Messages

26

RNA structures (DSSR) / Re: Figure 2. Molecular images of RNA secondary structural motifs incorporating each

« on: June 10, 2019, 01:02:46 pm »

Figure 2.d
pymol 4qlm.pdb
select AA, chain A and resi 42-49+64-72+81-89
select AAa, chain A and resi 44-47+66-67+86-87
select BB, chain A and resi 68+45
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain A and resi 68+45
zoom AA
set cartoon_ring_transparency, 1, 2-d
set_color mycolor, [255,51,51] #m-m
set_color mycolor2, [255,178,102] #loop
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC

27

RNA structures (DSSR) / Re: Figure 2. Molecular images of RNA secondary structural motifs incorporating each

« on: June 10, 2019, 01:02:21 pm »

Figure 2.c
pymol 2HW8.cif
select AA, chain B and resi 7-15+20-32
select AAa, chain B and resi 11-12+23-28
select BB, chain B and resi 13+28
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain B and resi 13+28
zoom AA
set cartoon_ring_transparency, 1, 2HW8
set_color mycolor, [255,51,153]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC
show spheres,BB
set sphere_scale, 0.15
hide spheres, BB and name OP2+OP1
set cartoon_ring_transparency, 0, CC

28

RNA structures (DSSR) / Re: Figure 2. Molecular images of RNA secondary structural motifs incorporating each

« on: June 10, 2019, 01:02:06 pm »

Figure 2.b
pymol 4Y4O.cif
select AA, resi 605-612 or resi 628-633
select AAa, resi 606-611 or resi 629-632
select BB, resi 611+629
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, resi 611+629
zoom AA
set cartoon_ring_transparency, 1, 2-b
set_color mycolor, [160,160,160]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC
show spheres,BB
set sphere_scale, 0.15
hide spheres, BB and name OP2+OP1
set cartoon_ring_transparency, 0, CC

29

RNA structures (DSSR) / Re: Figure 2. Molecular images of RNA secondary structural motifs incorporating each

« on: June 10, 2019, 12:58:52 pm »

Figure 2.a
pymol 2Z75.cif
select AA, chain B and resi 111-120
select AAa, chain B and resi 114-117
select BB, chain B and resi 114+117
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain B and resi 114+117
zoom AA
set cartoon_ring_transparency, 1, 2Z75
set_color mycolor, [51,51,255]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC
show spheres,BB
set sphere_scale, 0.15
hide spheres, BB and name OP2+OP1
set cartoon_ring_transparency, 0, CC

30

RNA structures (DSSR) / Figure 2. Molecular images of RNA secondary structural motifs incorporating each

« on: June 10, 2019, 12:56:44 pm »

Figure 2. Molecular images of RNA secondary structural motifs incorporating each of the dominant modes of G·A base pairing. Motifs correspond to one of the common settings of the designated pairs: (a) sheared m–M pair closing the GNRA tetraloop at the end of the P4 helix of the glmS ribozyme bound to glucosamine 6-phosphate;(35) (b) imino W–W pair at the end of an asymmetric internal loop in the Thermus thermophilus 70S ribosome in complex with the hibernation factor pY;(36) (c) m+m pair linking the G in a double-helical stem and the A in an internal loop of the complex of Thermus thermophilus ribosomal protein L1 with a fragment of the L1 RNA from Methanoccocus vannielii;(37) (d) m–m pair joining a stem and single-stranded fragment within a three-way junction of the Thermoanaerobacter tengcongenesis ydaO riboswitch bound to cyclic di-AMP;(38) (e) m+W pair connecting the D and T hairpin loops of yeast initiator tRNA;(39) (f) m–W pair linking two hairpin loops of the 5S rRNA within the structure of the hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.(40) The G·A pairs are color-coded as in Figure 1 and shown at the nucleotide level within each structural element and in a separate local depiction to the right of each example. Loops are depicted in gold and canonical base pairs at the ends of loops or within double-helical stems in white. Ribbons connect phosphorus atoms in successive nucleotides. See Table S3 for Protein Data Bank identifiers, chain names, and residue numbers of the depicted pairs and Figure S2 for simple secondary structural diagrams of the associated motifs.

