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Calcium in PDB 3rax: DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion, PDB code: 3rax was solved by O.Rechkoblit, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.880, 61.645, 92.684, 98.50, 103.82, 93.29
R / Rfree (%) 19.7 / 23

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion (pdb code 3rax). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion, PDB code: 3rax:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rax

Go back to Calcium Binding Sites List in 3rax
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:20.4
occ:1.00
 O A:HOH519 2.2 18.1 1.0
O A:HOH567 2.3 22.4 1.0
OE2 A:GLU106 2.3 26.1 1.0
OD1 A:ASP105 2.3 22.7 1.0
OD2 A:ASP7 2.3 24.4 1.0
O2A A:DGT414 2.3 29.7 1.0
CG A:ASP105 3.3 20.2 1.0
C3' D:2DT814 3.4 65.7 1.0
OD2 A:ASP105 3.5 21.9 1.0
PA A:DGT414 3.5 26.1 1.0
CD A:GLU106 3.5 25.9 1.0
CG A:ASP7 3.5 22.2 1.0
CA A:CA416 3.6 18.8 1.0
O A:HOH589 3.9 42.8 1.0
O1A A:DGT414 3.9 23.0 1.0
O5' A:DGT414 4.0 23.5 1.0
OG A:SER103 4.1 22.2 1.0
CB A:GLU106 4.1 21.0 1.0
C5' A:DGT414 4.2 23.5 1.0
CG A:GLU106 4.3 22.9 1.0
OD1 A:ASP7 4.3 25.9 1.0
C4' D:2DT814 4.4 63.4 1.0
OE1 A:GLU106 4.5 28.6 1.0
CB A:ASP7 4.5 19.4 1.0
O A:ASP105 4.6 20.7 1.0
C2' D:2DT814 4.6 66.5 1.0
OP1 D:2DT814 4.6 50.5 1.0
C A:ASP105 4.7 20.9 1.0
CB A:ASP105 4.7 21.4 1.0
C5' D:2DT814 4.8 61.6 1.0
O1G A:DGT414 4.9 24.2 1.0
NZ A:LYS152 4.9 35.1 1.0
O5' D:2DT814 4.9 57.6 1.0
O3A A:DGT414 4.9 22.6 1.0
N A:GLU106 5.0 20.3 1.0
O A:HOH661 5.0 28.8 1.0

Calcium binding site 2 out of 6 in 3rax

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Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:18.8
occ:1.00
 OD2 A:ASP105 2.3 21.9 1.0
O A:PHE8 2.3 21.5 1.0
O1B A:DGT414 2.3 26.3 1.0
O2A A:DGT414 2.3 29.7 1.0
OD1 A:ASP7 2.4 25.9 1.0
O1G A:DGT414 2.4 24.2 1.0
OD2 A:ASP7 2.6 24.4 1.0
CG A:ASP7 2.8 22.2 1.0
PG A:DGT414 3.3 28.9 1.0
PB A:DGT414 3.4 23.0 1.0
CG A:ASP105 3.4 20.2 1.0
PA A:DGT414 3.5 26.1 1.0
C A:PHE8 3.5 20.5 1.0
CA A:CA415 3.6 20.4 1.0
O3A A:DGT414 3.7 22.6 1.0
OD1 A:ASP105 3.8 22.7 1.0
O A:HOH613 3.9 30.4 1.0
N A:PHE8 3.9 19.6 1.0
O3B A:DGT414 3.9 24.0 1.0
C5' A:DGT414 4.2 23.5 1.0
NZ A:LYS159 4.2 35.1 1.0
O2G A:DGT414 4.3 25.6 1.0
CA A:PHE8 4.3 20.1 1.0
O A:HOH519 4.3 18.1 1.0
CB A:ASP7 4.3 19.4 1.0
C A:ASP7 4.3 19.1 1.0
O5' A:DGT414 4.3 23.5 1.0
N A:ASP9 4.5 20.8 1.0
O3G A:DGT414 4.5 25.1 1.0
N A:TYR10 4.5 20.6 1.0
CA A:ASP9 4.5 20.9 1.0
CB A:ASP105 4.6 21.4 1.0
O1A A:DGT414 4.7 23.0 1.0
O2B A:DGT414 4.7 22.9 1.0
C A:ASP9 4.7 20.8 1.0
O A:ASP7 4.8 19.9 1.0
CA A:ASP7 4.8 19.6 1.0
N A:PHE11 4.8 19.6 1.0
O A:ASP105 4.9 20.7 1.0
CB A:PHE11 5.0 18.7 1.0
CB A:PHE8 5.0 20.3 1.0

