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Sodium in PDB 5j0r: Binary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus

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

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

Protein crystallography data

The structure of Binary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus, PDB code: 5j0r 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) 19.13 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.590, 79.490, 55.000, 90.00, 105.58, 90.00
R / Rfree (%) 20.8 / 27.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with C:A Mismatch at the Primer Terminus (pdb code 5j0r). 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 C:A Mismatch at the Primer Terminus, PDB code: 5j0r:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5j0r

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

b:10.7
occ:1.00
 O A:THR101 2.2 14.0 1.0
O A:ILE106 2.4 9.4 1.0
O A:VAL103 2.4 9.3 1.0
OP1 P:DG9 2.5 9.9 1.0
O P:HOH106 2.6 10.2 1.0
O A:HOH752 2.7 12.3 1.0
C A:THR101 3.3 10.6 1.0
C A:VAL103 3.3 13.0 1.0
NA A:NA403 3.3 19.4 1.0
C A:ILE106 3.3 9.3 1.0
P P:DG9 3.5 12.3 1.0
OP2 P:DG9 3.7 10.2 1.0
N A:ILE106 3.7 9.8 1.0
CA A:THR101 3.8 8.8 1.0
CA A:SER104 3.9 9.1 1.0
N A:SER104 4.0 11.2 1.0
N A:GLY105 4.0 9.7 1.0
CA A:ILE106 4.0 9.2 1.0
N A:VAL103 4.1 8.9 1.0
C A:ARG102 4.3 11.5 1.0
N A:ARG102 4.3 12.8 1.0
C A:SER104 4.3 9.0 1.0
N A:GLY107 4.3 9.5 1.0
CA A:VAL103 4.3 8.9 1.0
CB A:THR101 4.4 10.6 1.0
CB A:ILE106 4.4 10.6 1.0
O P:HOH107 4.5 28.1 1.0
O3' P:DC8 4.5 9.8 1.0
CA A:ARG102 4.6 10.9 1.0
C A:GLY105 4.6 10.8 1.0
CA A:GLY107 4.6 10.2 1.0
O5' P:DG9 4.7 11.2 1.0
O A:LEU100 4.8 8.3 1.0
O A:ARG102 4.8 11.2 1.0
CA A:GLY105 4.9 8.6 1.0
O A:HOH734 5.0 13.4 1.0

Sodium binding site 2 out of 4 in 5j0r

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

b:16.1
occ:1.00
 O D:HOH116 2.2 17.6 1.0
O A:VAL65 2.3 19.1 1.0
O A:LYS60 2.3 18.0 1.0
O A:LEU62 2.5 21.0 1.0
O A:HOH728 2.7 21.1 1.0
OP1 D:DC3 2.9 19.6 1.0
C A:VAL65 3.3 17.2 1.0
C A:LYS60 3.4 21.7 1.0
C A:LEU62 3.5 22.1 1.0
N A:VAL65 3.6 17.8 1.0
P D:DC3 3.8 17.4 1.0
CA A:VAL65 3.9 15.3 1.0
OP2 D:DC3 3.9 12.7 1.0
O D:HOH115 4.0 28.1 1.0
N A:LEU62 4.1 20.7 1.0
N A:GLY64 4.1 20.5 1.0
C A:LYS61 4.1 21.9 1.0
CA A:LYS60 4.2 16.3 1.0
CB A:VAL65 4.2 18.0 1.0
CA A:PRO63 4.2 19.7 1.0
N A:PRO63 4.3 18.8 1.0
O A:LYS61 4.4 31.9 1.0
N A:LYS61 4.4 21.8 1.0
N A:GLY66 4.4 14.2 1.0
CA A:LEU62 4.5 20.7 1.0
CG A:LYS60 4.5 26.3 1.0
CA A:LYS61 4.5 22.7 1.0
C A:PRO63 4.5 21.1 1.0
C A:GLY64 4.6 20.1 1.0
O3' D:DT2 4.6 14.8 1.0
CD A:LYS60 4.7 19.2 1.0
O A:ALA59 4.8 21.1 1.0
CA A:GLY66 4.8 12.1 1.0
CB A:LYS60 4.9 19.7 1.0
CA A:GLY64 4.9 21.6 1.0
CG1 A:VAL65 5.0 18.4 1.0

Sodium binding site 3 out of 4 in 5j0r

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Sodium binding site 3 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with C:A 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 C:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.4
occ:1.00
 O A:HOH734 2.4 13.4 1.0
O A:HOH766 2.4 19.9 1.0
O A:HOH827 2.5 18.0 1.0
O A:HOH752 2.6 12.3 1.0
O A:THR101 2.6 14.0 1.0
O P:HOH106 2.9 10.2 1.0
NA A:NA401 3.3 10.7 1.0
C A:THR101 3.5 10.6 1.0
O P:HOH107 3.9 28.1 1.0
CA A:ARG102 3.9 10.9 1.0
O P:HOH148 3.9 27.8 1.0
N A:ARG102 4.1 12.8 1.0
O A:HOH507 4.3 24.1 1.0
C A:ARG102 4.4 11.5 1.0
CB A:THR101 4.5 10.6 1.0
NZ A:LYS27 4.5 27.9 1.0
CA A:THR101 4.6 8.8 1.0
OG1 A:THR101 4.6 14.0 1.0
O A:ARG102 4.7 11.2 1.0
O P:HOH109 4.8 22.7 1.0
OP1 P:DG9 4.9 9.9 1.0
O A:HOH815 4.9 21.8 1.0
OP2 P:DG9 4.9 10.2 1.0

Sodium binding site 4 out of 4 in 5j0r

Go back to Sodium Binding Sites List in 5j0r
Sodium binding site 4 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with C:A 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 C:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:23.1
occ:1.00
 OG A:SER171 2.3 14.4 1.0
O A:HOH714 2.4 18.0 1.0
O A:HOH573 2.7 24.5 1.0
CB A:SER171 3.5 12.6 1.0
N A:SER171 3.9 10.8 1.0
O A:HOH597 4.2 22.8 1.0
CA A:SER171 4.3 11.6 1.0
OD1 A:ASP170 4.6 13.3 1.0
O A:HOH834 4.7 27.5 1.0
O A:HOH528 4.9 21.6 1.0
C A:SER171 5.0 15.6 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 Oct 7 21:45:29 2024

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