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Sodium in PDB 5j0y: Binary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus

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

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus, PDB code: 5j0y 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 (°) 54.600, 79.100, 54.500, 90.00, 106.10, 90.00
R / Rfree (%) 18.9 / 24.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus (pdb code 5j0y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Binary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus, PDB code: 5j0y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5j0y

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Sodium binding site 1 out of 6 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:11.6
occ:1.00
 O A:THR101 2.3 10.5 1.0
OP1 P:DG9 2.4 11.6 1.0
O A:ILE106 2.4 10.0 1.0
O A:VAL103 2.5 9.1 1.0
O P:HOH204 2.5 11.8 1.0
O A:HOH765 2.5 12.9 1.0
NA A:NA403 3.3 19.6 1.0
C A:THR101 3.3 11.7 1.0
C A:VAL103 3.4 10.7 1.0
C A:ILE106 3.4 9.8 1.0
P P:DG9 3.5 12.0 1.0
N A:ILE106 3.7 9.0 1.0
OP2 P:DG9 3.8 7.9 1.0
CA A:THR101 3.9 11.1 1.0
CA A:SER104 3.9 9.0 1.0
N A:GLY105 4.0 10.3 1.0
N A:SER104 4.0 9.8 1.0
N A:VAL103 4.0 12.1 1.0
CA A:ILE106 4.1 9.6 1.0
C A:ARG102 4.3 12.3 1.0
N A:ARG102 4.3 12.4 1.0
C A:SER104 4.3 8.7 1.0
CA A:VAL103 4.3 10.6 1.0
N A:GLY107 4.4 11.7 1.0
CB A:THR101 4.4 11.2 1.0
CB A:ILE106 4.5 10.4 1.0
O3' P:DC8 4.5 11.4 1.0
O P:HOH243 4.5 30.2 1.0
CA A:ARG102 4.6 13.1 1.0
CA A:GLY107 4.6 11.4 1.0
C A:GLY105 4.6 10.7 1.0
O5' P:DG9 4.7 13.6 1.0
O A:ARG102 4.8 14.3 1.0
O A:HOH536 4.8 26.4 1.0
O A:HOH812 4.9 26.1 1.0
O A:LEU100 4.9 11.6 1.0
CA A:GLY105 4.9 9.5 1.0
O A:HOH630 5.0 15.7 1.0
O A:HOH721 5.0 27.1 1.0

Sodium binding site 2 out of 6 in 5j0y

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Sodium binding site 2 out of 6 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:28.9
occ:1.00
 O A:HOH793 2.3 27.9 1.0
O A:LYS60 2.4 23.9 1.0
O D:HOH116 2.5 29.7 1.0
O A:VAL65 2.5 17.2 1.0
O A:LEU62 2.6 20.9 1.0
OP1 D:DC3 2.6 19.5 1.0
C A:VAL65 3.6 17.8 1.0
C A:LYS60 3.6 24.8 1.0
C A:LEU62 3.6 22.3 1.0
P D:DC3 3.7 18.0 1.0
OP2 D:DC3 3.8 16.4 1.0
N A:VAL65 3.9 17.8 1.0
CA A:VAL65 4.2 18.0 1.0
C A:LYS61 4.2 24.9 1.0
N A:GLY64 4.2 21.1 1.0
N A:LEU62 4.2 23.3 1.0
CA A:PRO63 4.2 22.7 1.0
N A:PRO63 4.3 22.3 1.0
O A:LYS61 4.4 24.9 1.0
CB A:VAL65 4.4 18.4 1.0
CA A:LYS60 4.5 23.4 1.0
N A:LYS61 4.5 24.6 1.0
CA A:LYS61 4.5 25.2 1.0
CA A:LEU62 4.5 22.4 1.0
C A:PRO63 4.6 22.3 1.0
O3' D:DT2 4.6 17.0 1.0
N A:GLY66 4.7 15.6 1.0
NZ A:LYS60 4.7 26.1 1.0
CD A:LYS60 4.8 27.4 1.0
O5' D:DC3 4.8 17.0 1.0
C A:GLY64 4.8 19.5 1.0
CG A:LYS60 4.9 28.7 1.0
O A:ALA59 4.9 20.7 1.0
CA A:GLY66 5.0 16.8 1.0

