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Calcium in PDB 5vrx: Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation

Enzymatic activity of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation

All present enzymatic activity of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation, PDB code: 5vrx was solved by A.J.Reed, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.72 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.000, 80.100, 55.600, 90.00, 107.20, 90.00
R / Rfree (%) 18.7 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation (pdb code 5vrx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation, PDB code: 5vrx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5vrx

Go back to Calcium Binding Sites List in 5vrx
Calcium binding site 1 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca101

b:28.8
occ:1.00
 OD1 A:ASP192 2.3 20.0 1.0
O3' P:DC10 2.3 22.4 1.0
OD2 A:ASP190 2.3 29.4 1.0
OD2 A:ASP256 2.4 25.8 1.0
O A:HOH571 2.6 27.3 1.0
O2A P:TTP103 2.6 23.3 1.0
OD1 A:ASP190 2.6 22.9 1.0
CG A:ASP190 2.8 24.9 1.0
O5' P:TTP103 3.3 26.7 1.0
CG A:ASP192 3.3 18.8 1.0
PA P:TTP103 3.5 24.0 1.0
CG A:ASP256 3.5 22.3 1.0
C3' P:DC10 3.5 22.6 1.0
OD2 A:ASP192 3.7 19.8 1.0
CA A:CA401 3.8 21.2 1.0
O1A P:TTP103 4.0 26.8 1.0
CB A:ASP256 4.1 21.4 1.0
C4' P:DC10 4.1 21.5 1.0
C5' P:DC10 4.2 21.4 1.0
O P:HOH207 4.2 25.9 1.0
CB A:ASP190 4.3 22.2 1.0
C5' P:TTP103 4.4 22.6 1.0
OD1 A:ASP256 4.5 23.7 1.0
O A:MET191 4.6 18.6 1.0
CB A:ASP192 4.6 19.3 1.0
C2' P:DC10 4.8 22.3 1.0
O5' P:DC10 4.9 20.9 1.0
NH2 A:ARG254 4.9 23.3 1.0
C A:MET191 4.9 19.0 1.0
O3A P:TTP103 4.9 24.1 1.0
OP1 P:DC10 4.9 20.6 1.0

Calcium binding site 2 out of 5 in 5vrx

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Calcium binding site 2 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca102

b:44.5
occ:1.00
 OP1 P:DC9 2.3 19.8 1.0
O P:HOH210 2.4 28.2 1.0
O A:THR101 2.5 26.6 1.0
O P:HOH202 2.5 26.4 1.0
O A:VAL103 2.6 17.5 1.0
O A:ILE106 2.7 19.5 1.0
P P:DC9 3.3 22.8 1.0
C A:THR101 3.4 25.2 1.0
OP2 P:DC9 3.4 21.6 1.0
C A:VAL103 3.5 20.3 1.0
C A:ILE106 3.7 20.3 1.0
N A:GLY105 3.8 19.1 1.0
CA A:SER104 3.9 19.6 1.0
N A:ILE106 3.9 21.4 1.0
N A:SER104 4.0 20.6 1.0
CA A:THR101 4.1 27.4 1.0
N A:VAL103 4.2 20.0 1.0
C A:ARG102 4.2 20.6 1.0
C A:SER104 4.2 19.3 1.0
O3' P:DG8 4.3 22.4 1.0
CA A:ILE106 4.3 20.2 1.0
N A:ARG102 4.4 22.3 1.0
O5' P:DC9 4.5 20.2 1.0
CA A:VAL103 4.5 20.5 1.0
CA A:ARG102 4.5 22.3 1.0
CB A:THR101 4.6 28.2 1.0
N A:GLY107 4.6 21.4 1.0
C A:GLY105 4.6 19.3 1.0
CB A:ILE106 4.7 21.4 1.0
O A:ARG102 4.7 20.1 1.0
CA A:GLY105 4.7 20.8 1.0
CA A:GLY107 4.9 21.9 1.0