31

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:23:36 am »

Use Photoshop to add labels and dashed lines on each figure.

1-a.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-A    6.816843 -4.527391  0.343299   5.599746  -2.494629   -8.234822   0.000     0.000     0.000     0.000     0.000     0.000

1-b.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-A    0.048750  1.525968 -0.338185   7.312177  -9.915202  -16.193871   0.000     0.000     0.000     0.000     0.000     0.000

1-c.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G+A    -2.676827   -7.299808   -0.098718   -10.314647   9.461635   -152.17256   0.000     0.000     0.000     0.000     0.000     0.000

1-d.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-A    -1.880278  7.232870 -0.008889 -3.494259  -12.964537  148.270648   0.000     0.000     0.000     0.000     0.000     0.000

1-e.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G+A    1.798861 -4.956085 -0.004733  -4.433452  11.665907  -94.003630   0.000     0.000     0.000     0.000     0.000     0.000

1-f.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-A    3.762906  3.367692  0.284957  -7.853162 -13.928718  101.603333   0.000     0.000     0.000     0.000     0.000     0.000

1-g.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-C   -0.37   -0.44   -0.18   9.31   -10.39   -1.3  0.000     0.000     0.000     0.000     0.000     0.000

32

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:18:35 am »

Figure 1.g
x3dna_utils cp_std rna
rebuild -atomic 1-g.par 1-g.pdb
pymol 1-g.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,255,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

33

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:16:53 am »

Figure 1.f
x3dna_utils cp_std rna
rebuild -atomic 1-f.par 1-f.pdb
pymol 1-f.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,51,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

34

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:16:35 am »

Figure 1.e
x3dna_utils cp_std rna
rebuild -atomic 1-e.par 1-e.pdb
pymol 1-e.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [51,153,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

35

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:16:22 am »

Figure 1.d
x3dna_utils cp_std rna
rebuild -atomic 1-d.par 1-d.pdb
pymol 1-d.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,51,51]
set_bond stick_color, mycolor, all
color mycolor, all
ray

36

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:15:32 am »

Figure 1.c
x3dna_utils cp_std rna
rebuild -atomic 1-c.par 1-c.pdb
pymol 1-c.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,51,153]
set_bond stick_color, mycolor, all
color mycolor, all
ray

37

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:12:29 am »

Figure 1.b
x3dna_utils cp_std rna
rebuild -atomic 1-b.par
pymol 1-b.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [160,160,160]
set_bond stick_color, mycolor, all
color mycolor, all
ray

38

RNA structures (DSSR) / Re: Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:11:26 am »

Figure 1.a
x3dna_utils cp_std rna
rebuild -atomic 1-a.par 1-a.pdb
pymol 1-a.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [51,51,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

39

RNA structures (DSSR) / Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

« on: June 10, 2019, 10:06:15 am »

Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures, and relative spatial arrangements of nucleotides in the six dominant modes of G·A pairing and in a canonical Watson–Crick G–C pair. Hydrogen bonds are shown by thin dashed lines, with arrows directed toward base/backbone atoms capable of accepting protons. Structures were generated with 3DNA(24) and rendered in PyMOL (www.pymol.org) using the average rigid-body parameters in Table 1 and a canonical A-RNA backbone.(34) Structures are depicted in the standard reference frame of G.(30) Color-coding denotes the mode of base association: sheared m–M (dark blue); imino W–W (gray); m+m (pink); m–m (red); m+W (light blue); m–W (magenta); canonical (white), where the combinations of signs and letters denote the orientation (parallel + /antiparallel –) and the approximate sites (minor, m; major, M; Watson–Crick, W edges) of base association.(27) Interestingly, less than 10% of the + states reflect an anti-to-syn sugar–base rearrangement, and these examples all involve adenine.

40

RNA structures (DSSR) / Re: no nucleotide in some structures

« on: February 11, 2019, 11:41:21 am »

Thank you so much for the explanation and an option to solve my problem.

Best,
Shuxiang

41

RNA structures (DSSR) / no nucleotide in some structures

« on: February 11, 2019, 10:24:32 am »

Hi Xiang-Jun,

I'm using DSSR to analyze some structures and it showed there is no nucleotide was found. When I visualized these structures using pymol. I indeed saw nucleotides are there. For example (6CEV):

x3dna-dssr -i=6cev.pdb

Thanks.

Best,
Shuxiang

42

w3DNA -- web interface to 3DNA / Web 3DNA 2.0 is up and running

« on: December 18, 2018, 09:15:17 pm »

Web 3DNA 2.0 (http://web.x3dna.org/) is a significantly enhanced interface for the analysis, visualization, and modeling of 3D nucleic-acid structures. The new server employs modern web technologies and takes advantages of the latest 3DNA version 2.4.0. As a result, the original w3DNA website (http://w3dna.rutgers.edu/) is obsolete and users are strongly encouraged to use web 3DNA 2.0 (http://web.x3dna.org/).

Web 3DNA 2.0 has six major modules: Analysis, Visualization, Rebuilding, Composite, Fiber and Mutation. Each module has its default setting and users can just click the buttons to have a feeling of what the new server has to offer.

Any questions and bug reports are welcome!

Shuxiang & Xiang-Jun

43

w3DNA -- web interface to 3DNA / Re: Notes on w3DNA v2

« on: December 06, 2018, 03:30:49 pm »

Hi Xiang-Jun,

I found an interesting base (TNT) when calculating the torsion angles of a structure (pdbid: 102D). I found this because my code was killed to extract the base name and cannot import the data into a local database.
the command I used:  analyze -t=test.tor 102D.pdb
the result:
              base      chi A/S     alpha    beta   gamma   delta  epsilon   zeta     e-z BI/BII
   1 A:...1_:[.DC]C  -110.9 anti     ---     ---    162.9   155.9  -177.3  -105.1   -72.2  BI
   2 A:...2_:[.DG]G   -96.2 anti    -48.5  -172.5    22.9   149.7  -176.0  -111.9   -64.1  BI
   3 A:...3_:[.DC]C  -113.1 anti    -68.6   172.1    55.5   132.3  -168.4  -105.4   -63.0  BI
   4 A:...4_:[.DA]A   -89.3 anti    -57.8  -159.4    40.9   144.7   171.5  -105.3   -83.3  BI
   5 A:...5_:[.DA]A   -97.6 anti    -61.0   178.3    54.8   152.7  -169.7  -114.6   -55.1  BI
   6 A:...6_:[.DA]A  -102.2 anti    -66.1  -176.1    48.1   142.8   178.2   -92.7   -89.1  BI
   7 A:...7_:[.DT]T  -101.7 anti    -80.5   177.5    55.4   148.6   -91.5   175.7    92.7  BII
   8 A:...8_:[.DT]T   -99.5 anti    -45.3   168.6    -4.0   150.3  -168.8  -102.8   -66.0  BI
   9 A:...9_:[.DT]T   -94.3 anti    -76.5  -165.2    41.7   136.8  -176.4  -109.3   -67.1  BI
  10 A:..10_:[.DG]G   -87.6 anti    -51.9   170.2    42.6   152.9  -134.3  -169.8    35.5  BII
  11 A:..11_:[.DC]C  -105.4 anti    -66.5   169.1    47.4   143.7  -169.3   -95.4   -73.9  BI
  12 A:..12_:[.DG]G   -77.2 anti    -74.8  -176.4    46.8   148.5    ---     ---     ---   ---
  13 B:..13_:[.DC]C   -98.7 anti     ---     ---    -63.7   161.9  -125.0  -178.8    53.8  BII
  14 B:..14_:[.DG]G  -110.4 anti    -50.4   154.6    25.0   146.5  -170.5  -108.0   -62.5  BI
  15 B:..15_:[.DC]C  -118.7 anti    -59.8   170.6    52.8   140.4  -155.7  -134.9   -20.8  BI
  16 B:..16_:[.DA]A   -98.2 anti    -57.8   158.8    61.9   152.0  -168.7  -114.0   -54.7  BI
  17 B:..17_:[.DA]A  -103.2 anti    -63.8   175.0    52.4   143.3  -166.0  -105.7   -60.2  BI
  18 B:..18_:[.DA]A  -104.3 anti    -55.4   177.7    40.6   145.7  -177.8   -98.8   -79.0  BI
  19 B:..19_:[.DT]T  -103.1 anti    -73.4   175.6    58.0   147.4  -141.7  -160.8    19.1  BI
  20 B:..20_:[.DT]T   -99.1 anti     10.2   173.1   -35.0   157.6   178.5   -98.2   -83.3  BI
  21 B:..21_:[.DT]T  -106.8 anti    -69.9   177.9    55.3   139.2  -155.6  -118.1   -37.5  BI
  22 B:..22_:[.DG]G   -80.4 anti    -41.0   155.2    33.8   148.7  -104.0   174.8    81.2  BII
  23 B:..23_:[.DC]C  -109.9 anti    -62.5   156.8    15.6   150.0  -160.2  -123.2   -37.0  BI
  24 B:..24_:[.DG]G  -116.0 anti    -62.7   162.5    57.1   138.2    ---     ---     ---   ---
  25 -:..25_:[TNT]     ---  ---      ---     ---     ---     ---     ---     ---     ---   ---

