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Sodium in PDB 3rje: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position, PDB code: 3rje 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) 22.11 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.490, 79.170, 54.890, 90.00, 105.58, 90.00
R / Rfree (%) 19.8 / 25.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position (pdb code 3rje). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position, PDB code: 3rje:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3rje

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Sodium binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na336

b:6.7
occ:1.00
 O A:THR101 2.2 10.0 1.0
O A:ILE106 2.4 11.8 1.0
OP1 P:DG9 2.4 9.6 1.0
O P:HOH67 2.5 11.7 1.0
O A:VAL103 2.5 11.6 1.0
O P:HOH11 2.7 19.1 1.0
C A:THR101 3.2 10.1 1.0
NA A:NA338 3.3 27.5 1.0
C A:ILE106 3.4 8.6 1.0
C A:VAL103 3.4 12.0 1.0
P P:DG9 3.5 12.5 1.0
OP2 P:DG9 3.7 12.6 1.0
N A:ILE106 3.7 6.8 1.0
CA A:THR101 3.8 9.4 1.0
CA A:SER104 3.9 9.8 1.0
N A:GLY105 4.0 9.9 1.0
N A:SER104 4.0 9.9 1.0
N A:VAL103 4.0 9.8 1.0
CA A:ILE106 4.1 8.8 1.0
N A:ARG102 4.3 10.9 1.0
CB A:THR101 4.3 10.9 1.0
C A:SER104 4.3 9.0 1.0
C A:ARG102 4.3 12.1 1.0
N A:GLY107 4.4 7.8 1.0
CA A:VAL103 4.4 10.4 1.0
CB A:ILE106 4.5 10.2 1.0
O3' P:DC8 4.5 15.3 1.0
CA A:GLY107 4.6 8.7 1.0
CA A:ARG102 4.6 11.4 1.0
C A:GLY105 4.6 7.5 1.0
O5' P:DG9 4.6 13.9 1.0
O A:HOH395 4.7 39.8 1.0
O A:LEU100 4.8 10.0 1.0
O A:ARG102 4.9 12.3 1.0
CA A:GLY105 4.9 8.6 1.0

Sodium binding site 2 out of 4 in 3rje

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Sodium binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na337

b:16.4
occ:1.00
 O D:HOH26 2.1 20.8 1.0
O A:LYS60 2.2 24.8 1.0
O A:VAL65 2.3 16.2 1.0
O A:LEU62 2.5 23.3 1.0
OP1 D:DC3 2.7 19.6 1.0
O A:HOH593 2.7 29.5 1.0
C A:LYS60 3.3 24.2 1.0
C A:VAL65 3.4 13.4 1.0
C A:LEU62 3.6 22.4 1.0
P D:DC3 3.7 16.4 1.0
N A:VAL65 3.7 14.1 1.0
OP2 D:DC3 3.8 13.1 1.0
CA A:VAL65 4.0 13.7 1.0
CA A:LYS60 4.1 20.8 1.0
N A:LEU62 4.1 22.9 1.0
C A:LYS61 4.2 24.9 1.0
N A:GLY64 4.2 19.5 1.0
CB A:VAL65 4.2 13.9 1.0
CG A:LYS60 4.2 22.2 1.0
CA A:PRO63 4.3 21.2 1.0
N A:LYS61 4.3 25.4 1.0
N A:PRO63 4.3 23.1 1.0
N A:GLY66 4.4 11.9 1.0
CA A:LEU62 4.5 22.3 1.0
O A:LYS61 4.5 26.1 1.0
CA A:LYS61 4.5 24.9 1.0
O3' D:DT2 4.6 17.4 1.0
C A:PRO63 4.6 20.0 1.0
CA A:GLY66 4.7 10.6 1.0
C A:GLY64 4.8 16.5 1.0
CB A:LYS60 4.8 20.9 1.0
O A:ALA59 4.8 17.6 1.0
NZ A:LYS60 4.9 21.2 1.0
CG1 A:VAL65 4.9 11.2 1.0
O5' D:DC3 5.0 15.5 1.0

Sodium binding site 3 out of 4 in 3rje

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Sodium binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na338

b:27.5
occ:1.00
 O A:HOH389 2.4 23.5 1.0
O A:THR101 2.6 10.0 1.0
O A:HOH494 2.6 17.3 1.0
O A:HOH343 2.6 19.1 1.0
O P:HOH11 2.7 19.1 1.0
O P:HOH67 2.7 11.7 1.0
NA A:NA336 3.3 6.7 1.0
C A:THR101 3.5 10.1 1.0
O A:HOH457 3.8 38.4 1.0
O A:HOH449 4.0 36.3 1.0
CA A:ARG102 4.0 11.4 1.0
N A:ARG102 4.2 10.9 1.0
O A:HOH395 4.3 39.8 1.0
CB A:THR101 4.4 10.9 1.0
OG1 A:THR101 4.5 9.8 1.0
C A:ARG102 4.5 12.1 1.0
NZ A:LYS27 4.5 30.4 1.0
CA A:THR101 4.6 9.4 1.0
O A:HOH623 4.6 22.1 1.0
O A:HOH558 4.7 37.1 1.0
O P:HOH387 4.8 24.3 1.0
OP1 P:DG9 4.8 9.6 1.0
O A:ARG102 4.8 12.3 1.0
OP2 P:DG9 4.9 12.6 1.0

Sodium binding site 4 out of 4 in 3rje

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Sodium binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na339

b:27.6
occ:1.00
 OG A:SER171 2.1 9.8 1.0
O A:HOH483 2.6 21.5 1.0
O A:HOH418 2.7 16.4 1.0
CB A:SER171 3.3 12.8 1.0
N A:SER171 3.9 14.3 1.0
O A:HOH542 4.1 22.2 1.0
CA A:SER171 4.2 14.1 1.0
OD1 A:ASP170 4.6 16.0 1.0
C A:SER171 4.8 15.2 1.0
O A:HOH362 4.8 31.5 1.0
N A:GLU172 5.0 14.2 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: Mon Oct 7 12:48:01 2024

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