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Sodium in PDB 5j0x: Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus

Enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus, PDB code: 5j0x was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.400, 79.300, 54.700, 90.00, 105.50, 90.00
R / Rfree (%) 19.3 / 24.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus (pdb code 5j0x). 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 Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus, PDB code: 5j0x:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5j0x

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Sodium binding site 1 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the 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 Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:11.5
occ:1.00
 O A:THR101 2.3 14.3 1.0
OP1 P:DG9 2.3 9.3 1.0
O A:VAL103 2.4 13.2 1.0
O A:ILE106 2.4 11.8 1.0
O P:HOH119 2.5 13.8 1.0
O A:HOH786 2.7 18.6 1.0
NA A:NA404 3.3 23.3 1.0
C A:THR101 3.3 13.2 1.0
C A:VAL103 3.4 13.0 1.0
C A:ILE106 3.4 11.9 1.0
P P:DG9 3.5 13.4 1.0
N A:ILE106 3.7 10.2 1.0
OP2 P:DG9 3.7 13.3 1.0
CA A:SER104 3.8 10.5 1.0
N A:GLY105 3.9 9.5 1.0
CA A:THR101 3.9 12.8 1.0
N A:SER104 4.0 12.1 1.0
CA A:ILE106 4.0 11.0 1.0
N A:VAL103 4.1 11.4 1.0
C A:SER104 4.2 9.0 1.0
C A:ARG102 4.3 13.9 1.0
N A:ARG102 4.4 13.9 1.0
N A:GLY107 4.4 10.9 1.0
CA A:VAL103 4.4 12.7 1.0
CB A:THR101 4.4 12.6 1.0
O3' P:DC8 4.4 11.9 1.0
CB A:ILE106 4.4 12.5 1.0
C A:GLY105 4.6 10.2 1.0
O5' P:DG9 4.6 13.1 1.0
CA A:GLY107 4.6 12.9 1.0
CA A:ARG102 4.6 12.5 1.0
CA A:GLY105 4.9 9.4 1.0
O A:ARG102 4.9 13.4 1.0
O A:HOH540 4.9 24.1 1.0
O A:LEU100 4.9 16.2 1.0

Sodium binding site 2 out of 4 in 5j0x

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Sodium binding site 2 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the 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 Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.1
occ:1.00
 O A:VAL65 2.2 20.7 1.0
O D:HOH119 2.3 19.6 1.0
O A:LYS60 2.3 25.7 1.0
OP1 D:DC3 2.6 21.8 1.0
O A:HOH777 2.7 34.0 1.0
O A:LEU62 2.7 20.4 1.0
C A:VAL65 3.3 18.2 1.0
C A:LYS60 3.4 24.8 1.0
P D:DC3 3.7 19.8 1.0
C A:LEU62 3.7 21.1 1.0
N A:VAL65 3.7 17.4 1.0
O D:HOH115 3.7 37.6 1.0
OP2 D:DC3 3.8 19.5 1.0
CA A:VAL65 4.0 17.9 1.0
CA A:LYS60 4.1 22.1 1.0
CG A:LYS60 4.1 24.2 1.0
N A:GLY64 4.1 20.1 1.0
N A:LEU62 4.3 23.6 1.0
CB A:VAL65 4.3 16.7 1.0
CA A:PRO63 4.3 21.7 1.0
N A:GLY66 4.3 17.6 1.0
C A:LYS61 4.4 25.0 1.0
N A:PRO63 4.4 21.7 1.0
N A:LYS61 4.5 25.1 1.0
O3' D:DT2 4.6 19.5 1.0
CA A:GLY66 4.6 17.6 1.0
CA A:LEU62 4.6 21.9 1.0
C A:PRO63 4.6 20.2 1.0
CA A:LYS61 4.7 24.7 1.0
O A:LYS61 4.7 25.1 1.0
CB A:LYS60 4.7 23.2 1.0
C A:GLY64 4.7 18.8 1.0
NZ A:LYS60 4.8 22.4 1.0
O A:ALA59 4.9 20.8 1.0
O5' D:DC3 4.9 18.2 1.0

Sodium binding site 3 out of 4 in 5j0x

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Sodium binding site 3 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:18.3
occ:1.00
 OG A:SER171 2.1 12.7 1.0
O A:HOH730 2.3 20.9 1.0
O A:HOH762 2.4 25.4 1.0
CB A:SER171 3.3 15.3 1.0
N A:SER171 3.9 14.2 1.0
CA A:SER171 4.2 14.6 1.0
O A:HOH597 4.2 20.0 1.0
O A:HOH846 4.3 35.7 1.0
OD1 A:ASP170 4.6 16.8 1.0
O A:HOH815 4.7 48.5 1.0
C A:SER171 4.9 15.0 1.0
N A:GLU172 4.9 14.0 1.0

Sodium binding site 4 out of 4 in 5j0x

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Sodium binding site 4 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Binary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:23.3
occ:1.00
 O A:HOH835 2.3 28.2 1.0
O P:HOH119 2.5 13.8 1.0
O A:HOH692 2.6 15.8 1.0
O A:HOH786 2.6 18.6 1.0
O A:THR101 2.6 14.3 1.0
O A:HOH856 2.7 27.7 1.0
NA A:NA401 3.3 11.5 1.0
C A:THR101 3.6 13.2 1.0
O A:HOH590 3.7 40.4 1.0
CA A:ARG102 4.1 12.5 1.0
N A:ARG102 4.2 13.9 1.0
NZ A:LYS27 4.3 22.9 1.0
O A:HOH540 4.4 24.1 1.0
CB A:THR101 4.4 12.6 1.0
OG1 A:THR101 4.5 13.5 1.0
C A:ARG102 4.6 13.9 1.0
CA A:THR101 4.6 12.8 1.0
O A:HOH855 4.7 16.5 1.0
O P:HOH111 4.7 22.1 1.0
OP1 P:DG9 4.7 9.3 1.0
OP2 P:DG9 4.8 13.3 1.0
O A:HOH533 4.9 25.1 1.0
O A:ARG102 4.9 13.4 1.0
O A:HOH805 5.0 36.8 1.0

Reference:

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006
Page generated: Mon Aug 18 00:24:49 2025

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