Atomistry » Sodium » PDB 3r9b-3rn1 » 3rjg
Atomistry »
  Sodium »
    PDB 3r9b-3rn1 »
      3rjg »

Sodium in PDB 3rjg: Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus

Enzymatic activity of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus

All present enzymatic activity of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus, PDB code: 3rjg was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.660, 79.590, 55.000, 90.00, 105.79, 90.00
R / Rfree (%) 20.8 / 25.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus (pdb code 3rjg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus, PDB code: 3rjg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3rjg

Go back to Sodium Binding Sites List in 3rjg
Sodium binding site 1 out of 2 in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na336

b:8.7
occ:1.00
OP1 P:DG9 2.3 8.2 1.0
O A:THR101 2.4 11.4 1.0
O A:ILE106 2.4 9.8 1.0
O A:VAL103 2.5 10.9 1.0
O P:HOH20 2.6 11.4 1.0
O P:HOH11 2.7 16.0 1.0
C A:THR101 3.3 12.5 1.0
O A:HOH345 3.4 17.6 1.0
C A:ILE106 3.4 8.5 1.0
P P:DG9 3.4 12.8 1.0
C A:VAL103 3.4 10.0 1.0
OP2 P:DG9 3.6 10.5 1.0
N A:ILE106 3.7 7.4 1.0
CA A:THR101 3.9 10.6 1.0
CA A:SER104 3.9 7.9 1.0
N A:GLY105 4.0 9.0 1.0
N A:SER104 4.0 8.9 1.0
CA A:ILE106 4.1 8.4 1.0
N A:VAL103 4.1 10.3 1.0
C A:SER104 4.3 8.9 1.0
CB A:THR101 4.3 10.9 1.0
N A:GLY107 4.3 8.8 1.0
C A:ARG102 4.4 11.9 1.0
N A:ARG102 4.4 11.9 1.0
O3' P:DC8 4.4 9.5 1.0
CA A:VAL103 4.5 10.0 1.0
CB A:ILE106 4.5 12.2 1.0
O P:HOH261 4.5 37.5 1.0
O5' P:DG9 4.5 11.1 1.0
CA A:GLY107 4.6 9.2 1.0
C A:GLY105 4.6 8.8 1.0
O A:HOH655 4.6 39.6 1.0
CA A:ARG102 4.7 11.0 1.0
O P:HOH141 4.8 22.4 1.0
O A:ARG102 4.9 11.7 1.0
CA A:GLY105 4.9 7.7 1.0
O A:LEU100 5.0 14.1 1.0

Sodium binding site 2 out of 2 in 3rjg

Go back to Sodium Binding Sites List in 3rjg
Sodium binding site 2 out of 2 in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na337

b:17.0
occ:1.00
O D:HOH233 1.9 21.8 1.0
O A:LYS60 2.3 23.5 1.0
O A:LEU62 2.4 23.6 1.0
O A:VAL65 2.4 20.1 1.0
O A:HOH378 2.7 32.3 1.0
OP1 D:DC3 2.8 21.0 1.0
C A:LYS60 3.4 24.6 1.0
C A:LEU62 3.4 23.5 1.0
C A:VAL65 3.5 16.9 1.0
N A:VAL65 3.7 17.5 1.0
P D:DC3 3.8 17.7 1.0
OP2 D:DC3 4.0 15.6 1.0
N A:LEU62 4.0 23.7 1.0
N A:GLY64 4.0 22.2 1.0
CA A:VAL65 4.0 17.1 1.0
C A:LYS61 4.0 25.7 1.0
CA A:PRO63 4.1 22.7 1.0
N A:PRO63 4.1 23.6 1.0
CA A:LYS60 4.2 22.9 1.0
CB A:VAL65 4.2 16.5 1.0
O A:LYS61 4.3 25.4 1.0
N A:LYS61 4.3 25.6 1.0
CA A:LEU62 4.3 23.6 1.0
CA A:LYS61 4.4 26.6 1.0
CG A:LYS60 4.4 25.6 1.0
C A:PRO63 4.5 22.8 1.0
N A:GLY66 4.6 18.1 1.0
O3' D:DT2 4.7 16.8 1.0
C A:GLY64 4.7 19.4 1.0
O A:ALA59 4.7 21.2 1.0
O D:HOH381 4.8 37.9 1.0
CB A:LYS60 4.9 24.2 1.0
CA A:GLY66 5.0 17.0 1.0
CA A:GLY64 5.0 19.9 1.0

Reference:

V.K.Batra, D.D.Shock, W.A.Beard, C.E.Mckenna, S.H.Wilson. Binary Complex Crystal Structure of Dna Polymerase Beta Reveals Multiple Conformations of the Templating 8-Oxoguanine Lesion Proc.Natl.Acad.Sci.Usa V. 109 113 2012.
ISSN: ISSN 0027-8424
PubMed: 22178760
DOI: 10.1073/PNAS.1112235108
Page generated: Tue Dec 15 06:23:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy