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Sodium in PDB 3isb: Binary Complex of Human Dna Polymerase Beta with A Gapped Dna

Enzymatic activity of Binary Complex of Human Dna Polymerase Beta with A Gapped Dna

All present enzymatic activity of Binary Complex of Human Dna Polymerase Beta with A Gapped Dna:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex of Human Dna Polymerase Beta with A Gapped Dna, PDB code: 3isb was solved by W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.86 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.380, 79.240, 54.880, 90.00, 105.49, 90.00
R / Rfree (%) 21.1 / 27.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex of Human Dna Polymerase Beta with A Gapped Dna (pdb code 3isb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Binary Complex of Human Dna Polymerase Beta with A Gapped Dna, PDB code: 3isb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3isb

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Sodium binding site 1 out of 4 in the Binary Complex of Human Dna Polymerase Beta with A Gapped Dna


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 Human Dna Polymerase Beta with A Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:7.7
occ:1.00
 O A:THR101 2.3 13.8 1.0
OP1 P:DG9 2.4 8.3 1.0
O A:ILE106 2.4 10.1 1.0
O P:HOH12 2.4 11.4 1.0
O A:VAL103 2.5 12.9 1.0
O P:HOH11 2.7 11.1 1.0
NA A:NA403 3.2 24.2 1.0
C A:THR101 3.3 13.3 1.0
C A:VAL103 3.4 11.9 1.0
C A:ILE106 3.4 8.8 1.0
P P:DG9 3.5 10.4 1.0
OP2 P:DG9 3.7 10.3 1.0
N A:ILE106 3.8 9.2 1.0
CA A:THR101 3.9 12.4 1.0
CA A:SER104 3.9 10.5 1.0
N A:GLY105 3.9 10.0 1.0
N A:SER104 4.0 10.8 1.0
N A:VAL103 4.1 12.3 1.0
CA A:ILE106 4.2 8.7 1.0
C A:SER104 4.3 10.5 1.0
C A:ARG102 4.3 12.4 1.0
CB A:THR101 4.3 12.1 1.0
N A:ARG102 4.3 13.7 1.0
N A:GLY107 4.4 8.0 1.0
CA A:VAL103 4.4 12.0 1.0
O3' P:DC8 4.5 9.8 1.0
CB A:ILE106 4.6 10.2 1.0
CA A:GLY107 4.6 9.8 1.0
C A:GLY105 4.6 9.1 1.0
O5' P:DG9 4.6 10.6 1.0
CA A:ARG102 4.6 12.7 1.0
O A:ARG102 4.8 10.6 1.0
CA A:GLY105 4.9 9.3 1.0
O A:LEU100 4.9 10.5 1.0
O A:HOH566 5.0 15.2 1.0
O A:HOH739 5.0 33.0 1.0

Sodium binding site 2 out of 4 in 3isb

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Sodium binding site 2 out of 4 in the Binary Complex of Human Dna Polymerase Beta with A Gapped Dna


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 Human Dna Polymerase Beta with A Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.1
occ:1.00
 O A:VAL65 2.1 19.2 1.0
O D:HOH6 2.2 23.0 1.0
O A:LYS60 2.3 25.1 1.0
OP1 D:DC3 2.7 21.2 1.0
O A:LEU62 2.8 28.0 1.0
O A:HOH690 2.9 32.2 1.0
C A:VAL65 3.2 16.8 1.0
C A:LYS60 3.4 25.8 1.0
P D:DC3 3.7 18.3 1.0
C A:LEU62 3.8 27.4 1.0
OP2 D:DC3 3.8 15.9 1.0
N A:VAL65 3.8 18.4 1.0
CG A:LYS60 3.9 26.6 1.0
CA A:VAL65 4.0 16.3 1.0
CA A:LYS60 4.0 24.2 1.0
O D:HOH533 4.2 43.2 1.0
N A:GLY66 4.2 16.6 1.0
CB A:VAL65 4.3 14.2 1.0
N A:LEU62 4.3 27.3 1.0
C A:LYS61 4.3 28.2 1.0
N A:GLY64 4.4 23.3 1.0
CA A:GLY66 4.4 13.7 1.0
CA A:PRO63 4.4 25.5 1.0
N A:LYS61 4.4 26.4 1.0
N A:PRO63 4.5 27.1 1.0
NZ A:LYS60 4.6 28.2 1.0
O3' D:DT2 4.6 20.0 1.0
O A:LYS61 4.6 29.1 1.0
CB A:LYS60 4.6 24.3 1.0
CA A:LEU62 4.6 28.1 1.0
CA A:LYS61 4.7 27.1 1.0
C A:PRO63 4.8 23.8 1.0
C A:GLY64 4.9 19.7 1.0
O5' D:DC3 4.9 20.7 1.0
O A:ALA59 4.9 21.4 1.0
CG1 A:VAL65 5.0 11.3 1.0

Sodium binding site 3 out of 4 in 3isb

Go back to Sodium Binding Sites List in 3isb
Sodium binding site 3 out of 4 in the Binary Complex of Human Dna Polymerase Beta with A Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex of Human Dna Polymerase Beta with A Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:24.2
occ:1.00
 O P:HOH12 2.4 11.4 1.0
O A:HOH566 2.5 15.2 1.0
O A:THR101 2.6 13.8 1.0
O A:HOH687 2.6 22.8 1.0
O A:HOH341 2.7 26.1 1.0
O P:HOH11 2.7 11.1 1.0
NA A:NA401 3.2 7.7 1.0
C A:THR101 3.6 13.3 1.0
O A:HOH491 4.1 32.1 1.0
CA A:ARG102 4.2 12.7 1.0
N A:ARG102 4.3 13.7 1.0
CB A:THR101 4.4 12.1 1.0
O A:HOH739 4.4 33.0 1.0
NZ A:LYS27 4.4 22.6 1.0
OG1 A:THR101 4.5 12.5 1.0
CA A:THR101 4.6 12.4 1.0
C A:ARG102 4.6 12.4 1.0
O P:HOH134 4.7 18.0 1.0
OP1 P:DG9 4.7 8.3 1.0
OP2 P:DG9 4.7 10.3 1.0
O A:HOH688 4.8 26.6 1.0
O A:HOH552 4.8 22.2 1.0
O A:ARG102 4.9 10.6 1.0

Sodium binding site 4 out of 4 in 3isb

Go back to Sodium Binding Sites List in 3isb
Sodium binding site 4 out of 4 in the Binary Complex of Human Dna Polymerase Beta with A Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Binary Complex of Human Dna Polymerase Beta with A Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:21.8
occ:1.00
 O A:HOH722 2.1 33.5 1.0
O A:HOH568 2.1 16.6 1.0
OG A:SER171 2.3 13.9 1.0
CB A:SER171 3.4 13.8 1.0
N A:SER171 3.8 11.4 1.0
O A:HOH382 3.9 38.5 1.0
CA A:SER171 4.2 12.9 1.0
O A:HOH549 4.3 16.4 1.0
OD1 A:ASP170 4.5 16.1 1.0
C A:SER171 4.8 15.3 1.0
N A:GLU172 4.9 15.4 1.0
C A:ASP170 4.9 12.1 1.0

Reference:

W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson. Dna Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-Rule". J.Biol.Chem. V. 284 31680 2009.
ISSN: ISSN 0021-9258
PubMed: 19759017
DOI: 10.1074/JBC.M109.029843
Page generated: Sun Aug 17 15:50:37 2025

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