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Calcium in PDB 3raq: DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) Lesion:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) Lesion, PDB code: 3raq 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 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.194, 62.077, 91.459, 98.97, 103.82, 93.72
R / Rfree (%) 19.4 / 23.5

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) Lesion (pdb code 3raq). 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 C Base Opposite the 1-Methylguanine (MG1) Lesion, PDB code: 3raq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3raq

Go back to Calcium Binding Sites List in 3raq
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) 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 C Base Opposite the 1-Methylguanine (MG1) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:22.4
occ:1.00
 O A:HOH519 2.3 14.1 1.0
O A:HOH538 2.3 17.1 1.0
OD2 A:ASP7 2.3 26.4 1.0
OE2 A:GLU106 2.3 28.8 1.0
O1A A:DGT414 2.3 25.6 1.0
OD1 A:ASP105 2.3 25.1 1.0
CG A:ASP105 3.3 24.4 1.0
OD2 A:ASP105 3.4 24.9 1.0
PA A:DGT414 3.5 23.3 1.0
CG A:ASP7 3.5 23.7 1.0
CD A:GLU106 3.6 28.6 1.0
CA A:CA416 3.7 20.7 1.0
O2A A:DGT414 3.9 23.1 1.0
O5' A:DGT414 3.9 22.5 1.0
OG A:SER103 4.0 22.4 1.0
CB A:GLU106 4.2 23.9 1.0
C5' A:DGT414 4.2 21.1 1.0
OD1 A:ASP7 4.2 26.9 1.0
CG A:GLU106 4.3 25.7 1.0
OE1 A:GLU106 4.5 30.9 1.0
CB A:ASP7 4.5 21.9 1.0
O A:ASP105 4.7 22.6 1.0
CB A:ASP105 4.7 23.2 1.0
O D:HOH50 4.7 41.8 1.0
C A:ASP105 4.7 22.9 1.0
O A:HOH537 4.8 27.1 1.0
O1G A:DGT414 4.9 20.4 1.0
O3A A:DGT414 4.9 24.1 1.0
NZ A:LYS152 4.9 37.1 1.0
CB A:SER103 5.0 22.8 1.0

Calcium binding site 2 out of 6 in 3raq

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Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) 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 C Base Opposite the 1-Methylguanine (MG1) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:20.7
occ:1.00
 O A:PHE8 2.3 23.5 1.0
OD2 A:ASP105 2.3 24.9 1.0
OD1 A:ASP7 2.3 26.9 1.0
O1B A:DGT414 2.3 26.8 1.0
O1A A:DGT414 2.4 25.6 1.0
O1G A:DGT414 2.5 20.4 1.0
OD2 A:ASP7 2.7 26.4 1.0
CG A:ASP7 2.8 23.7 1.0
PG A:DGT414 3.2 24.1 1.0
CG A:ASP105 3.4 24.4 1.0
PB A:DGT414 3.4 22.0 1.0
C A:PHE8 3.4 22.4 1.0
PA A:DGT414 3.6 23.3 1.0
CA A:CA415 3.7 22.4 1.0
O3A A:DGT414 3.8 24.1 1.0
OD1 A:ASP105 3.9 25.1 1.0
N A:PHE8 3.9 21.4 1.0
O3B A:DGT414 3.9 23.2 1.0
O A:HOH532 4.1 42.2 1.0
O2G A:DGT414 4.2 21.8 1.0
C A:ASP7 4.2 21.4 1.0
CB A:ASP7 4.2 21.9 1.0
NZ A:LYS159 4.3 40.2 1.0
CA A:PHE8 4.3 22.1 1.0
C5' A:DGT414 4.3 21.1 1.0
N A:ASP9 4.4 22.6 1.0
O3G A:DGT414 4.4 20.4 1.0
CA A:ASP9 4.4 22.7 1.0
O5' A:DGT414 4.4 22.5 1.0
N A:TYR10 4.5 22.6 1.0
O A:ASP7 4.5 21.8 1.0
O A:HOH519 4.6 14.1 1.0
CB A:ASP105 4.7 23.2 1.0
C A:ASP9 4.7 22.7 1.0
CA A:ASP7 4.7 21.5 1.0
O2B A:DGT414 4.8 24.1 1.0
O2A A:DGT414 4.8 23.1 1.0
N A:PHE11 4.9 21.1 1.0
O A:ASP105 4.9 22.6 1.0
CB A:PHE8 5.0 22.5 1.0

Calcium binding site 3 out of 6 in 3raq

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Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) 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 C Base Opposite the 1-Methylguanine (MG1) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:42.1
occ:1.00
 O A:HOH515 2.2 26.5 1.0
O A:HOH513 2.3 27.6 1.0
O A:ALA181 2.3 47.5 1.0
O A:ILE186 2.3 46.0 1.0
O A:HOH516 2.4 36.9 1.0
OP2 D:DG813 3.3 39.5 1.0
C A:ALA181 3.5 46.0 1.0
C A:ILE186 3.5 43.9 1.0
CA A:GLY187 3.9 44.6 1.0
N A:GLY187 4.2 44.5 1.0
CA A:ALA181 4.3 46.8 1.0
O A:HOH660 4.5 42.6 1.0
N A:ASP182 4.5 45.4 1.0
CB A:ALA181 4.5 47.2 1.0
P D:DG813 4.6 37.3 1.0
C A:GLY187 4.6 46.0 1.0
CA A:ASP182 4.7 44.1 1.0
CA A:ILE186 4.7 43.1 1.0
O A:VAL183 4.7 39.2 1.0
OP1 D:DG813 4.9 39.2 1.0
CB A:ILE186 5.0 43.6 1.0
O A:GLY187 5.0 46.4 1.0

