Messages

1

General discussions (Q&As) / Re: Helical parametrs for 2′,5′-Linked RNA or DNA

« on: March 21, 2013, 08:06:54 am »

Dear Sir,

I am sorry for not specify the pdb code.
Structure has 2KD4 code.

Output file after processing structure 2KD4 using x3dna can be found in the attachment.
I am sending also file with x3dna information from terminal.

Sincerely
Paul

2

General discussions (Q&As) / Helical parametrs for 2′,5′-Linked RNA or DNA

« on: March 20, 2013, 11:51:04 am »

Dear Sir,

I would like to ask whether is it possible (or will be) using x3DNA program to calculate helical parameters for DNA or RNA structures with
2' - 5' linklage ?
eg:
http://pubs.acs.org/doi/abs/10.1021/ja810068e

Sincerely

Paul

3

General discussions (Q&As) / Re: Large value of ZpH and inclination for Z-DNA

« on: December 10, 2012, 08:14:24 pm »

Dear Sir,

Thank you for your answer.

 The rmsd for this base step between my Z-DNA structures (according to superpose program from CCP4) 
is 
RMS     XYZ DISPLACEMENT =   0.355
AVERAGE XYZ DISPLACEMENT =   0.293
 MAXIMUM XYZ DISPLACEMENT =   0.867
and between the entire two structures
is
RMS     XYZ DISPLACEMENT =   0.593
AVERAGE XYZ DISPLACEMENT =   0.409
MAXIMUM XYZ DISPLACEMENT =   4.240
Are these values significantly large ?

I am sending also two figures with superposition of my Z-DNA structures at the local base-pair step number 3.
Are these figures show differences in inclination and X-disp for base-pair step number 3 ?
At this base step we can see ZI to ZII rotation of the phosphate group at this dinucleotide step ?
Is it possible that differences in backbone ZI/ZII conformation would affect how X3DNA calculates some of the parameters (the Zp in
particular) ?

Thank you for your help !
Paul

4

General discussions (Q&As) / Large value of ZpH and inclination for Z-DNA

« on: December 02, 2012, 06:14:23 am »

Dear Sir,

I would like to know your opinion about the high value of inclination and ZpH in the my structure of  Z-DNA.
For local base-pair number 3 in my first Z-DNA I have values:
      step       X-disp    Y-disp   h-Rise     Incl.       Tip     h-Twist
3 CG/CG     11.88     -0.10      6.56     63.77      1.19     -6.06
    step              Xp      Yp      Zp     XpH     YpH     ZpH    Form
   3 CG/CG    5.82    5.30   -1.92   17.69    4.06    3.91
and for the my second Z-DNA structure I have values:
     step       X-disp    Y-disp   h-Rise     Incl.       Tip     h-Twist
   3 CG/CG    -26.29      0.88      5.98     29.64      2.06     -6.31
 step           Xp      Yp      Zp     XpH     YpH       ZpH    Form
3 CG/CG    5.49    5.42   -2.51  -20.76    5.96    0.50
Is it possible to find something specific by comparing the values of ZpH ​​for the two structures Z-DNA?
Does it matter that the ZpH value is close to 4 A (which in your paper is considered as threshold for TA-DNA (> 4A) ?
Is such a large value of η is associated with a width of the minor groove (8.5 Å for step 3 = 3CG-10GC) ?
What can we say about the differences in X-disp for my two Z-DNA structures ?
It seems to me that X-disp = 11.88 differs from other values for this step in Z-DNA structures. ?
I would like ask one more thing. The average value of helical twist for Z-DNA is around -60.  How to calculate this value having these data ?  :
    step           h-Twist
   1 CG/CG    -6.15
   2 GC/GC       -53.30
   3 CG/CG     -6.31
   4 GC/GC      -53.77
   5 CG/CG        -6.86
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          ave.     -25.28

As yoou can see I am beginner in the field of explanation the relationship between the helical parameters - therefore can please you to propose me some publication explanatory  for example how depends the width of small groove of the other helical parameters . ?

Thank you for your time and help

Yours sincerely,

paul