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

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

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer C 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 C Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rbd 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.852, 109.339, 100.680, 90.00, 101.12, 90.00
R / Rfree (%) 20.4 / 23.8

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3rbd

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

b:53.1
occ:1.00
 OD1 A:ASP105 2.3 49.9 1.0
O A:HOH400 2.4 12.8 1.0
O2A A:DGT414 2.6 41.4 1.0
OD1 A:ASP7 2.9 40.9 1.0
OD2 A:ASP105 3.0 39.2 1.0
CG A:ASP105 3.0 38.3 1.0
OD2 A:ASP7 3.1 40.3 1.0
O A:HOH343 3.1 29.3 1.0
OE1 A:GLU106 3.2 37.6 1.0
CG A:ASP7 3.3 38.8 1.0
OE2 A:GLU106 3.3 44.5 1.0
CD A:GLU106 3.3 40.2 1.0
CA A:CA416 3.6 35.4 1.0
C3' D:DOC814 3.7 46.5 1.0
PA A:DGT414 3.8 36.9 1.0
OP1 D:DOC814 3.9 47.3 1.0
O1A A:DGT414 4.2 42.1 1.0
C5' D:DOC814 4.2 47.5 1.0
O5' A:DGT414 4.2 37.4 1.0
CB A:GLU106 4.2 39.5 1.0
C5' A:DGT414 4.2 34.1 1.0
C4' D:DOC814 4.3 48.1 1.0
CG A:GLU106 4.3 40.0 1.0
O5' D:DOC814 4.4 48.4 1.0
OG A:SER103 4.5 38.8 1.0
CB A:ASP105 4.5 37.9 1.0
CB A:ASP7 4.6 36.8 1.0
P D:DOC814 4.8 45.3 1.0
C A:ASP105 4.8 37.8 1.0
O A:ASP105 4.8 37.0 1.0
NZ A:LYS159 4.9 41.8 1.0

Calcium binding site 2 out of 6 in 3rbd

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

b:35.4
occ:1.00
 O A:PHE8 2.3 38.1 1.0
OD1 A:ASP7 2.3 40.9 1.0
OD2 A:ASP105 2.3 39.2 1.0
O1B A:DGT414 2.3 39.9 1.0
O2A A:DGT414 2.3 41.4 1.0
O1G A:DGT414 2.7 36.0 1.0
PG A:DGT414 3.2 35.6 1.0
PB A:DGT414 3.3 35.6 1.0
CG A:ASP7 3.5 38.8 1.0
C A:PHE8 3.5 37.7 1.0
CG A:ASP105 3.5 38.3 1.0
PA A:DGT414 3.5 36.9 1.0
CA A:CA415 3.6 53.1 1.0
O3A A:DGT414 3.8 38.0 1.0
O3B A:DGT414 3.8 37.6 1.0
N A:PHE8 4.0 37.1 1.0
OD2 A:ASP7 4.1 40.3 1.0
OD1 A:ASP105 4.2 49.9 1.0
C5' A:DGT414 4.2 34.1 1.0
O2G A:DGT414 4.3 36.3 1.0
NZ A:LYS159 4.3 41.8 1.0
O A:HOH343 4.3 29.3 1.0
CA A:PHE8 4.3 37.4 1.0
C A:ASP7 4.3 37.5 1.0
O5' A:DGT414 4.4 37.4 1.0
O3G A:DGT414 4.4 35.2 1.0
N A:ASP9 4.5 37.8 1.0
N A:TYR10 4.5 36.0 1.0
CB A:ASP7 4.5 36.8 1.0
CA A:ASP9 4.6 37.4 1.0
CB A:ASP105 4.6 37.9 1.0
O2B A:DGT414 4.6 37.5 1.0
O1A A:DGT414 4.7 42.1 1.0
C A:ASP9 4.7 37.0 1.0
O A:ASP7 4.7 38.5 1.0
CA A:ASP7 4.8 37.1 1.0
CE A:LYS159 4.8 41.6 1.0
N A:PHE11 4.8 34.2 1.0
CB A:PHE8 4.9 37.0 1.0

Calcium binding site 3 out of 6 in 3rbd

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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 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 C Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:48.0
occ:1.00
 O A:HOH388 2.2 38.8 1.0
O A:ALA181 2.3 56.1 1.0
O A:ILE186 2.3 56.2 1.0
O D:HOH2 2.4 24.4 1.0
O A:HOH342 2.5 53.2 1.0
C A:ALA181 3.5 54.4 1.0
C A:ILE186 3.6 54.6 1.0
CA A:GLY187 4.1 54.1 1.0
CA A:ALA181 4.3 55.7 1.0
N A:GLY187 4.3 54.6 1.0
OP1 D:DG813 4.4 46.1 1.0
OP2 D:DG813 4.4 45.2 1.0
CB A:ALA181 4.5 55.5 1.0
N A:ASP182 4.5 54.1 1.0
C A:GLY187 4.6 56.0 1.0
CA A:ASP182 4.7 51.9 1.0
CA A:ILE186 4.7 54.6 1.0
O A:VAL183 4.8 49.3 1.0
CB A:ILE186 4.9 55.9 1.0
O A:GLY187 4.9 56.9 1.0
P D:DG813 5.0 43.9 1.0