Calcium binding site 3 out of 6 in 3rax

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Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:36.2
occ:1.00
 O A:HOH516 2.3 29.7 1.0
O D:HOH511 2.3 30.6 1.0
O A:HOH513 2.3 30.1 1.0
O A:ALA181 2.3 39.3 1.0
O A:HOH639 2.4 41.8 1.0
O D:HOH515 2.5 28.2 1.0
O A:ILE186 2.5 33.8 1.0
C A:ALA181 3.4 38.0 1.0
C A:ILE186 3.7 34.0 1.0
OP2 D:DG813 4.2 37.5 1.0
CA A:GLY187 4.2 35.0 1.0
CA A:ALA181 4.2 38.7 1.0
O A:HOH652 4.3 58.7 1.0
N A:GLY187 4.4 34.4 1.0
N A:ASP182 4.4 37.2 1.0
CB A:ALA181 4.5 39.5 1.0
OP1 D:DG813 4.5 34.9 1.0
CA A:ASP182 4.5 36.4 1.0
C A:GLY187 4.6 36.6 1.0
O A:GLY187 4.7 36.6 1.0
O A:VAL183 4.7 32.1 1.0
CA A:ILE186 4.8 34.1 1.0
P D:DG813 4.9 36.8 1.0
CB A:ILE186 4.9 34.9 1.0

Calcium binding site 4 out of 6 in 3rax

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Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:29.1
occ:1.00
 O B:HOH1519 2.1 21.6 1.0
O B:HOH107 2.3 29.9 1.0
OE2 B:GLU1106 2.3 39.9 1.0
OD1 B:ASP1105 2.3 34.9 1.0
O2A B:DGT1414 2.3 42.5 1.0
OD1 B:ASP1007 2.7 36.2 1.0
CD B:GLU1106 3.0 37.4 1.0
OD2 B:ASP1007 3.1 40.5 1.0
CG B:GLU1106 3.1 36.8 1.0
CG B:ASP1007 3.2 34.2 1.0
CG B:ASP1105 3.2 32.0 1.0
OD2 B:ASP1105 3.4 33.9 1.0
PA B:DGT1414 3.5 35.0 1.0
CA B:CA1416 3.6 26.9 1.0
O1A B:DGT1414 3.8 33.7 1.0
O5' B:DGT1414 4.0 32.2 1.0
OG B:SER1103 4.0 33.9 1.0
C3' H:2DT1814 4.1 72.8 1.0
C5' B:DGT1414 4.2 31.4 1.0
OE1 B:GLU1106 4.2 40.1 1.0
CB B:GLU1106 4.3 33.9 1.0
OP1 H:2DT1814 4.6 62.9 1.0
CB B:ASP1007 4.6 31.9 1.0
O B:ASP1105 4.6 30.6 1.0
CB B:ASP1105 4.6 31.1 1.0
C B:ASP1105 4.7 31.5 1.0
C5' H:2DT1814 4.8 69.7 1.0
O1G B:DGT1414 4.8 30.8 1.0
C4' H:2DT1814 4.8 71.2 1.0
O5' H:2DT1814 4.8 66.3 1.0
O B:HOH289 4.9 37.6 1.0
O3A B:DGT1414 4.9 32.8 1.0
NZ B:LYS1152 4.9 41.0 1.0
O B:HOH65 4.9 38.8 1.0
N B:GLU1106 4.9 31.6 1.0
O1B B:DGT1414 5.0 41.0 1.0

