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Calcium in PDB 3rbe: DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion

Enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer T 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 T Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rbe 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.904, 109.860, 101.291, 90.00, 100.99, 90.00
R / Rfree (%) 22.6 / 26.6

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T Base Opposite the 3-Methylcytosine (M3C) Lesion (pdb code 3rbe). 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 3-Methylcytosine (M3C) Lesion, PDB code: 3rbe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T 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 T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:38.6
occ:1.00
 O2A A:DGT414 2.1 42.2 1.0
OD2 A:ASP7 2.4 39.0 1.0
OE2 A:GLU106 2.4 42.6 1.0
OD1 A:ASP105 2.6 38.0 1.0
OD2 A:ASP105 2.8 35.0 1.0
CG A:ASP105 3.0 36.5 1.0
CG A:ASP7 3.1 36.5 1.0
CA A:CA416 3.3 28.6 1.0
PA A:DGT414 3.4 34.1 1.0
OD1 A:ASP7 3.4 36.0 1.0
C3' D:2DT814 3.4 74.2 1.0
CD A:GLU106 3.5 40.3 1.0
O1A A:DGT414 3.8 35.8 1.0
CB A:GLU106 4.1 37.7 1.0
O5' A:DGT414 4.2 35.2 1.0
C5' A:DGT414 4.2 33.4 1.0
CG A:GLU106 4.3 39.1 1.0
CB A:ASP7 4.3 34.9 1.0
OE1 A:GLU106 4.3 40.7 1.0
NZ A:LYS159 4.3 45.3 1.0
C4' D:2DT814 4.4 74.1 1.0
C5' D:2DT814 4.4 71.3 1.0
O3A A:DGT414 4.5 35.5 1.0
O1G A:DGT414 4.5 38.2 1.0
CB A:ASP105 4.6 36.4 1.0
OG A:SER103 4.6 34.2 1.0
C2' D:2DT814 4.7 74.9 1.0
OP1 D:2DT814 4.8 61.4 1.0
O5' D:2DT814 4.9 64.4 1.0
C A:ASP105 4.9 37.3 1.0
O A:ASP105 4.9 38.1 1.0
CA A:ASP7 5.0 35.0 1.0

Calcium binding site 2 out of 6 in 3rbe

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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 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 T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:28.6
occ:1.00
 OD1 A:ASP7 2.3 36.0 1.0
O A:PHE8 2.3 33.9 1.0
O1B A:DGT414 2.3 39.7 1.0
OD2 A:ASP105 2.3 35.0 1.0
O2A A:DGT414 2.3 42.2 1.0
O1G A:DGT414 2.5 38.2 1.0
PG A:DGT414 3.1 39.0 1.0
PB A:DGT414 3.2 33.5 1.0
O3A A:DGT414 3.2 35.5 1.0
CG A:ASP7 3.2 36.5 1.0
PA A:DGT414 3.3 34.1 1.0
CA A:CA415 3.3 38.6 1.0
OD2 A:ASP7 3.5 39.0 1.0
C A:PHE8 3.6 33.5 1.0
CG A:ASP105 3.6 36.5 1.0
O3B A:DGT414 3.8 37.0 1.0
NZ A:LYS159 4.0 45.3 1.0
C5' A:DGT414 4.2 33.4 1.0
N A:PHE8 4.2 33.7 1.0
O5' A:DGT414 4.2 35.2 1.0
O2G A:DGT414 4.2 38.1 1.0
OD1 A:ASP105 4.3 38.0 1.0
O3G A:DGT414 4.3 39.1 1.0
C A:ASP7 4.4 34.8 1.0
CA A:PHE8 4.4 33.7 1.0
N A:ASP9 4.5 33.8 1.0
O2B A:DGT414 4.5 31.8 1.0
O1A A:DGT414 4.5 35.8 1.0
N A:TYR10 4.6 31.8 1.0
CB A:ASP7 4.6 34.9 1.0
CA A:ASP9 4.6 33.4 1.0
CB A:ASP105 4.6 36.4 1.0
O A:ASP7 4.7 35.3 1.0
CE A:LYS159 4.7 43.7 1.0
C A:ASP9 4.8 32.7 1.0
N A:PHE11 4.9 30.7 1.0
CA A:ASP7 5.0 35.0 1.0

Calcium binding site 3 out of 6 in 3rbe

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

b:51.5
occ:1.00
 O A:ALA181 2.3 63.6 1.0
O A:HOH366 2.4 23.8 1.0
O A:ILE186 2.6 49.0 1.0
C A:ALA181 3.5 61.9 1.0
C A:ILE186 3.7 49.8 1.0
CA A:GLY187 4.0 50.0 1.0
C A:GLY187 4.3 52.9 1.0
CA A:ALA181 4.3 64.0 1.0
O A:GLY187 4.3 54.8 1.0
N A:GLY187 4.3 49.8 1.0
OP1 D:DG813 4.4 44.9 1.0
CB A:ALA181 4.5 64.7 1.0
N A:ASP182 4.6 60.9 1.0
OP2 D:DG813 4.6 41.9 1.0
CA A:ASP182 4.8 57.8 1.0
CA A:ILE186 5.0 50.9 1.0