Calcium binding site 3 out of 5 in 5vrx

Go back to Calcium Binding Sites List in 5vrx
Calcium binding site 3 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:59.8
occ:1.00
 O A:HOH572 2.3 30.8 1.0
O A:LYS60 2.3 37.1 1.0
O A:LEU62 2.4 36.1 1.0
O A:VAL65 2.6 39.6 1.0
OP1 D:DC3 2.7 40.6 1.0
C A:LYS60 3.5 38.4 1.0
C A:LEU62 3.5 34.1 1.0
C A:VAL65 3.7 34.5 1.0
OP2 D:DC3 3.7 30.8 1.0
P D:DC3 3.7 38.8 1.0
N A:VAL65 4.0 33.0 1.0
N A:LEU62 4.1 33.2 1.0
C A:LYS61 4.1 35.5 1.0
N A:GLY64 4.2 35.9 1.0
CA A:PRO63 4.2 35.3 1.0
CA A:VAL65 4.3 33.3 1.0
N A:PRO63 4.3 34.4 1.0
O A:LYS61 4.3 35.6 1.0
CA A:LYS60 4.4 36.5 1.0
N A:LYS61 4.4 36.0 1.0
CA A:LEU62 4.4 34.2 1.0
CB A:VAL65 4.5 32.4 1.0
CA A:LYS61 4.5 34.5 1.0
C A:PRO63 4.6 36.5 1.0
N A:GLY66 4.7 34.7 1.0
O3' D:DT2 4.7 37.7 1.0
CG A:LYS60 4.8 48.1 1.0
O5' D:DC3 4.8 38.4 1.0
O A:ALA59 4.9 25.6 1.0
C A:GLY64 5.0 35.2 1.0
CA A:GLY66 5.0 32.8 1.0

Calcium binding site 4 out of 5 in 5vrx

Go back to Calcium Binding Sites List in 5vrx
Calcium binding site 4 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:21.2
occ:1.00
 O2A P:TTP103 2.2 23.3 1.0
OD1 A:ASP190 2.3 22.9 1.0
O A:HOH539 2.3 18.0 1.0
OD2 A:ASP192 2.4 19.8 1.0
O2B P:TTP103 2.4 22.4 1.0
O3G P:TTP103 2.4 24.7 1.0
O A:ASP190 3.1 20.4 1.0
CG A:ASP192 3.3 18.8 1.0
PB P:TTP103 3.4 20.7 1.0
CG A:ASP190 3.5 24.9 1.0
PA P:TTP103 3.5 24.0 1.0
OD1 A:ASP192 3.6 20.0 1.0
C A:ASP190 3.6 20.7 1.0
PG P:TTP103 3.6 24.6 1.0
O3A P:TTP103 3.7 24.1 1.0
CA P:CA101 3.8 28.8 1.0
N A:ASP190 3.9 20.3 1.0
O3B P:TTP103 3.9 25.4 1.0
O P:HOH207 3.9 25.9 1.0
O5' P:TTP103 4.0 26.7 1.0
O A:HOH564 4.1 19.5 1.0
CA A:ASP190 4.1 20.8 1.0
O1G P:TTP103 4.3 25.9 1.0
OD2 A:ASP190 4.3 29.4 1.0
CB A:ASP190 4.3 22.2 1.0
OG A:SER180 4.4 20.9 1.0
N A:MET191 4.5 21.9 1.0
N A:SER180 4.6 20.2 1.0
CB A:ASP192 4.7 19.3 1.0
CA A:GLY179 4.7 19.2 1.0
O1B P:TTP103 4.7 21.8 1.0
N A:ASP192 4.8 18.8 1.0
O1A P:TTP103 4.8 26.8 1.0
CA A:MET191 4.8 22.1 1.0
O2G P:TTP103 4.8 27.0 1.0
C A:MET191 4.8 19.0 1.0
C A:GLY189 5.0 21.4 1.0
N A:GLY189 5.0 22.9 1.0

Calcium binding site 5 out of 5 in 5vrx

Go back to Calcium Binding Sites List in 5vrx
Calcium binding site 5 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Watson-Crick Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:65.2
occ:1.00
 O A:HOH581 2.2 32.1 1.0
OE2 A:GLU249 2.6 37.4 1.0
OE1 A:GLU249 2.9 36.1 1.0
CD A:GLU249 3.1 35.8 1.0
OE1 A:GLN240 4.4 25.3 1.0
CG A:GLU249 4.6 32.4 1.0
O A:HOH544 4.7 28.9 1.0
NE2 A:GLN240 4.9 23.3 1.0

Reference:

A.J.Reed, Z.Suo. Time-Dependent Extension From An 8-Oxoguanine Lesion By Human Dna Polymerase Beta. J. Am. Chem. Soc. V. 139 9684 2017.
ISSN: ESSN 1520-5126
PubMed: 28682600
DOI: 10.1021/JACS.7B05048
Page generated: Wed Jul 9 10:51:53 2025

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