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Calcium in PDB 3rb6: DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rb6 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.915, 109.328, 100.828, 90.00, 101.07, 90.00
R / Rfree (%) 20.3 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) Lesion (pdb code 3rb6). 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rb6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:53.3
occ:1.00
 O2A A:DGT414 2.3 47.5 1.0
OE2 A:GLU106 2.3 55.3 1.0
OD1 A:ASP105 2.4 41.7 1.0
O D:HOH65 2.5 30.5 1.0
OD2 A:ASP105 3.0 39.1 1.0
CG A:ASP105 3.1 37.6 1.0
OD2 A:ASP7 3.1 47.2 1.0
OD1 A:ASP7 3.1 46.5 1.0
CA A:CA416 3.3 39.1 1.0
CG A:ASP7 3.4 45.1 1.0
CD A:GLU106 3.5 52.6 1.0
C3' D:2DA814 3.5 51.0 1.0
PA A:DGT414 3.6 37.5 1.0
O1A A:DGT414 3.9 39.0 1.0
C5' D:2DA814 3.9 51.3 1.0
C4' D:2DA814 4.0 52.4 1.0
O5' D:2DA814 4.1 48.4 1.0
O5' A:DGT414 4.2 37.4 1.0
OE1 A:GLU106 4.2 56.2 1.0
C5' A:DGT414 4.2 34.9 1.0
CG A:GLU106 4.4 47.8 1.0
CB A:GLU106 4.4 44.6 1.0
CB A:ASP105 4.5 39.0 1.0
OP1 D:2DA814 4.5 50.1 1.0
CB A:ASP7 4.7 42.1 1.0
NZ A:LYS159 4.7 53.0 1.0
O1B A:DGT414 4.8 43.0 1.0
OG A:SER103 4.8 41.6 1.0
O3A A:DGT414 4.8 40.8 1.0
O A:ASP105 4.9 41.1 1.0
C2' D:2DA814 4.9 51.9 1.0
C A:ASP105 4.9 40.6 1.0
P D:2DA814 5.0 48.7 1.0

Calcium binding site 2 out of 6 in 3rb6

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Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:39.1
occ:1.00
 O A:PHE8 2.3 41.6 1.0
OD2 A:ASP105 2.3 39.1 1.0
OD1 A:ASP7 2.3 46.5 1.0
O2A A:DGT414 2.3 47.5 1.0
O1B A:DGT414 2.3 43.0 1.0
O2G A:DGT414 2.6 42.9 1.0
PB A:DGT414 3.3 39.4 1.0
CA A:CA415 3.3 53.3 1.0
PG A:DGT414 3.4 43.2 1.0
C A:PHE8 3.4 41.8 1.0
CG A:ASP105 3.5 37.6 1.0
PA A:DGT414 3.5 37.5 1.0
CG A:ASP7 3.5 45.1 1.0
O3A A:DGT414 3.6 40.8 1.0
O3B A:DGT414 3.7 43.4 1.0
N A:PHE8 3.9 39.1 1.0
OD1 A:ASP105 4.0 41.7 1.0
OD2 A:ASP7 4.1 47.2 1.0
C5' A:DGT414 4.1 34.9 1.0
O3G A:DGT414 4.2 41.9 1.0
CA A:PHE8 4.2 40.1 1.0
NZ A:LYS159 4.3 53.0 1.0
C A:ASP7 4.3 40.5 1.0
O5' A:DGT414 4.3 37.4 1.0
N A:ASP9 4.5 41.5 1.0
CB A:ASP105 4.6 39.0 1.0
N A:TYR10 4.6 35.8 1.0
O1A A:DGT414 4.6 39.0 1.0
CA A:ASP9 4.7 40.3 1.0
O2B A:DGT414 4.7 40.0 1.0
CB A:ASP7 4.7 42.1 1.0
CE A:LYS159 4.7 51.3 1.0
O A:ASP7 4.8 41.3 1.0
C A:ASP9 4.8 38.8 1.0
O1G A:DGT414 4.8 45.9 1.0
CA A:ASP7 4.9 41.1 1.0
CB A:PHE8 4.9 40.5 1.0
N A:PHE11 4.9 35.3 1.0

Calcium binding site 3 out of 6 in 3rb6

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Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:58.6
occ:1.00
 O A:HOH358 2.3 60.7 1.0
O A:ALA181 2.3 61.9 1.0
O A:ILE186 2.3 61.7 1.0
O A:HOH343 2.3 65.1 1.0
O D:HOH40 2.4 57.6 1.0
O D:HOH5 2.4 43.8 1.0
C A:ALA181 3.5 58.1 1.0
C A:ILE186 3.5 56.2 1.0
CA A:GLY187 4.1 53.6 1.0
OP1 D:DG813 4.2 47.7 1.0
N A:GLY187 4.3 53.7 1.0
OP2 D:DG813 4.3 47.5 1.0
CA A:ALA181 4.4 59.2 1.0
N A:ASP182 4.5 59.1 1.0
O A:VAL183 4.6 54.5 1.0
CB A:ALA181 4.6 58.2 1.0
C A:GLY187 4.6 57.2 1.0
CA A:ILE186 4.7 56.5 1.0
CA A:ASP182 4.7 56.3 1.0
P D:DG813 4.8 46.9 1.0
O A:GLY187 4.8 59.1 1.0
CB A:ILE186 4.8 58.9 1.0

