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Calcium in PDB 5vrw: Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar Conformation

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

All present enzymatic activity of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar 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 Non-Planar Conformation, PDB code: 5vrw 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) 52.85 / 2.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 79.500, 55.300, 90.00, 107.10, 90.00
R / Rfree (%) 23.4 / 30.6

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 Non-Planar Conformation (pdb code 5vrw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar Conformation, PDB code: 5vrw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5vrw

Go back to Calcium Binding Sites List in 5vrw
Calcium binding site 1 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar 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 Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca101

b:41.7
occ:1.00
 OD2 A:ASP190 2.3 32.4 1.0
O3' P:DC10 2.4 31.2 1.0
OD1 A:ASP192 2.4 31.4 1.0
OD2 A:ASP256 2.4 27.6 1.0
O2A P:TTP103 2.6 36.2 1.0
CG A:ASP190 3.1 32.5 1.0
OD1 A:ASP190 3.2 32.6 1.0
CG A:ASP192 3.4 31.0 1.0
PA P:TTP103 3.4 36.3 1.0
C3' P:DC10 3.5 31.3 1.0
O1A P:TTP103 3.6 36.1 1.0
CG A:ASP256 3.7 27.5 1.0
OD2 A:ASP192 3.7 31.4 1.0
O5' P:TTP103 4.0 36.7 1.0
C5' P:DC10 4.1 30.5 1.0
C4' P:DC10 4.1 31.2 1.0
C5' P:TTP103 4.1 36.6 1.0
CA A:CA401 4.2 46.1 1.0
O5' P:DC10 4.2 29.7 1.0
CB A:ASP256 4.4 27.3 1.0
OP1 P:DC10 4.5 28.9 1.0
CB A:ASP190 4.6 32.2 1.0
OD1 A:ASP256 4.6 27.6 1.0
CB A:ASP192 4.8 30.5 1.0
C2' P:DC10 4.8 31.4 1.0
O A:MET191 4.8 30.0 1.0
O3A P:TTP103 4.9 35.6 1.0

Calcium binding site 2 out of 7 in 5vrw

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Calcium binding site 2 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar 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 Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca102

b:46.2
occ:1.00
 OP1 P:DC9 2.2 29.2 1.0
O A:THR101 2.3 29.9 1.0
O P:HOH201 2.4 19.5 1.0
O A:VAL103 2.7 28.5 1.0
O A:ILE106 2.8 31.8 1.0
OP2 P:DC9 2.9 28.7 1.0
P P:DC9 2.9 29.3 1.0
C A:THR101 3.5 29.8 1.0
C A:VAL103 3.6 28.9 1.0
C A:ILE106 3.8 31.5 1.0
CA A:SER104 4.0 29.1 1.0
O3' P:DG8 4.0 29.4 1.0
N A:GLY105 4.0 29.4 1.0
N A:ILE106 4.0 30.6 1.0
O5' P:DC9 4.2 29.3 1.0
N A:SER104 4.2 29.1 1.0
CA A:THR101 4.3 30.0 1.0
C A:ARG102 4.3 29.3 1.0
N A:VAL103 4.4 29.1 1.0
N A:ARG102 4.5 29.8 1.0
CA A:ILE106 4.5 31.1 1.0
C A:SER104 4.5 29.1 1.0
O A:ARG102 4.6 29.2 1.0
CA A:ARG102 4.6 29.5 1.0
CA A:VAL103 4.7 29.1 1.0
N A:GLY107 4.8 31.9 1.0
CB A:THR101 4.8 30.1 1.0
C A:GLY105 4.9 30.1 1.0
C3' P:DG8 5.0 29.3 1.0

Calcium binding site 3 out of 7 in 5vrw

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Calcium binding site 3 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar 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 Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:63.6
occ:1.00
 O A:LYS60 2.4 36.9 1.0
OP1 D:DC3 2.6 42.5 1.0
O A:LEU62 2.8 35.7 1.0
O A:VAL65 2.9 38.9 1.0
O D:HOH202 3.0 36.6 1.0
C A:LYS60 3.6 37.0 1.0
P D:DC3 3.7 42.2 1.0
C A:LEU62 3.7 35.5 1.0
OP2 D:DC3 3.8 42.2 1.0
C A:VAL65 3.9 37.8 1.0
N A:VAL65 4.1 37.1 1.0
C A:LYS61 4.1 36.1 1.0
CA A:PRO63 4.1 35.6 1.0
O A:LYS61 4.2 36.3 1.0
N A:PRO63 4.3 35.3 1.0
N A:GLY64 4.3 36.8 1.0
N A:LEU62 4.3 35.7 1.0
CG A:LYS60 4.5 38.4 1.0
CA A:VAL65 4.5 37.4 1.0
CA A:LYS60 4.5 37.3 1.0
N A:LYS61 4.5 36.9 1.0
CA A:LYS61 4.6 36.7 1.0
C A:PRO63 4.6 36.2 1.0
CA A:LEU62 4.6 35.6 1.0
O5' D:DC3 4.7 44.5 1.0
O3' D:DT2 4.8 41.0 1.0
CB A:VAL65 4.8 37.3 1.0

