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

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

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

Resolution Low / High (Å) 22.10 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.510, 79.400, 54.710, 90.00, 105.75, 90.00
R / Rfree (%) 17.4 / 22.9

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 5tzv

Go back to Sodium Binding Sites List in 5tzv
Sodium binding site 1 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with G:T 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:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:5.4
occ:1.00
 O A:THR101 2.3 7.7 1.0
O A:ILE106 2.4 5.6 1.0
OP1 P:DG9 2.4 6.5 1.0
O A:VAL103 2.5 7.2 1.0
O P:HOH116 2.5 8.6 1.0
O A:HOH805 2.6 11.8 1.0
NA A:NA404 3.3 19.8 1.0
C A:ILE106 3.4 6.0 1.0
C A:THR101 3.4 7.4 1.0
C A:VAL103 3.4 7.6 1.0
P P:DG9 3.4 9.6 1.0
OP2 P:DG9 3.7 10.4 1.0
N A:ILE106 3.8 4.5 1.0
CA A:SER104 3.9 8.6 1.0
CA A:THR101 3.9 6.8 1.0
N A:SER104 4.0 5.6 1.0
N A:GLY105 4.0 8.4 1.0
CA A:ILE106 4.1 5.2 1.0
N A:VAL103 4.2 8.5 1.0
C A:SER104 4.3 6.7 1.0
O P:HOH144 4.3 30.4 1.0
N A:GLY107 4.3 7.0 1.0
C A:ARG102 4.4 8.1 1.0
CB A:THR101 4.4 9.0 1.0
N A:ARG102 4.4 9.4 1.0
O A:HOH794 4.4 26.7 1.0
CA A:VAL103 4.4 8.2 1.0
O3' P:DC8 4.5 7.6 1.0
O5' P:DG9 4.5 8.8 1.0
CB A:ILE106 4.5 7.7 1.0
C A:GLY105 4.6 6.3 1.0
CA A:GLY107 4.6 7.3 1.0
CA A:ARG102 4.7 7.8 1.0
O A:HOH803 4.8 22.2 1.0
CA A:GLY105 4.9 7.9 1.0
O A:ARG102 4.9 8.5 1.0
O A:HOH619 4.9 12.1 1.0
O A:LEU100 5.0 9.8 1.0

Sodium binding site 2 out of 4 in 5tzv

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

b:17.2
occ:1.00
 O A:VAL65 2.3 16.9 1.0
O D:HOH116 2.3 17.4 1.0
O A:LYS60 2.4 17.1 1.0
O A:LEU62 2.4 17.0 1.0
O A:HOH811 2.8 26.1 1.0
OP1 D:DC3 2.8 18.5 1.0
C A:VAL65 3.3 14.9 1.0
C A:LEU62 3.4 17.3 1.0
C A:LYS60 3.5 19.6 1.0
N A:VAL65 3.6 11.2 1.0
O A:HOH752 3.8 30.6 1.0
P D:DC3 3.8 14.1 1.0
O D:HOH118 3.9 24.2 1.0
CA A:VAL65 3.9 11.8 1.0
OP2 D:DC3 4.0 9.9 1.0
N A:LEU62 4.0 16.3 1.0
N A:GLY64 4.0 18.2 1.0
CA A:PRO63 4.0 16.8 1.0
N A:PRO63 4.1 18.9 1.0
C A:LYS61 4.2 20.2 1.0
CA A:LYS60 4.2 14.1 1.0
CB A:VAL65 4.2 12.6 1.0
CA A:LEU62 4.3 15.4 1.0
C A:PRO63 4.4 15.0 1.0
N A:GLY66 4.4 11.3 1.0
N A:LYS61 4.5 18.7 1.0
O A:LYS61 4.5 19.2 1.0
CA A:LYS61 4.6 18.7 1.0
C A:GLY64 4.6 16.0 1.0
O3' D:DT2 4.6 12.5 1.0
CG A:LYS60 4.7 24.7 1.0
CD A:LYS60 4.7 22.6 1.0
CA A:GLY66 4.8 11.9 1.0
O A:ALA59 4.8 13.7 1.0
CA A:GLY64 4.9 14.3 1.0

Sodium binding site 3 out of 4 in 5tzv

Go back to Sodium Binding Sites List in 5tzv
Sodium binding site 3 out of 4 in the Binary Complex Crystal Structure of Dna Polymerase Beta with G:T 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:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:16.2
occ:1.00
 OG A:SER171 2.4 8.3 1.0
O A:HOH774 2.4 15.3 1.0
O A:HOH620 2.5 14.6 1.0
CB A:SER171 3.6 12.2 1.0
N A:SER171 4.0 9.8 1.0
O A:HOH606 4.3 12.4 1.0
CA A:SER171 4.4 11.3 1.0
O A:HOH833 4.5 25.1 1.0
O A:HOH893 4.5 23.5 1.0
OD1 A:ASP170 4.6 11.0 1.0
C A:SER171 5.0 14.0 1.0

Sodium binding site 4 out of 4 in 5tzv

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

b:19.8
occ:1.00
 O A:HOH871 2.3 17.7 1.0
O A:HOH803 2.4 22.2 1.0
O A:HOH805 2.5 11.8 1.0
O A:THR101 2.5 7.7 1.0
O A:HOH659 2.6 18.2 1.0
O P:HOH116 2.7 8.6 1.0
NA A:NA401 3.3 5.4 1.0
C A:THR101 3.5 7.4 1.0
O P:HOH144 3.6 30.4 1.0
O A:HOH798 3.9 28.2 1.0
CA A:ARG102 3.9 7.8 1.0
O A:HOH794 4.0 26.7 1.0
N A:ARG102 4.1 9.4 1.0
O P:HOH156 4.1 26.2 1.0
NZ A:LYS27 4.4 19.5 1.0
C A:ARG102 4.5 8.1 1.0
CB A:THR101 4.5 9.0 1.0
OG1 A:THR101 4.5 8.2 1.0
CA A:THR101 4.6 6.8 1.0
O A:HOH641 4.6 17.0 1.0
O A:HOH619 4.6 12.1 1.0
O A:HOH875 4.8 19.5 1.0
O A:ARG102 4.8 8.5 1.0
OP1 P:DG9 4.9 6.5 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: Tue Oct 8 00:19:57 2024

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