Calcium binding site 4 out of 6 in 3rbd

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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 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 C Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:64.7
occ:1.00
 O2A B:DGT1414 2.3 88.3 1.0
O H:HOH4 2.5 22.7 1.0
OD1 B:ASP1105 2.6 77.5 1.0
OE2 B:GLU1106 2.9 78.3 1.0
OD1 B:ASP1007 3.1 85.5 1.0
OD2 B:ASP1007 3.1 82.1 1.0
CD B:GLU1106 3.2 78.2 1.0
CG B:GLU1106 3.3 78.3 1.0
CG B:ASP1105 3.3 76.9 1.0
OD2 B:ASP1105 3.3 83.1 1.0
CG B:ASP1007 3.4 80.7 1.0
PA B:DGT1414 3.5 78.0 1.0
CA B:CA1416 3.5 53.3 1.0
O1A B:DGT1414 3.7 79.0 1.0
C5' H:DOC1814 3.9 90.5 1.0
C3' H:DOC1814 3.9 88.9 1.0
C5' B:DGT1414 4.0 71.5 1.0
O5' H:DOC1814 4.0 88.7 1.0
O5' B:DGT1414 4.0 75.8 1.0
OE1 B:GLU1106 4.1 78.1 1.0
O B:HOH1501 4.2 35.6 1.0
OP1 H:DOC1814 4.2 92.7 1.0
O B:HOH1502 4.4 55.7 1.0
C4' H:DOC1814 4.4 89.5 1.0
OG B:SER1103 4.4 74.7 1.0
CB B:GLU1106 4.7 79.4 1.0
P H:DOC1814 4.7 89.5 1.0
CB B:ASP1105 4.8 75.7 1.0
O3A B:DGT1414 4.8 80.5 1.0
O3G B:DGT1414 4.8 79.9 1.0
O1B B:DGT1414 4.8 84.0 1.0
CB B:ASP1007 4.9 80.8 1.0
O B:ASP1105 4.9 78.7 1.0
C B:ASP1105 4.9 77.8 1.0

Calcium binding site 5 out of 6 in 3rbd

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

b:53.3
occ:1.00
 O B:PHE1008 2.3 79.6 1.0
OD2 B:ASP1105 2.3 83.1 1.0
OD1 B:ASP1007 2.3 85.5 1.0
O1B B:DGT1414 2.3 84.0 1.0
O2A B:DGT1414 2.3 88.3 1.0
O3G B:DGT1414 2.5 79.9 1.0
PB B:DGT1414 3.3 79.5 1.0
CG B:ASP1105 3.4 76.9 1.0
CG B:ASP1007 3.4 80.7 1.0
C B:PHE1008 3.5 77.7 1.0
PA B:DGT1414 3.5 78.0 1.0
CA B:CA1415 3.5 64.7 1.0
O1G B:DGT1414 3.6 86.6 1.0
O3A B:DGT1414 3.7 80.5 1.0
O3B B:DGT1414 3.7 83.4 1.0
PG B:DGT1414 3.8 83.1 1.0
O B:HOH1501 3.8 35.6 1.0
OD1 B:ASP1105 3.9 77.5 1.0
OD2 B:ASP1007 4.0 82.1 1.0
N B:PHE1008 4.0 78.6 1.0
C5' B:DGT1414 4.2 71.5 1.0
CA B:PHE1008 4.3 78.6 1.0
O5' B:DGT1414 4.4 75.8 1.0
C B:ASP1007 4.4 80.2 1.0
N B:ASP1009 4.4 77.7 1.0
CA B:ASP1009 4.6 76.1 1.0
O2G B:DGT1414 4.6 82.1 1.0
N B:TYR1010 4.6 71.1 1.0
CB B:ASP1007 4.6 80.8 1.0
CB B:ASP1105 4.6 75.7 1.0
O2B B:DGT1414 4.6 78.5 1.0
O1A B:DGT1414 4.7 79.0 1.0
O H:HOH4 4.7 22.7 1.0
C B:ASP1009 4.7 73.3 1.0
O B:ASP1007 4.8 81.4 1.0
N B:PHE1011 4.8 64.4 1.0
CA B:ASP1007 4.9 80.6 1.0
CB B:PHE1008 4.9 77.1 1.0

Calcium binding site 6 out of 6 in 3rbd

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

b:61.4
occ:1.00
 O B:ALA1181 2.3 97.1 1.0
O B:HOH7 2.4 10.2 1.0
O B:HOH1516 2.4 26.8 1.0
O B:HOH1512 2.5 41.3 1.0
O B:HOH5 2.5 26.5 1.0
O B:ILE1186 2.6 83.3 1.0
O H:HOH1514 2.8 36.9 1.0
C B:ALA1181 3.5 94.9 1.0
C B:ILE1186 3.8 84.2 1.0
OP2 H:DG1813 4.0 79.8 1.0
OP1 H:DG1813 4.1 83.5 1.0
CA B:ASP1182 4.4 92.6 1.0
N B:ASP1182 4.4 95.1 1.0
CA B:GLY1187 4.5 84.0 1.0
CA B:ALA1181 4.5 96.0 1.0
O B:VAL1183 4.5 87.3 1.0
N B:GLY1187 4.6 84.3 1.0
P H:DG1813 4.6 79.6 1.0
CA B:ILE1186 4.8 85.3 1.0
CB B:ALA1181 4.8 96.2 1.0
C B:ASP1182 4.9 91.8 1.0
C B:GLY1187 4.9 86.2 1.0
CB B:ILE1186 5.0 86.9 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 16:16:32 2025

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