Atomistry » Calcium » PDB 5vlk-5w4t » 5vrx
Atomistry »
  Calcium »
    PDB 5vlk-5w4t »
      5vrx »

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

Go back to Calcium Binding Sites List in 5vrx
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: Mon Jul 15 12:35:43 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy