Atomistry » Sodium » PDB 2x5x-2xjq » 2xhb
Atomistry »
  Sodium »
    PDB 2x5x-2xjq »
      2xhb »

Sodium in PDB 2xhb: Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna

Enzymatic activity of Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna

All present enzymatic activity of Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna, PDB code: 2xhb was solved by T.Killelea, S.Ghosh, S.S.Tan, P.Heslop, S.J.Firbank, E.T.Kool, B.A.Connolly, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.01 / 2.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.450, 98.370, 116.630, 90.00, 90.00, 90.00
R / Rfree (%) 23.361 / 29.455

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna (pdb code 2xhb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna, PDB code: 2xhb:

Sodium binding site 1 out of 1 in 2xhb

Go back to Sodium Binding Sites List in 2xhb
Sodium binding site 1 out of 1 in the Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dna Polymerase From Thermococcus Gorgonarius in Complex with Hypoxanthine-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1758

b:29.0
occ:1.00
 O A:HIS103 2.3 19.9 1.0
O A:VAL106 2.3 18.8 1.0
O A:HOH2005 2.3 24.7 1.0
O A:LYS101 2.4 18.9 1.0
O A:HOH2006 2.7 15.0 1.0
C A:HIS103 3.4 19.4 1.0
C A:VAL106 3.5 17.9 1.0
C A:LYS101 3.7 20.0 1.0
C A:GLU102 4.0 20.4 1.0
CA A:PRO104 4.0 18.4 1.0
N A:VAL106 4.0 17.6 1.0
N A:HIS103 4.1 19.8 1.0
O A:GLU102 4.1 20.8 1.0
CA A:VAL106 4.1 17.3 1.0
N A:PRO104 4.1 19.1 1.0
C A:PRO104 4.2 18.3 1.0
O A:PRO104 4.2 18.3 1.0
CB A:VAL106 4.3 17.0 1.0
CA A:HIS103 4.3 19.3 1.0
CA A:GLU102 4.4 21.3 1.0
N A:GLU102 4.5 20.6 1.0
N A:VAL107 4.5 17.3 1.0
CA A:LYS101 4.7 20.1 1.0
CA A:VAL107 4.7 17.0 1.0
O A:VAL107 4.7 19.8 1.0
C A:VAL107 4.8 18.1 1.0
N A:ALA105 4.9 18.3 1.0
CG1 A:VAL106 4.9 16.2 1.0

Reference:

T.Killelea, S.Ghosh, S.S.Tan, P.Heslop, S.J.Firbank, E.T.Kool, B.A.Connolly. Probing the Interaction of Archaeal Dna Polymerases with Deaminated Bases Using X-Ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues. Biochemistry V. 49 5772 2010.
ISSN: ISSN 0006-2960
PubMed: 20527806
DOI: 10.1021/BI100421R
Page generated: Mon Oct 7 05:10:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy