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Calcium in PDB 5vs1: Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Da Extension Complex with Dttp Bound in Non-Planar Conformation

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

All present enzymatic activity of Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Da 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:Da Extension Complex with Dttp Bound in Non-Planar Conformation, PDB code: 5vs1 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) 52.91 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.600, 80.500, 55.300, 90.00, 106.90, 90.00
R / Rfree (%) 21.1 / 27.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Da Extension Complex with Dttp Bound in Non-Planar Conformation (pdb code 5vs1). 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:Da Extension Complex with Dttp Bound in Non-Planar Conformation, PDB code: 5vs1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5vs1

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

b:55.1
occ:1.00
 O2A P:TTP103 2.1 47.8 1.0
O3' P:DA10 2.3 64.4 1.0
OD1 A:ASP190 2.4 33.1 1.0
OD1 A:ASP192 2.5 38.3 1.0
OD2 A:ASP256 2.5 28.3 1.0
CG A:ASP190 3.2 33.6 1.0
OD2 A:ASP190 3.4 36.7 1.0
C3' P:DA10 3.4 68.5 1.0
PA P:TTP103 3.5 58.0 1.0
CG A:ASP192 3.5 31.1 1.0
CG A:ASP256 3.6 28.6 1.0
OD2 A:ASP192 3.8 31.3 1.0
O5' P:DA10 4.0 53.5 1.0
C4' P:DA10 4.0 62.9 1.0
CA A:CA401 4.1 48.5 1.0
C5' P:TTP103 4.1 56.8 1.0
C5' P:DA10 4.1 57.3 1.0
O5' P:TTP103 4.1 57.4 1.0
O1A P:TTP103 4.1 46.1 1.0
CB A:ASP256 4.2 26.9 1.0
OP1 P:DA10 4.5 47.1 1.0
O3A P:TTP103 4.6 52.1 1.0
OD1 A:ASP256 4.6 30.2 1.0
CB A:ASP190 4.7 31.2 1.0
C2' P:DA10 4.7 70.5 1.0
CB A:ASP192 4.8 28.9 1.0
O A:MET191 4.9 24.9 1.0
P P:DA10 4.9 47.4 1.0
NH2 A:ARG254 5.0 27.3 1.0

Calcium binding site 2 out of 5 in 5vs1

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Calcium binding site 2 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Da 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:Da Extension Complex with Dttp Bound in Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca102

b:54.6
occ:1.00
 OP1 P:DC9 2.2 25.4 1.0
O A:THR101 2.5 27.4 1.0
O A:VAL103 2.5 25.0 1.0
O A:ILE106 2.9 24.8 1.0
P P:DC9 3.1 26.0 1.0
OP2 P:DC9 3.1 25.9 1.0
C A:VAL103 3.5 23.8 1.0
C A:THR101 3.5 27.9 1.0
N A:GLY105 3.8 24.6 1.0
C A:ILE106 3.8 23.4 1.0
CA A:SER104 3.9 24.6 1.0
N A:ILE106 4.0 23.5 1.0
O3' P:DG8 4.0 28.9 1.0
N A:SER104 4.1 23.8 1.0
CA A:THR101 4.1 30.2 1.0
N A:VAL103 4.3 23.5 1.0
C A:SER104 4.3 25.3 1.0
O5' P:DC9 4.3 29.0 1.0
C A:ARG102 4.4 24.9 1.0
CA A:ILE106 4.4 23.6 1.0
N A:ARG102 4.5 26.9 1.0
CA A:VAL103 4.5 22.9 1.0
CB A:THR101 4.6 31.3 1.0
O A:ARG102 4.7 23.7 1.0
N A:GLY107 4.7 24.2 1.0
CA A:ARG102 4.7 25.9 1.0
C A:GLY105 4.8 23.1 1.0
CA A:GLY105 4.8 24.3 1.0
CB A:ILE106 4.9 23.5 1.0
CA A:GLY107 4.9 26.9 1.0
C3' P:DG8 5.0 27.2 1.0

Calcium binding site 3 out of 5 in 5vs1

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Calcium binding site 3 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Da 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:Da Extension Complex with Dttp Bound in Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:68.2
occ:1.00
 OP1 D:DC3 2.3 40.9 1.0
O A:LYS60 2.4 38.2 1.0
O A:LEU62 2.5 41.6 1.0
O A:VAL65 2.6 36.2 1.0
P D:DC3 3.5 46.4 1.0
C A:LEU62 3.5 41.1 1.0
C A:LYS60 3.6 38.0 1.0
OP2 D:DC3 3.8 47.1 1.0
C A:VAL65 3.8 35.0 1.0
CA A:PRO63 4.1 38.1 1.0
N A:VAL65 4.2 38.5 1.0
N A:GLY64 4.2 41.6 1.0
N A:LEU62 4.2 44.4 1.0
N A:PRO63 4.2 37.9 1.0
C A:LYS61 4.3 42.6 1.0
CG A:LYS60 4.4 42.3 1.0
CA A:VAL65 4.5 35.5 1.0
CA A:LYS60 4.5 38.5 1.0
CA A:LEU62 4.5 42.1 1.0
O5' D:DC3 4.6 46.3 1.0
N A:LYS61 4.6 39.1 1.0
O3' D:DT2 4.6 43.4 1.0
C A:PRO63 4.6 40.2 1.0
CA A:LYS61 4.6 42.1 1.0
O A:LYS61 4.7 40.8 1.0
CB A:VAL65 4.7 34.5 1.0
N A:GLY66 4.8 36.7 1.0

Calcium binding site 4 out of 5 in 5vs1

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Calcium binding site 4 out of 5 in the Human Dna Polymerase Beta Pre-Catalytic 8-Oxog:Da 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:Da Extension Complex with Dttp Bound in Non-Planar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:48.5
occ:1.00
 OD2 A:ASP192 2.2 31.3 1.0
OD2 A:ASP190 2.3 36.7 1.0
O3A P:TTP103 2.3 52.1 1.0
O2A P:TTP103 2.4 47.8 1.0
PA P:TTP103 2.9 58.0 1.0
O2G P:TTP103 3.1 43.5 1.0
CG A:ASP192 3.3 31.1 1.0
O5' P:TTP103 3.4 57.4 1.0
CG A:ASP190 3.4 33.6 1.0
PB P:TTP103 3.6 45.4 1.0
O A:ASP190 3.6 31.3 1.0
OD1 A:ASP192 3.8 38.3 1.0
O3B P:TTP103 3.8 47.5 1.0
C A:ASP190 4.0 30.6 1.0
O1B P:TTP103 4.0 47.0 1.0
CA P:CA101 4.1 55.1 1.0
OD1 A:ASP190 4.1 33.1 1.0
PG P:TTP103 4.1 42.0 1.0
CA A:GLY179 4.1 25.9 1.0
N A:ASP190 4.3 29.6 1.0
O1A P:TTP103 4.3 46.1 1.0
N A:SER180 4.4 28.5 1.0
CA A:ASP190 4.5 30.8 1.0
CB A:ASP192 4.5 28.9 1.0
C5' P:TTP103 4.5 56.8 1.0
CB A:ASP190 4.6 31.2 1.0
N A:MET191 4.6 29.1 1.0
OG A:SER180 4.6 28.9 1.0
N A:ASP192 4.7 25.3 1.0
O3G P:TTP103 4.7 43.2 1.0
O2B P:TTP103 4.8 56.7 1.0
C A:GLY179 4.8 27.3 1.0
C A:MET191 4.9 26.5 1.0
CA A:MET191 4.9 28.6 1.0

Calcium binding site 5 out of 5 in 5vs1

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

b:61.8
occ:1.00
 OE2 A:GLU249 2.9 45.1 1.0
OE1 A:GLU249 3.4 52.5 1.0
CD A:GLU249 3.5 46.5 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 12:35:47 2024

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