I'm not sure this base should be in the torsion angle file. I cannot find it in any other 3dna output files including .inp, .out.

Thank you.

Best regards,
Shuxiang

44

w3DNA -- web interface to 3DNA / Re: Notes on w3DNA v2

« on: December 03, 2018, 02:43:55 pm »

Hi Xiang-Jun,

Thank you so much for above wonderful suggestions. I have finished some of them and will update the public server as soon as I finish all.

One thing I want to mention is about the high resolution image in the Visualization part. I compared the high resolution png file (converted from eps file with high resolution option)  with the default svg file (convert eps to pdf then to svg) in our web sever.  It looks like the high resolution png file is better than the default svg file (see the attached image, the top one is png file and the bottom is svg file). I will use the png file currently.

Best regards,
Shuxiang

45

General discussions (Q&As) / Re: How to calculate two reference frames for each base in a base pair

« on: October 29, 2018, 04:59:25 pm »

Both methods work. Thank you so much.

46

General discussions (Q&As) / How to calculate two reference frames for each base in a base pair

« on: October 29, 2018, 03:57:11 pm »

Hi Xiang-Jun,

I encounter a question when plotting separate frames for each base in a base pair. See the attached picture, each base has its own reference frame.


From the ref_frames.dat file, I get the information like following.  If I understand correctly, it looks like the reference frames here are the averaged frames for a base pair.
...     6 A-T   # A:...6_:[.DA]A - B:..19_:[.DT]T
   14.8825    20.6882    10.2718  # origin
    0.9873    -0.1230    -0.1006  # x-axis
   -0.0859    -0.9457     0.3135  # y-axis
   -0.1337    -0.3009    -0.9442  # z-axis

I want to obtain the reference frame for each base in a paired bases. Thank you.

Best,
Shuxiang

47

RNA structures (DSSR) / Re: Web 3DNA Error

« on: October 18, 2018, 12:43:20 pm »

The error you got is because our current web 3DNA version cann't recognize the A3 residue in your structure.  The web 3DNA  was developed 10 years ago and it uses an old version of 3DNA for analyzing DNA structures and the "A3" residue is not in the base list.  As Xiang-Jun suggested, you can use DSSR to analyze your structure. By the way, we're working on an updated version of web 3DNA.

48

Bug reports / Re: 5-hydroxy methyl cytosine

« on: September 06, 2018, 01:22:27 pm »

I have modified web 3DNA to deal with modified cytosine like 5HM.

49

RNA structures (DSSR) / Re: strange residue number after dssr --view option

« on: August 06, 2018, 05:40:26 pm »

Hi Xiang-Jun,

Thank you very much for your explanation. I will fix the server to correctly represent these structures (such as 3mgp)  with conflicts between "_atom_site.label_seq_id" and "_atom_site.auth_seq_id".

