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Sodium in PDB 5j0u: Binary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus

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

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with G: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 G:G Mismatch at the Primer Terminus, PDB code: 5j0u 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) 20.68 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.509, 79.473, 54.952, 90.00, 105.66, 90.00
R / Rfree (%) 20.5 / 28.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus (pdb code 5j0u). 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:G Mismatch at the Primer Terminus, PDB code: 5j0u:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5j0u

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

b:13.1
occ:1.00
 O A:ILE106 2.2 15.3 1.0
O A:VAL103 2.4 13.4 1.0
O A:THR101 2.4 14.9 1.0
OP1 P:DG9 2.4 14.5 1.0
O P:HOH116 2.5 13.4 1.0
O A:HOH733 2.8 18.6 1.0
C A:ILE106 3.1 16.6 1.0
C A:VAL103 3.3 17.9 1.0
C A:THR101 3.4 14.6 1.0
NA A:NA404 3.4 25.5 1.0
P P:DG9 3.5 15.2 1.0
N A:ILE106 3.6 13.2 1.0
OP2 P:DG9 3.7 14.1 1.0
CA A:ILE106 3.8 14.5 1.0
CA A:THR101 3.9 13.7 1.0
N A:GLY105 3.9 13.8 1.0
CA A:SER104 3.9 14.4 1.0
N A:SER104 4.0 13.5 1.0
O P:HOH129 4.1 27.4 1.0
N A:GLY107 4.1 15.4 1.0
N A:VAL103 4.1 17.8 1.0
C A:SER104 4.2 11.6 1.0
CB A:ILE106 4.3 15.5 1.0
C A:ARG102 4.3 17.0 1.0
CA A:VAL103 4.4 13.3 1.0
CB A:THR101 4.4 13.5 1.0
C A:GLY105 4.4 14.1 1.0
N A:ARG102 4.4 16.4 1.0
CA A:GLY107 4.5 14.5 1.0
O3' P:DC8 4.5 17.9 1.0
O5' P:DG9 4.6 14.4 1.0
CA A:ARG102 4.7 16.1 1.0
CA A:GLY105 4.8 12.2 1.0
O A:ARG102 4.8 14.8 1.0
O A:LEU100 4.9 15.9 1.0

Sodium binding site 2 out of 4 in 5j0u

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

b:24.2
occ:1.00
 O D:HOH109 2.2 21.4 1.0
O A:VAL65 2.4 24.3 1.0
O A:LYS60 2.5 23.7 1.0
O A:LEU62 2.6 26.8 1.0
O A:HOH597 2.7 28.9 1.0
OP1 D:DC3 2.8 26.5 1.0
C A:VAL65 3.5 18.5 1.0
C A:LEU62 3.6 23.2 1.0
C A:LYS60 3.6 28.0 1.0
P D:DC3 3.7 20.2 1.0
OP2 D:DC3 3.7 17.9 1.0
N A:VAL65 3.9 18.1 1.0
C A:LYS61 4.2 25.0 1.0
CA A:PRO63 4.2 22.9 1.0
CA A:VAL65 4.2 20.4 1.0
N A:GLY64 4.3 21.9 1.0
N A:LEU62 4.3 25.5 1.0
CG A:LYS60 4.3 25.1 1.0
N A:PRO63 4.3 24.1 1.0
O A:LYS61 4.3 28.2 1.0
CA A:LYS60 4.3 24.1 1.0
CB A:VAL65 4.5 21.6 1.0
N A:GLY66 4.5 17.2 1.0
N A:LYS61 4.5 26.3 1.0
CA A:LEU62 4.6 22.6 1.0
C A:PRO63 4.6 26.5 1.0
CA A:LYS61 4.6 26.9 1.0
O3' D:DT2 4.7 22.4 1.0
CA A:GLY66 4.8 14.1 1.0
C A:GLY64 4.9 20.6 1.0
CB A:LYS60 4.9 22.9 1.0
O A:HOH749 4.9 37.8 1.0
NZ A:LYS60 4.9 25.9 1.0
O5' D:DC3 5.0 20.3 1.0

Sodium binding site 3 out of 4 in 5j0u

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

b:24.4
occ:1.00
 OG A:SER171 2.2 18.3 1.0
O A:HOH702 2.5 21.0 1.0
O A:HOH680 2.5 23.1 1.0
CB A:SER171 3.3 22.2 1.0
N A:SER171 4.0 19.4 1.0
O A:HOH542 4.1 21.3 1.0
O A:HOH742 4.2 33.0 1.0
CA A:SER171 4.2 17.4 1.0
OD1 A:ASP170 4.8 21.5 1.0
C A:SER171 4.9 20.9 1.0

Sodium binding site 4 out of 4 in 5j0u

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

b:25.5
occ:1.00
 O A:HOH639 2.5 19.4 1.0
O P:HOH116 2.5 13.4 1.0
O A:THR101 2.5 14.9 1.0
O A:HOH745 2.7 29.1 1.0
O A:HOH775 2.8 30.4 1.0
O A:HOH733 2.8 18.6 1.0
NA A:NA401 3.4 13.1 1.0
C A:THR101 3.5 14.6 1.0
O A:HOH579 3.5 30.8 1.0
O P:HOH129 3.7 27.4 1.0
CA A:ARG102 4.0 16.1 1.0
O A:HOH518 4.1 21.1 1.0
N A:ARG102 4.1 16.4 1.0
NZ A:LYS27 4.2 23.0 1.0
OG1 A:THR101 4.3 13.8 1.0
CB A:THR101 4.3 13.5 1.0
CA A:THR101 4.5 13.7 1.0
C A:ARG102 4.6 17.0 1.0
O A:HOH773 4.8 27.5 1.0
O A:HOH600 4.8 34.0 1.0
O A:ARG102 4.8 14.8 1.0
OP2 P:DG9 4.9 14.1 1.0
O A:ILE106 5.0 15.3 1.0
OP1 P:DG9 5.0 14.5 1.0
O P:HOH118 5.0 17.2 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 21:46:03 2024

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