Calcium binding site 4 out of 6 in 3rb6

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Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:73.5
occ:1.00
 O2A B:DGT1414 2.3 0.9 1.0
OD1 B:ASP1105 2.3 94.3 1.0
OD2 B:ASP1007 2.3 96.9 1.0
O B:HOH6 2.7 53.4 1.0
CG B:ASP1007 3.0 91.2 1.0
OE2 B:GLU1106 3.0 87.9 1.0
OD1 B:ASP1007 3.0 94.3 1.0
CG B:ASP1105 3.1 86.2 1.0
OD2 B:ASP1105 3.1 90.2 1.0
CG B:GLU1106 3.2 85.8 1.0
CD B:GLU1106 3.3 87.6 1.0
CA B:CA1416 3.3 63.9 1.0
C3' H:2DA1814 3.6 0.2 1.0
PA B:DGT1414 3.7 91.8 1.0
C5' H:2DA1814 3.9 0.6 1.0
O5' H:2DA1814 4.0 0.9 1.0
O1A B:DGT1414 4.1 93.7 1.0
C4' H:2DA1814 4.2 0.0 1.0
OE1 B:GLU1106 4.2 87.5 1.0
C5' B:DGT1414 4.2 87.7 1.0
O5' B:DGT1414 4.3 90.6 1.0
CB B:ASP1007 4.4 89.6 1.0
OG B:SER1103 4.5 82.3 1.0
CB B:GLU1106 4.5 85.0 1.0
CB B:ASP1105 4.6 83.3 1.0
O1B B:DGT1414 4.6 0.3 1.0
O B:ASP1105 4.7 83.5 1.0
C B:ASP1105 4.7 83.0 1.0
OP1 H:2DA1814 4.8 0.1 1.0
O3A B:DGT1414 4.9 96.5 1.0
N B:GLU1106 4.9 84.5 1.0
C2' H:2DA1814 5.0 0.6 1.0

Calcium binding site 5 out of 6 in 3rb6

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Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:63.9
occ:1.00
 OD1 B:ASP1007 2.3 94.3 1.0
OD2 B:ASP1105 2.3 90.2 1.0
O2A B:DGT1414 2.3 0.9 1.0
O B:PHE1008 2.3 85.0 1.0
O1B B:DGT1414 2.3 0.3 1.0
O3G B:DGT1414 2.8 95.0 1.0
O3B B:DGT1414 3.1 99.9 1.0
PB B:DGT1414 3.1 96.7 1.0
CA B:CA1415 3.3 73.5 1.0
PA B:DGT1414 3.4 91.8 1.0
CG B:ASP1007 3.4 91.2 1.0
CG B:ASP1105 3.4 86.2 1.0
O3A B:DGT1414 3.5 96.5 1.0
C B:PHE1008 3.5 81.2 1.0
PG B:DGT1414 3.8 97.8 1.0
OD2 B:ASP1007 3.9 96.9 1.0
OD1 B:ASP1105 3.9 94.3 1.0
C5' B:DGT1414 4.1 87.7 1.0
N B:PHE1008 4.2 82.5 1.0
O5' B:DGT1414 4.2 90.6 1.0
O1G B:DGT1414 4.3 0.4 1.0
CA B:PHE1008 4.4 82.0 1.0
O2B B:DGT1414 4.5 96.6 1.0
N B:ASP1009 4.5 82.2 1.0
O2G B:DGT1414 4.5 95.3 1.0
C B:ASP1007 4.5 85.5 1.0
O1A B:DGT1414 4.6 93.7 1.0
N B:TYR1010 4.6 78.1 1.0
O B:HOH6 4.6 53.4 1.0
CA B:ASP1009 4.6 82.4 1.0
CB B:ASP1105 4.7 83.3 1.0
CB B:ASP1007 4.7 89.6 1.0
C B:ASP1009 4.8 80.0 1.0
N B:PHE1011 4.9 72.7 1.0
O B:ASP1007 5.0 86.8 1.0

Calcium binding site 6 out of 6 in 3rb6

Go back to Calcium Binding Sites List in 3rb6
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer A Base Opposite the 3-Methylcytosine (M3C) 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 A Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:68.8
occ:1.00
 O B:ALA1181 2.3 0.4 1.0
O B:ILE1186 2.3 99.5 1.0
O H:HOH3 2.5 44.4 1.0
O B:HOH9 2.5 53.9 1.0
O B:HOH8 2.6 57.0 1.0
O B:HOH1 3.1 73.7 1.0
C B:ALA1181 3.4 0.5 1.0
C B:ILE1186 3.5 94.7 1.0
OP1 H:DG1813 3.8 98.0 1.0
CA B:ALA1181 4.0 0.0 1.0
CA B:GLY1187 4.1 93.9 1.0
N B:GLY1187 4.3 94.7 1.0
CB B:ALA1181 4.3 0.6 1.0
N B:ASP1182 4.5 1.0 1.0
C B:GLY1187 4.6 96.8 1.0
O B:VAL1183 4.6 89.4 1.0
CA B:ILE1186 4.6 94.0 1.0
CB B:ILE1186 4.7 94.6 1.0
O B:GLY1187 4.8 99.6 1.0
CA B:ASP1182 4.8 100.0 1.0
P H:DG1813 4.9 95.2 1.0
OP2 H:DG1813 4.9 95.1 1.0
CG2 B:ILE1186 4.9 96.1 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 16:15:37 2025

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