Calcium binding site 4 out of 7 in 5vrw

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Calcium binding site 4 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar 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 Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:46.1
occ:1.00
 O2B P:TTP103 2.2 34.1 1.0
O2A P:TTP103 2.3 36.2 1.0
OD1 A:ASP190 2.4 32.6 1.0
OD2 A:ASP192 2.5 31.4 1.0
O2G P:TTP103 2.5 34.1 1.0
O A:ASP190 3.2 32.6 1.0
PA P:TTP103 3.4 36.3 1.0
PB P:TTP103 3.4 34.2 1.0
CG A:ASP192 3.5 31.0 1.0
PG P:TTP103 3.6 34.2 1.0
CG A:ASP190 3.6 32.5 1.0
O3A P:TTP103 3.6 35.6 1.0
O5' P:TTP103 3.7 36.7 1.0
O1G P:TTP103 3.8 34.3 1.0
O3B P:TTP103 3.9 34.4 1.0
C A:ASP190 3.9 32.4 1.0
N A:ASP190 3.9 32.4 1.0
OD1 A:ASP192 4.0 31.4 1.0
CA P:CA101 4.2 41.7 1.0
OD2 A:ASP190 4.3 32.4 1.0
CA A:GLY179 4.4 27.1 1.0
CA A:ASP190 4.4 32.3 1.0
N A:SER180 4.4 27.3 1.0
OG A:SER180 4.5 27.9 1.0
CB A:ASP190 4.6 32.2 1.0
N A:GLY189 4.7 32.9 1.0
O1B P:TTP103 4.7 34.3 1.0
O1A P:TTP103 4.8 36.1 1.0
CB A:ASP192 4.8 30.5 1.0
N A:MET191 4.9 31.7 1.0
C5' P:TTP103 4.9 36.6 1.0
O3G P:TTP103 4.9 34.6 1.0
C A:GLY189 4.9 32.6 1.0
C A:GLY179 5.0 27.2 1.0

Calcium binding site 5 out of 7 in 5vrw

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Calcium binding site 5 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar 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 Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:81.4
occ:1.00
 OD1 A:ASP318 2.8 40.8 1.0
OD1 A:ASP314 2.8 44.6 1.0
O A:HOH537 3.2 16.2 1.0
OD2 A:ASP318 3.3 41.6 1.0
CG A:ASP318 3.4 40.5 1.0
OD2 A:ASP314 3.5 44.9 1.0
CG A:ASP314 3.6 44.0 1.0
O A:HOH512 3.8 30.5 1.0
OG A:SER315 4.3 41.1 1.0
CB A:SER315 4.9 41.0 1.0
CB A:ASP318 4.9 39.6 1.0

Calcium binding site 6 out of 7 in 5vrw

Go back to Calcium Binding Sites List in 5vrw
Calcium binding site 6 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:60.4
occ:1.00
 OE2 A:GLU249 2.9 39.4 1.0
OE1 A:GLU249 3.0 40.2 1.0
CD A:GLU249 3.3 40.0 1.0
OE1 A:GLN240 4.7 31.5 1.0
NE2 A:GLN240 4.8 31.4 1.0
CG A:GLU249 4.8 39.8 1.0
CE1 A:HIS252 4.9 30.4 1.0

Calcium binding site 7 out of 7 in 5vrw

Go back to Calcium Binding Sites List in 5vrw
Calcium binding site 7 out of 7 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Dc Extension Complex with Dttp Bound in Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:72.2
occ:1.00
 O A:GLU335 2.9 44.7 1.0
O A:HOH540 3.3 29.7 1.0
C A:GLU335 4.0 44.2 1.0
O1 A:PEG406 4.0 47.1 1.0
O A:ALA47 4.1 34.3 1.0
C A:ALA47 4.7 34.2 1.0
CG2 A:THR10 4.9 42.5 1.0
CB A:ALA47 4.9 34.2 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 12:35:40 2024

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