Calcium binding site 5 out of 6 in 3rax

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Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:26.9
occ:1.00
 OD2 B:ASP1105 2.3 33.9 1.0
O B:PHE1008 2.3 31.3 1.0
O1B B:DGT1414 2.3 41.0 1.0
OD1 B:ASP1007 2.3 36.2 1.0
O2A B:DGT1414 2.4 42.5 1.0
O1G B:DGT1414 2.4 30.8 1.0
O B:HOH65 2.5 38.8 1.0
PG B:DGT1414 3.3 36.4 1.0
CG B:ASP1007 3.4 34.2 1.0
CG B:ASP1105 3.4 32.0 1.0
PB B:DGT1414 3.4 32.0 1.0
C B:PHE1008 3.5 30.0 1.0
PA B:DGT1414 3.5 35.0 1.0
CA B:CA1415 3.6 29.1 1.0
O3A B:DGT1414 3.8 32.8 1.0
N B:PHE1008 3.9 30.0 1.0
OD1 B:ASP1105 3.9 34.9 1.0
O3B B:DGT1414 4.0 31.2 1.0
OD2 B:ASP1007 4.0 40.5 1.0
C B:ASP1007 4.2 30.6 1.0
NZ B:LYS1159 4.2 42.3 1.0
CA B:PHE1008 4.2 30.2 1.0
O2G B:DGT1414 4.3 33.2 1.0
C5' B:DGT1414 4.3 31.4 1.0
O B:HOH1519 4.4 21.6 1.0
N B:ASP1009 4.4 30.3 1.0
O5' B:DGT1414 4.4 32.2 1.0
O3G B:DGT1414 4.4 32.0 1.0
CB B:ASP1007 4.4 31.9 1.0
N B:TYR1010 4.5 29.2 1.0
CA B:ASP1009 4.5 29.9 1.0
O B:HOH30 4.5 25.6 1.0
O B:ASP1007 4.6 30.6 1.0
CB B:ASP1105 4.6 31.1 1.0
C B:ASP1009 4.7 29.5 1.0
O1A B:DGT1414 4.7 33.7 1.0
CA B:ASP1007 4.7 31.2 1.0
O2B B:DGT1414 4.7 29.9 1.0
N B:PHE1011 4.9 28.2 1.0
O B:ASP1105 5.0 30.6 1.0
CB B:PHE1008 5.0 30.0 1.0

Calcium binding site 6 out of 6 in 3rax

Go back to Calcium Binding Sites List in 3rax
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:43.0
occ:1.00
 O H:HOH1516 2.2 24.3 1.0
O B:ALA1181 2.3 58.5 1.0
O B:ILE1186 2.3 56.3 1.0
O H:HOH1511 2.4 31.1 1.0
O B:HOH1515 2.4 39.7 1.0
O B:HOH1514 2.5 33.5 1.0
C B:ALA1181 3.5 57.7 1.0
C B:ILE1186 3.5 53.9 1.0
CA B:GLY1187 4.0 53.3 1.0
N B:GLY1187 4.2 53.7 1.0
OP2 H:DG1813 4.3 49.1 1.0
CA B:ALA1181 4.3 59.5 1.0
N B:ASP1182 4.4 57.3 1.0
OP1 H:DG1813 4.5 48.3 1.0
CA B:ASP1182 4.5 55.1 1.0
C B:GLY1187 4.6 55.0 1.0
CB B:ALA1181 4.6 59.9 1.0
O B:VAL1183 4.6 50.4 1.0
CA B:ILE1186 4.7 53.9 1.0
O B:GLY1187 4.8 56.4 1.0
CB B:ILE1186 4.8 55.4 1.0
P H:DG1813 4.9 47.6 1.0
OD1 B:ASP1182 5.0 58.6 1.0

Reference:

O.Rechkoblit, J.C.Delaney, J.M.Essigmann, D.J.Patel. Implications For Damage Recognition During DPO4-Mediated Mutagenic Bypass of M1G and M3C Lesions. Structure V. 19 821 2011.
ISSN: ISSN 0969-2126
PubMed: 21645853
DOI: 10.1016/J.STR.2011.03.020
Page generated: Sat Jul 13 17:55:29 2024

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