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Calcium in PDB 3rb0: DPO4 Extension Ternary Complex with 3'-Terminal Primer G Base Opposite the 1-Methylguanine (M1G) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer G Base Opposite the 1-Methylguanine (M1G) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion, PDB code: 3rb0 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 / 3.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.421, 110.362, 102.268, 90.00, 101.28, 90.00
R / Rfree (%) 22.3 / 29.4

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G Base Opposite the 1-Methylguanine (M1G) Lesion (pdb code 3rb0). 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 G Base Opposite the 1-Methylguanine (M1G) Lesion, PDB code: 3rb0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rb0

Go back to Calcium Binding Sites List in 3rb0
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:48.0
occ:1.00
 OE2 A:GLU106 2.3 62.0 1.0
O2A A:DGT414 2.3 83.0 1.0
OD1 A:ASP105 2.3 59.1 1.0
OD2 A:ASP7 2.3 61.6 1.0
O A:HOH519 2.9 60.5 1.0
CG A:ASP105 3.1 54.9 1.0
CG A:ASP7 3.2 60.6 1.0
OD2 A:ASP105 3.2 53.8 1.0
PA A:DGT414 3.4 67.8 1.0
O1A A:DGT414 3.4 67.9 1.0
OD1 A:ASP7 3.4 62.1 1.0
CD A:GLU106 3.5 59.8 1.0
O5' A:DGT414 3.9 66.2 1.0
OP1 D:DDG814 3.9 0.8 1.0
OG A:SER103 4.0 56.7 1.0
CA A:CA416 4.0 46.9 1.0
C5' A:DGT414 4.0 65.2 1.0
OE1 A:GLU106 4.3 62.4 1.0
CG A:GLU106 4.5 57.8 1.0
CB A:GLU106 4.5 56.9 1.0
CB A:ASP105 4.6 55.2 1.0
CB A:ASP7 4.6 60.3 1.0
O3A A:DGT414 4.8 67.2 1.0
CB A:SER103 4.9 56.2 1.0

Calcium binding site 2 out of 6 in 3rb0

Go back to Calcium Binding Sites List in 3rb0
Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:46.9
occ:1.00
 OD1 A:ASP7 2.3 62.1 1.0
O2A A:DGT414 2.3 83.0 1.0
O A:PHE8 2.3 60.4 1.0
OD2 A:ASP105 2.5 53.8 1.0
O1B A:DGT414 2.8 60.5 1.0
PG A:DGT414 3.0 66.6 1.0
O2G A:DGT414 3.1 69.1 1.0
CG A:ASP7 3.1 60.6 1.0
PB A:DGT414 3.3 62.2 1.0
O3A A:DGT414 3.3 67.2 1.0
PA A:DGT414 3.3 67.8 1.0
O3B A:DGT414 3.4 66.2 1.0
NZ A:LYS159 3.4 65.1 1.0
OD2 A:ASP7 3.4 61.6 1.0
C A:PHE8 3.5 60.9 1.0
CG A:ASP105 3.7 54.9 1.0
O1G A:DGT414 3.9 67.3 1.0
CA A:CA415 4.0 48.0 1.0
OD1 A:ASP105 4.3 59.1 1.0
O5' A:DGT414 4.3 66.2 1.0
CB A:ASP7 4.3 60.3 1.0
CE A:LYS159 4.3 66.2 1.0
C5' A:DGT414 4.4 65.2 1.0
N A:TYR10 4.4 59.7 1.0
CA A:ASP9 4.4 61.4 1.0
N A:ASP9 4.4 61.5 1.0
O1A A:DGT414 4.4 67.9 1.0
O3G A:DGT414 4.4 70.8 1.0
N A:PHE8 4.4 60.6 1.0
C A:ASP7 4.5 60.4 1.0
CA A:PHE8 4.5 61.2 1.0
C A:ASP9 4.6 60.6 1.0
O A:HOH519 4.6 60.5 1.0
O2B A:DGT414 4.7 62.5 1.0
O A:ASP7 4.8 60.7 1.0
CB A:ASP105 4.8 55.2 1.0
CA A:ASP7 5.0 60.3 1.0
N A:PHE11 5.0 57.1 1.0

Calcium binding site 3 out of 6 in 3rb0

Go back to Calcium Binding Sites List in 3rb0
Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:99.8
occ:1.00
 O A:HOH516 2.3 17.8 1.0
O A:ILE186 2.4 77.4 1.0
O A:ALA181 2.7 80.8 1.0
O6 D:DDG814 2.8 0.3 1.0
O D:HOH511 3.1 31.4 1.0
OP1 D:DG813 3.2 82.4 1.0
OP2 D:DG813 3.4 82.5 1.0
C A:ILE186 3.5 78.0 1.0
C6 D:DDG814 3.6 0.9 1.0
P D:DG813 3.8 80.3 1.0
O A:VAL183 3.8 78.8 1.0
C A:ALA181 3.9 82.8 1.0
N A:ILE186 4.3 77.1 1.0
N A:GLY187 4.3 78.2 1.0
CA A:GLY187 4.3 77.5 1.0
C5 D:DDG814 4.3 0.0 1.0
CA A:ILE186 4.3 79.1 1.0
N7 D:DDG814 4.4 0.8 1.0
O D:HOH11 4.5 44.9 1.0
N1 D:DDG814 4.5 0.6 1.0
CB A:ILE186 4.6 81.1 1.0
CA A:ALA181 4.7 85.5 1.0
O A:GLY187 4.7 81.0 1.0
C A:VAL183 4.7 78.6 1.0
N A:ASP182 4.8 82.9 1.0
CA A:PRO184 4.8 74.5 1.0
O5' D:DG813 4.9 82.1 1.0
CA A:ASP182 4.9 80.9 1.0
C A:ASP182 4.9 80.3 1.0
C A:GLY187 5.0 79.9 1.0
O3' D:DA812 5.0 75.8 1.0
N A:GLY185 5.0 74.4 1.0