Calcium binding site 4 out of 6 in 3raq

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Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) 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 C Base Opposite the 1-Methylguanine (MG1) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:28.8
occ:1.00
 OE2 B:GLU1106 2.3 37.5 1.0
O2A B:DGT1414 2.3 35.7 1.0
OD2 B:ASP1007 2.3 37.0 1.0
OD1 B:ASP1105 2.3 33.0 1.0
O B:HOH60 2.4 26.2 1.0
O B:HOH1519 2.4 16.9 1.0
CG B:ASP1007 3.1 31.1 1.0
OD1 B:ASP1007 3.1 31.7 1.0
CD B:GLU1106 3.1 36.4 1.0
CG B:ASP1105 3.2 31.0 1.0
CG B:GLU1106 3.3 34.8 1.0
OD2 B:ASP1105 3.3 30.8 1.0
PA B:DGT1414 3.5 30.2 1.0
CA B:CA1416 3.7 24.0 1.0
O1A B:DGT1414 3.9 29.9 1.0
O5' B:DGT1414 4.0 28.9 1.0
OG B:SER1103 4.1 29.5 1.0
O B:HOH312 4.1 40.8 1.0
C5' B:DGT1414 4.2 28.4 1.0
OE1 B:GLU1106 4.3 38.8 1.0
CB B:GLU1106 4.5 32.7 1.0
CB B:ASP1007 4.5 29.2 1.0
O B:HOH112 4.6 34.3 1.0
CB B:ASP1105 4.6 30.2 1.0
O B:ASP1105 4.6 30.8 1.0
C B:ASP1105 4.7 31.2 1.0
O1G B:DGT1414 4.8 29.8 1.0
O H:HOH122 4.8 28.0 1.0
O B:HOH12 4.9 34.1 1.0
O3A B:DGT1414 4.9 28.4 1.0

Calcium binding site 5 out of 6 in 3raq

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Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) 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 C Base Opposite the 1-Methylguanine (MG1) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:24.0
occ:1.00
 OD1 B:ASP1007 2.3 31.7 1.0
O2B B:DGT1414 2.3 31.7 1.0
OD2 B:ASP1105 2.3 30.8 1.0
O B:PHE1008 2.3 28.9 1.0
O1G B:DGT1414 2.4 29.8 1.0
O2A B:DGT1414 2.4 35.7 1.0
PG B:DGT1414 3.1 30.9 1.0
PB B:DGT1414 3.3 27.4 1.0
CG B:ASP1007 3.4 31.1 1.0
C B:PHE1008 3.5 28.4 1.0
CG B:ASP1105 3.5 31.0 1.0
PA B:DGT1414 3.5 30.2 1.0
O3A B:DGT1414 3.7 28.4 1.0
CA B:CA1415 3.7 28.8 1.0
O3B B:DGT1414 3.8 29.0 1.0
N B:PHE1008 3.9 27.4 1.0
OD2 B:ASP1007 4.0 37.0 1.0
OD1 B:ASP1105 4.0 33.0 1.0
O3G B:DGT1414 4.1 31.0 1.0
NZ B:LYS1159 4.2 41.5 1.0
C5' B:DGT1414 4.3 28.4 1.0
CA B:PHE1008 4.3 28.2 1.0
C B:ASP1007 4.3 28.1 1.0
O2G B:DGT1414 4.3 26.4 1.0
O5' B:DGT1414 4.4 28.9 1.0
N B:ASP1009 4.4 28.6 1.0
O B:HOH15 4.4 24.9 1.0
N B:TYR1010 4.4 27.8 1.0
CA B:ASP1009 4.5 28.6 1.0
CB B:ASP1007 4.5 29.2 1.0
O1B B:DGT1414 4.6 24.3 1.0
CB B:ASP1105 4.7 30.2 1.0
C B:ASP1009 4.7 28.1 1.0
O1A B:DGT1414 4.7 29.9 1.0
O B:ASP1007 4.7 27.7 1.0
N B:PHE1011 4.9 25.9 1.0
CA B:ASP1007 4.9 28.8 1.0
O B:HOH1519 4.9 16.9 1.0
CB B:PHE1008 5.0 27.9 1.0

Calcium binding site 6 out of 6 in 3raq

Go back to Calcium Binding Sites List in 3raq
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer C Base Opposite the 1-Methylguanine (MG1) 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 C Base Opposite the 1-Methylguanine (MG1) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:50.7
occ:1.00
 O B:HOH1515 2.3 36.0 1.0
O B:HOH1516 2.3 27.3 1.0
O B:ALA1181 2.3 64.5 1.0
O B:HOH1514 2.5 38.3 1.0
O B:ILE1186 2.7 50.3 1.0
C B:ALA1181 3.5 63.4 1.0
OP2 H:DG1813 3.6 46.1 1.0
C B:ILE1186 3.8 51.1 1.0
CA B:GLY1187 4.1 51.6 1.0
CA B:ALA1181 4.3 65.2 1.0
CB B:ALA1181 4.4 65.6 1.0
N B:GLY1187 4.4 51.4 1.0
N B:ASP1182 4.5 62.8 1.0
CA B:ASP1182 4.6 60.4 1.0
C B:GLY1187 4.6 54.0 1.0
P H:DG1813 4.8 45.0 1.0
O B:VAL1183 4.9 54.5 1.0
O B:GLY1187 4.9 55.3 1.0
OP1 H:DG1813 4.9 46.0 1.0
OD1 B:ASP1182 5.0 62.9 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: Tue Jul 8 16:13:46 2025

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