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Sodium in PDB 5j0t: Binary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus

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

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with G: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 G:A Mismatch at the Primer Terminus, PDB code: 5j0t 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, 79.200, 54.700, 90.00, 106.10, 90.00
R / Rfree (%) 20.1 / 25.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus (pdb code 5j0t). 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 G:A Mismatch at the Primer Terminus, PDB code: 5j0t:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5j0t

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

b:8.7
occ:1.00
 O A:THR101 2.3 13.9 1.0
OP1 P:DG9 2.4 10.7 1.0
O A:ILE106 2.4 12.2 1.0
O P:HOH113 2.4 13.1 1.0
O A:HOH740 2.5 16.0 1.0
O A:VAL103 2.5 11.4 1.0
NA A:NA403 3.3 20.9 1.0
C A:THR101 3.3 13.6 1.0
C A:ILE106 3.4 11.2 1.0
C A:VAL103 3.4 11.9 1.0
P P:DG9 3.5 12.4 1.0
OP2 P:DG9 3.7 11.9 1.0
N A:ILE106 3.8 10.2 1.0
CA A:THR101 3.9 14.4 1.0
N A:GLY105 4.0 11.0 1.0
CA A:SER104 4.0 10.9 1.0
N A:SER104 4.1 11.5 1.0
N A:VAL103 4.1 11.1 1.0
CA A:ILE106 4.1 10.3 1.0
C A:ARG102 4.3 13.7 1.0
N A:ARG102 4.3 12.3 1.0
C A:SER104 4.3 10.8 1.0
N A:GLY107 4.4 10.5 1.0
CB A:THR101 4.4 11.3 1.0
CA A:VAL103 4.4 11.2 1.0
O3' P:DC8 4.5 10.0 1.0
CB A:ILE106 4.5 12.0 1.0
O5' P:DG9 4.6 13.1 1.0
CA A:ARG102 4.6 13.0 1.0
C A:GLY105 4.6 11.6 1.0
CA A:GLY107 4.6 11.0 1.0
O A:ARG102 4.8 12.2 1.0
CA A:GLY105 4.9 12.1 1.0
O A:HOH501 4.9 31.5 1.0
O A:LEU100 5.0 15.3 1.0

Sodium binding site 2 out of 4 in 5j0t

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

b:22.1
occ:1.00
 O D:HOH114 2.1 20.6 1.0
O A:VAL65 2.3 19.9 1.0
O A:LYS60 2.4 24.8 1.0
O A:LEU62 2.7 19.1 1.0
OP1 D:DC3 2.7 20.9 1.0
O A:HOH773 2.7 36.9 1.0
C A:VAL65 3.4 17.6 1.0
C A:LYS60 3.5 24.7 1.0
P D:DC3 3.7 16.4 1.0
C A:LEU62 3.7 19.3 1.0
OP2 D:DC3 3.7 17.1 1.0
N A:VAL65 3.8 16.9 1.0
O D:HOH111 4.1 39.1 1.0
CA A:VAL65 4.1 17.1 1.0
N A:GLY64 4.2 19.2 1.0
CA A:LYS60 4.2 22.5 1.0
CG A:LYS60 4.2 25.0 1.0
N A:LEU62 4.3 21.7 1.0
C A:LYS61 4.3 23.0 1.0
CA A:PRO63 4.3 19.4 1.0
CB A:VAL65 4.4 17.2 1.0
N A:PRO63 4.4 20.1 1.0
N A:GLY66 4.5 17.2 1.0
N A:LYS61 4.5 23.9 1.0
O A:LYS61 4.5 24.9 1.0
O3' D:DT2 4.5 16.6 1.0
CA A:LEU62 4.6 20.1 1.0
CA A:LYS61 4.6 23.2 1.0
C A:PRO63 4.7 19.1 1.0
NZ A:LYS60 4.7 26.1 1.0
CA A:GLY66 4.7 17.5 1.0
C A:GLY64 4.8 17.1 1.0
CB A:LYS60 4.9 23.9 1.0
O5' D:DC3 4.9 15.6 1.0

Sodium binding site 3 out of 4 in 5j0t

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

b:20.9
occ:1.00
 O A:HOH806 2.4 21.2 1.0
O A:HOH833 2.5 25.6 1.0
O A:HOH740 2.5 16.0 1.0
O A:THR101 2.6 13.9 1.0
O P:HOH113 2.6 13.1 1.0
O A:HOH669 2.7 17.9 1.0
NA A:NA401 3.3 8.7 1.0
C A:THR101 3.6 13.6 1.0
O A:HOH522 3.9 27.6 1.0
CA A:ARG102 4.0 13.0 1.0
N A:ARG102 4.2 12.3 1.0
O A:HOH501 4.3 31.5 1.0
C A:ARG102 4.4 13.7 1.0
NZ A:LYS27 4.5 26.2 1.0
OG1 A:THR101 4.5 12.9 1.0
CB A:THR101 4.6 11.3 1.0
O A:HOH589 4.7 21.0 1.0
O A:ARG102 4.7 12.2 1.0
CA A:THR101 4.7 14.4 1.0
O A:HOH839 4.7 17.2 1.0
OP1 P:DG9 4.8 10.7 1.0

Sodium binding site 4 out of 4 in 5j0t

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Sodium binding site 4 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with G: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 G:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:17.9
occ:1.00
 OG A:SER171 2.2 10.2 1.0
O A:HOH692 2.3 15.4 1.0
O A:HOH734 2.4 15.6 1.0
CB A:SER171 3.5 11.6 1.0
O A:HOH820 3.8 34.5 1.0
N A:SER171 4.0 13.9 1.0
CA A:SER171 4.3 14.5 1.0
O A:HOH674 4.4 21.0 1.0
O A:HOH832 4.4 35.6 1.0
OD1 A:ASP170 4.7 12.7 1.0
C A:SER171 5.0 16.2 1.0
O A:HOH665 5.0 28.6 1.0
N A:GLU172 5.0 16.9 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 21:46:02 2024

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