Calcium binding site 4 out of 6 in 3rb0

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Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:73.6
occ:1.00
 O2A B:DGT1414 2.3 0.5 1.0
O H:HOH1501 2.6 23.3 1.0
OE2 B:GLU1106 2.9 0.3 1.0
OD2 B:ASP1007 3.0 0.7 1.0
O B:HOH1502 3.1 14.9 1.0
OD1 B:ASP1105 3.1 0.9 1.0
OD2 B:ASP1105 3.2 0.7 1.0
CA B:CA1416 3.3 61.5 1.0
PA B:DGT1414 3.5 0.4 1.0
C5' B:DGT1414 3.5 0.5 1.0
CG B:ASP1105 3.5 0.0 1.0
CG B:GLU1106 3.7 0.8 1.0
CD B:GLU1106 3.7 0.9 1.0
O5' B:DGT1414 3.8 0.1 1.0
CG B:ASP1007 3.9 0.3 1.0
O1A B:DGT1414 3.9 1.0 1.0
OD1 B:ASP1007 4.1 1.0 1.0
OP1 H:DDG1814 4.3 0.9 1.0
O1B B:DGT1414 4.5 0.9 1.0
OG B:SER1103 4.8 0.1 1.0
O3A B:DGT1414 4.8 0.1 1.0
OE1 B:GLU1106 4.9 0.6 1.0
C4' B:DGT1414 4.9 0.2 1.0
CB B:ASP1105 5.0 0.7 1.0
O B:ASP1105 5.0 0.8 1.0

Calcium binding site 5 out of 6 in 3rb0

Go back to Calcium Binding Sites List in 3rb0
Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:61.5
occ:1.00
 O1B B:DGT1414 2.3 0.9 1.0
O B:PHE1008 2.3 0.9 1.0
O2A B:DGT1414 2.4 0.5 1.0
O2G B:DGT1414 2.7 0.4 1.0
OD2 B:ASP1105 2.7 0.7 1.0
PG B:DGT1414 2.8 0.8 1.0
OD2 B:ASP1007 2.9 0.7 1.0
OD1 B:ASP1007 3.2 1.0 1.0
PB B:DGT1414 3.3 0.0 1.0
CA B:CA1415 3.3 73.6 1.0
CG B:ASP1007 3.4 0.3 1.0
O3B B:DGT1414 3.4 0.3 1.0
PA B:DGT1414 3.5 0.4 1.0
C B:PHE1008 3.6 0.7 1.0
O1G B:DGT1414 3.7 0.1 1.0
O3A B:DGT1414 3.8 0.1 1.0
CG B:ASP1105 3.9 0.0 1.0
C5' B:DGT1414 3.9 0.5 1.0
O5' B:DGT1414 4.2 0.1 1.0
N B:PHE1008 4.2 0.6 1.0
O3G B:DGT1414 4.2 0.1 1.0
CA B:PHE1008 4.4 0.4 1.0
OD1 B:ASP1105 4.5 0.9 1.0
N B:ASP1009 4.5 0.1 1.0
O2B B:DGT1414 4.6 0.7 1.0
CA B:ASP1009 4.7 0.2 1.0
O B:HOH1502 4.7 14.9 1.0
N B:TYR1010 4.7 0.8 1.0
O1A B:DGT1414 4.7 1.0 1.0
C B:ASP1009 4.8 0.4 1.0
CB B:ASP1007 4.8 0.8 1.0
C B:ASP1007 4.9 0.6 1.0
N B:PHE1011 4.9 98.1 1.0
CB B:ASP1105 4.9 0.7 1.0
CB B:PHE1011 5.0 95.9 1.0

Calcium binding site 6 out of 6 in 3rb0

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Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 1-Methylguanine (M1G) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:73.9
occ:1.00
 O B:ILE1186 2.3 0.6 1.0
O B:HOH1514 2.6 2.0 1.0
OP2 H:DG1813 2.9 0.5 1.0
O H:HOH1515 2.9 12.5 1.0
O B:ALA1181 3.4 0.2 1.0
C B:ILE1186 3.5 0.2 1.0
O B:VAL1183 3.6 0.6 1.0
OP1 H:DG1813 3.6 0.1 1.0
P H:DG1813 3.7 0.4 1.0
N B:VAL1183 3.8 0.5 1.0
C B:VAL1183 4.1 0.3 1.0
CA B:GLY1187 4.1 0.1 1.0
CA B:ASP1182 4.2 0.3 1.0
N B:GLY1187 4.3 0.6 1.0
C B:ASP1182 4.4 1.0 1.0
C B:ALA1181 4.5 0.5 1.0
CA B:VAL1183 4.6 0.3 1.0
CA B:ILE1186 4.6 0.1 1.0
N B:ILE1186 4.7 0.6 1.0
O B:GLY1187 4.7 0.7 1.0
N B:PRO1184 4.7 0.8 1.0
O5' H:DG1813 4.8 0.6 1.0
N B:ASP1182 4.8 0.2 1.0
C B:GLY1187 4.9 0.7 1.0
CB B:ILE1186 5.0 0.5 1.0
O3' H:DA1812 5.0 0.0 1.0
CA B:PRO1184 5.0 0.2 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 17:55:37 2024

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