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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

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