Best ,
Shuxiang

50

RNA structures (DSSR) / strange residue number after dssr --view option

« on: August 06, 2018, 01:10:13 pm »

Hi Xiang-Jun,

I'm using the following command to convert a DNA\protein structure into its best view conformation. (3mgp.cif is downloaded from PDB database).

x3dna-dssr -i=3mgp.cif -o=3mgp_view.cif --view

The weird thing is the residue number index of the DNA part from original file (3mgp.cif)  is from 1 to 147. However, the corresponding residue number index from best view file (3mgp_view.cif) is from -73 to 73. I'm wondering is there an opinion to keep the residue renumber same between the original file and dssr output file? Thank you. 

For example, the beginning DNA part of 3mgp.cif is:
ATOM   6161  O  "O5'" . DA  I  5 1   ? 2.638   0.163   93.308 1.00 166.52 ? -73  DA  I "O5'" 1
ATOM   6162  C  "C5'" . DA  I  5 1   ? 3.279   0.178   94.579 1.00 166.78 ? -73  DA  I "C5'" 1
ATOM   6163  C  "C4'" . DA  I  5 1   ? 3.645   -1.223  95.042 1.00 167.01 ? -73  DA  I "C4'" 1
ATOM   6164  O  "O4'" . DA  I  5 1   ? 2.489   -2.096  95.012 1.00 167.37 ? -73  DA  I "O4'" 1
ATOM   6165  C  "C3'" . DA  I  5 1   ? 4.650   -1.969  94.180 1.00 166.94 ? -73  DA  I "C3'" 1
ATOM   6166  O  "O3'" . DA  I  5 1   ? 5.972   -1.523  94.462 1.00 166.58 ? -73  DA  I "O3'" 1
ATOM   6167  C  "C2'" . DA  I  5 1   ? 4.428   -3.410  94.635 1.00 167.20 ? -73  DA  I "C2'" 1
ATOM   6168  C  "C1'" . DA  I  5 1   ? 2.941   -3.442  94.998 1.00 167.53 ? -73  DA  I "C1'" 1
ATOM   6169  N  N9    . DA  I  5 1   ? 2.097   -4.257  94.106 1.00 167.70 ? -73  DA  I N9    1
ATOM   6170  C  C8    . DA  I  5 1   ? 0.995   -3.832  93.410 1.00 167.66 ? -73  DA  I C8    1
ATOM   6171  N  N7    . DA  I  5 1   ? 0.415   -4.762  92.687 1.00 167.66 ? -73  DA  I N7    1
ATOM   6172  C  C5    . DA  I  5 1   ? 1.185   -5.889  92.920 1.00 167.82 ? -73  DA  I C5    1
ATOM   6173  C  C6    . DA  I  5 1   ? 1.094   -7.219  92.443 1.00 167.68 ? -73  DA  I C6    1
ATOM   6174  N  N6    . DA  I  5 1   ? 0.141   -7.629  91.598 1.00 167.61 ? -73  DA  I N6    1
ATOM   6175  N  N1    . DA  I  5 1   ? 2.020   -8.112  92.866 1.00 167.60 ? -73  DA  I N1    1
ATOM   6176  C  C2    . DA  I  5 1   ? 2.972   -7.698  93.715 1.00 167.61 ? -73  DA  I C2    1
ATOM   6177  N  N3    . DA  I  5 1   ? 3.161   -6.478  94.229 1.00 167.74 ? -73  DA  I N3    1
ATOM   6178  C  C4    . DA  I  5 1   ? 2.227   -5.603  93.793 1.00 167.85 ? -73  DA  I C4    1
ATOM   6179  P  P     . DT  I  5 2   ? 6.808   -0.641  93.411 1.00 166.33 ? -72  DT  I P     1
ATOM   6180  O  OP1   . DT  I  5 2   ? 6.500   0.779   93.692 1.00 166.34 ? -72  DT  I OP1   1
ATOM   6181  O  OP2   . DT  I  5 2   ? 6.588   -1.186  92.052 1.00 166.28 ? -72  DT  I OP2   1
ATOM   6182  O  "O5'" . DT  I  5 2   ? 8.341   -0.918  93.788 1.00 165.73 ? -72  DT  I "O5'" 1
ATOM   6183  C  "C5'" . DT  I  5 2   ? 8.715   -1.557  95.009 1.00 164.98 ? -72  DT  I "C5'" 1
ATOM   6184  C  "C4'" . DT  I  5 2   ? 9.072   -3.018  94.786 1.00 164.44 ? -72  DT  I "C4'" 1
ATOM   6185  O  "O4'" . DT  I  5 2   ? 7.900   -3.772  94.389 1.00 164.50 ? -72  DT  I "O4'" 1
ATOM   6186  C  "C3'" . DT  I  5 2   ? 10.122  -3.278  93.711 1.00 164.05 ? -72  DT  I "C3'" 1
ATOM   6187  O  "O3'" . DT  I  5 2   ? 11.270  -3.824  94.345 1.00 163.49 ? -72  DT  I "O3'" 1
ATOM   6188  C  "C2'" . DT  I  5 2   ? 9.469   -4.258  92.730 1.00 164.06 ? -72  DT  I "C2'" 1
ATOM   6189  C  "C1'" . DT  I  5 2   ? 8.302   -4.824  93.535 1.00 164.11 ? -72  DT  I "C1'" 1

The beginning DNA part of 3mgp_view.cif is:
ATOM   6161  O5'  DA I -73     -44.102 -28.116  24.446  1.00166.52           O
ATOM   6162  C5'  DA I -73     -45.300 -28.880  24.535  1.00166.78           C
ATOM   6163  C4'  DA I -73     -45.873 -29.191  23.161  1.00167.01           C
ATOM   6164  O4'  DA I -73     -46.042 -27.979  22.385  1.00167.37           O
ATOM   6165  C3'  DA I -73     -45.006 -30.049  22.255  1.00166.94           C
ATOM   6166  O3'  DA I -73     -45.116 -31.421  22.619  1.00166.58           O
ATOM   6167  C2'  DA I -73     -45.629 -29.773  20.889  1.00167.20           C
ATOM   6168  C1'  DA I -73     -46.128 -28.331  21.012  1.00167.53           C
ATOM   6169   N9  DA I -73     -45.409 -27.347  20.184  1.00167.70           N
ATOM   6170   C8  DA I -73     -44.776 -26.213  20.626  1.00167.66           C
ATOM   6171   N7  DA I -73     -44.212 -25.500  19.679  1.00167.66           N
ATOM   6172   C5  DA I -73     -44.491 -26.208  18.522  1.00167.82           C
ATOM   6173   C6  DA I -73     -44.167 -25.976  17.163  1.00167.68           C
ATOM   6174   N6  DA I -73     -43.462 -24.917  16.750  1.00167.61           N
ATOM   6175   N1  DA I -73     -44.595 -26.874  16.245  1.00167.60           N
ATOM   6176   C2  DA I -73     -45.305 -27.933  16.662  1.00167.61           C
ATOM   6177   N3  DA I -73     -45.667 -28.258  17.908  1.00167.74           N
ATOM   6178   C4  DA I -73     -45.229 -27.349  18.808  1.00167.85           C
ATOM   6179    P  DT I -72     -43.906 -32.208  23.323  1.00166.33           P
ATOM   6180  OP1  DT I -72     -44.062 -32.031  24.784  1.00166.34           O
ATOM   6181  OP2  DT I -72     -42.638 -31.816  22.667  1.00166.28           O
ATOM   6182  O5'  DT I -72     -44.167 -33.748  22.962  1.00165.73           O
ATOM   6183  C5'  DT I -72     -45.409 -34.196  22.418  1.00164.98           C
ATOM   6184  C4'  DT I -72     -45.310 -34.425  20.919  1.00164.44           C
ATOM   6185  O4'  DT I -72     -45.104 -33.169  20.226  1.00164.50           O
ATOM   6186  C3'  DT I -72     -44.176 -35.341  20.471  1.00164.05           C
ATOM   6187  O3'  DT I -72     -44.756 -36.505  19.899  1.00163.49           O
ATOM   6188  C2'  DT I -72     -43.369 -34.526  19.455  1.00164.06           C
ATOM   6189  C1'  DT I -72     -44.333 -33.408  19.066  1.00164.11           C


Best,
Shuxiang