Calcium binding site 4 out of 6 in 3rbe

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

b:56.6
occ:1.00
 O2A B:DGT1414 2.3 0.5 1.0
OD1 B:ASP1105 2.5 82.4 1.0
OD1 B:ASP1007 2.6 93.7 1.0
CG B:GLU1106 3.0 83.6 1.0
OD2 B:ASP1105 3.1 89.0 1.0
OD2 B:ASP1007 3.1 90.6 1.0
CG B:ASP1007 3.1 89.9 1.0
CD B:GLU1106 3.2 84.7 1.0
CG B:ASP1105 3.2 81.7 1.0
CA B:CA1416 3.3 47.2 1.0
OE1 B:GLU1106 3.5 84.1 1.0
PA B:DGT1414 3.6 99.8 1.0
OE2 B:GLU1106 3.7 87.0 1.0
O1A B:DGT1414 3.7 99.9 1.0
OP1 H:2DT1814 4.1 0.7 1.0
C5' B:DGT1414 4.2 94.7 1.0
O5' B:DGT1414 4.4 97.6 1.0
CB B:GLU1106 4.4 84.2 1.0
C5' H:2DT1814 4.4 0.6 1.0
CB B:ASP1007 4.4 91.1 1.0
O5' H:2DT1814 4.4 0.7 1.0
O1B B:DGT1414 4.5 0.4 1.0
O B:ASP1105 4.5 83.4 1.0
C B:ASP1105 4.6 82.1 1.0
CB B:ASP1105 4.6 79.7 1.0
OG B:SER1103 4.7 81.7 1.0
O3A B:DGT1414 4.7 0.2 1.0
CA B:ASP1007 4.8 90.4 1.0
P H:2DT1814 4.8 0.7 1.0
N B:GLU1106 4.9 82.6 1.0
CA B:GLU1106 5.0 84.2 1.0

Calcium binding site 5 out of 6 in 3rbe

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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 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 T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:47.2
occ:1.00
 O2A B:DGT1414 2.3 0.5 1.0
OD2 B:ASP1105 2.3 89.0 1.0
O B:PHE1008 2.3 88.6 1.0
OD1 B:ASP1007 2.3 93.7 1.0
O1B B:DGT1414 2.3 0.4 1.0
O3B B:DGT1414 2.7 0.4 1.0
PB B:DGT1414 2.9 0.2 1.0
O3G B:DGT1414 3.2 0.2 1.0
CA B:CA1415 3.3 56.6 1.0
CG B:ASP1007 3.3 89.9 1.0
O3A B:DGT1414 3.3 0.2 1.0
O B:HOH1 3.4 45.8 1.0
PA B:DGT1414 3.4 99.8 1.0
CG B:ASP1105 3.4 81.7 1.0
C B:PHE1008 3.5 86.9 1.0
OD2 B:ASP1007 3.7 90.6 1.0
OD1 B:ASP1105 3.9 82.4 1.0
PG B:DGT1414 3.9 0.2 1.0
N B:PHE1008 4.0 87.6 1.0
CA B:PHE1008 4.3 87.2 1.0
O2B B:DGT1414 4.3 0.5 1.0
O1A B:DGT1414 4.4 99.9 1.0
O5' B:DGT1414 4.4 97.6 1.0
CB B:ASP1007 4.5 91.1 1.0
C5' B:DGT1414 4.5 94.7 1.0
C B:ASP1007 4.5 89.9 1.0
N B:ASP1009 4.5 87.4 1.0
O2G B:DGT1414 4.6 1.0 1.0
CB B:ASP1105 4.7 79.7 1.0
O1G B:DGT1414 4.7 0.1 1.0
CA B:ASP1009 4.7 86.7 1.0
N B:TYR1010 4.7 82.4 1.0
CA B:ASP1007 4.8 90.4 1.0
CB B:PHE1008 4.9 84.9 1.0
N B:PHE1011 4.9 75.9 1.0
C B:ASP1009 4.9 83.8 1.0

Calcium binding site 6 out of 6 in 3rbe

Go back to Calcium Binding Sites List in 3rbe
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer T 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 T Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:61.5
occ:1.00
 O B:ALA1181 2.3 0.7 1.0
O B:HOH4 2.6 5.8 1.0
O B:ILE1186 2.7 0.6 1.0
C B:ALA1181 3.4 0.6 1.0
C B:ILE1186 3.9 0.3 1.0
OP1 H:DG1813 4.1 0.8 1.0
CA B:ALA1181 4.2 0.1 1.0
O B:VAL1183 4.2 0.2 1.0
CA B:GLY1187 4.3 0.5 1.0
N B:ASP1182 4.4 0.0 1.0
CB B:ALA1181 4.5 0.9 1.0
N B:VAL1183 4.5 0.0 1.0
N B:GLY1187 4.6 0.4 1.0
CA B:ASP1182 4.6 0.8 1.0
C B:ASP1182 4.9 0.0 1.0
C B:VAL1183 5.0 0.3 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 16:16:59 2025

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