Sodium binding site 3 out of 6 in 5j0y

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Sodium binding site 3 out of 6 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.6
occ:1.00
 O A:HOH859 2.3 22.7 1.0
O A:HOH812 2.4 26.1 1.0
O A:HOH765 2.5 12.9 1.0
O A:THR101 2.5 10.5 1.0
O A:HOH630 2.5 15.7 1.0
O P:HOH204 2.9 11.8 1.0
NA A:NA401 3.3 11.6 1.0
C A:THR101 3.5 11.7 1.0
CA A:ARG102 3.9 13.1 1.0
O P:HOH243 4.0 30.2 1.0
N A:ARG102 4.1 12.4 1.0
O A:HOH536 4.3 26.4 1.0
C A:ARG102 4.4 12.3 1.0
OG1 A:THR101 4.5 13.4 1.0
CB A:THR101 4.5 11.2 1.0
O A:HOH566 4.6 19.1 1.0
O A:HOH867 4.6 23.1 1.0
CA A:THR101 4.6 11.1 1.0
O A:ARG102 4.7 14.3 1.0
OP1 P:DG9 4.8 11.6 1.0
O A:HOH721 4.8 27.1 1.0
NZ A:LYS27 5.0 29.4 1.0
O P:HOH237 5.0 45.6 1.0
OP2 P:DG9 5.0 7.9 1.0

Sodium binding site 4 out of 6 in 5j0y

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Sodium binding site 4 out of 6 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:21.1
occ:1.00
 O A:HOH738 2.3 19.9 1.0
O A:HOH776 2.3 20.1 1.0
OG A:SER171 2.4 11.8 1.0
CB A:SER171 3.6 14.1 1.0
O A:HOH865 3.9 30.1 1.0
N A:SER171 4.1 14.2 1.0
CA A:SER171 4.4 14.3 1.0
O A:HOH647 4.4 16.5 1.0
OD1 A:ASP170 4.8 19.1 1.0
O A:HOH881 4.9 35.7 1.0
O A:HOH680 4.9 33.7 1.0

Sodium binding site 5 out of 6 in 5j0y

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Sodium binding site 5 out of 6 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 5 of Binary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:29.8
occ:1.00
 O T:HOH247 2.3 25.0 1.0
O4' T:DC8 2.3 24.1 1.0
O2 T:DT7 2.4 32.4 1.0
O A:HOH645 2.4 44.8 1.0
O2 T:DC8 2.6 16.9 1.0
O A:HOH766 2.6 34.0 1.0
C1' T:DC8 3.1 22.5 1.0
C4' T:DC8 3.2 25.9 1.0
C2 T:DC8 3.2 16.9 1.0
C2 T:DT7 3.5 31.7 1.0
N1 T:DC8 3.5 21.7 1.0
O A:HOH736 3.9 37.4 1.0
C5' T:DC8 4.0 28.2 1.0
N3 T:DC8 4.3 17.3 1.0
N3 T:DT7 4.3 30.1 1.0
C3' T:DC8 4.4 24.2 1.0
N1 T:DT7 4.4 32.7 1.0
C1' T:DT7 4.4 32.7 1.0
C2' T:DC8 4.4 23.0 1.0
OH A:TYR296 4.5 28.8 1.0
O2 P:DT10 4.6 25.5 1.0
O3' T:DC8 4.6 27.5 1.0
OE1 A:GLU295 4.7 29.1 1.0
C6 T:DC8 4.7 19.7 1.0
N2 P:DG9 4.7 13.7 1.0
O A:HOH696 4.8 37.4 1.0
NZ A:LYS234 4.8 31.2 1.0
O A:HOH627 4.9 33.1 1.0
O A:HOH505 4.9 35.4 1.0
O5' T:DC8 5.0 30.5 1.0

Sodium binding site 6 out of 6 in 5j0y

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Sodium binding site 6 out of 6 in the Binary Complex Crystal Structure of Dna Polymerase Beta with T: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 6 of Binary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:31.3
occ:1.00
 O P:HOH238 2.2 26.9 1.0
O T:HOH250 2.4 24.3 1.0
O2 P:DT3 2.4 24.6 1.0
O P:HOH224 2.5 21.9 1.0
O4' P:DG4 2.9 27.8 1.0
C4' P:DG4 3.6 27.4 1.0
C2 P:DT3 3.6 25.6 1.0
C1' P:DG4 3.7 26.6 1.0
N9 P:DG4 4.0 25.6 1.0
C2 T:DA14 4.2 18.9 1.0
C1' P:DT3 4.2 28.5 1.0
O T:HOH245 4.3 30.7 1.0
C5' P:DG4 4.3 28.0 1.0
N3 P:DG4 4.3 21.4 1.0
C4 P:DG4 4.3 21.5 1.0
N2 T:DG15 4.3 20.0 1.0
N1 P:DT3 4.5 26.0 1.0
O T:HOH231 4.5 28.6 1.0
N3 P:DT3 4.6 23.1 1.0
N3 T:DG15 4.8 21.6 1.0
N1 T:DA14 4.8 16.8 1.0
C8 P:DG4 4.8 24.1 1.0
C3' P:DG4 4.9 26.2 1.0
C2 T:DG15 4.9 21.7 1.0
N3 T:DA14 4.9 20.1 1.0
C2' P:DG4 5.0 27.5 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: Mon Oct 7 21:47:28 2024

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