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Calcium in PDB 3rb4: DPO4 Extension Ternary Complex with 3'-Terminal Primer G Base Opposite the 3-Methylcytosine (M3C) Lesion

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

All present enzymatic activity of DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 3-Methylcytosine (M3C) Lesion, PDB code: 3rb4 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 / 2.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.267, 109.995, 101.535, 90.00, 101.35, 90.00
R / Rfree (%) 20.5 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G Base Opposite the 3-Methylcytosine (M3C) Lesion (pdb code 3rb4). 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 3-Methylcytosine (M3C) Lesion, PDB code: 3rb4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3rb4

Go back to Calcium Binding Sites List in 3rb4
Calcium binding site 1 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:43.3
occ:1.00
 O D:HOH501 2.3 23.0 1.0
O2A A:DGT414 2.3 42.3 1.0
OE2 A:GLU106 2.3 43.2 1.0
OD1 A:ASP105 2.3 40.5 1.0
OD2 A:ASP7 2.9 34.6 1.0
OD1 A:ASP7 2.9 32.7 1.0
OD2 A:ASP105 2.9 31.5 1.0
CG A:ASP105 3.0 31.8 1.0
CG A:ASP7 3.2 31.0 1.0
C3' D:DDG814 3.3 72.3 1.0
CA A:CA416 3.4 30.6 1.0
PA A:DGT414 3.5 26.6 1.0
CD A:GLU106 3.5 39.6 1.0
O1A A:DGT414 3.7 28.5 1.0
O5' D:DDG814 4.1 63.5 1.0
O5' A:DGT414 4.2 27.7 1.0
O A:HOH502 4.2 26.4 1.0
CG A:GLU106 4.2 34.4 1.0
C5' D:DDG814 4.3 68.8 1.0
C4' D:DDG814 4.3 71.5 1.0
C2' D:DDG814 4.3 73.3 1.0
C5' A:DGT414 4.3 25.2 1.0
CB A:GLU106 4.4 32.6 1.0
OE1 A:GLU106 4.5 43.2 1.0
CB A:ASP105 4.5 31.8 1.0
OP1 D:DDG814 4.5 60.6 1.0
OG A:SER103 4.5 31.9 1.0
O1G A:DGT414 4.6 36.1 1.0
CB A:ASP7 4.6 28.2 1.0
O A:ASP105 4.7 32.7 1.0
O3A A:DGT414 4.7 27.3 1.0
C A:ASP105 4.8 32.3 1.0
O1B A:DGT414 5.0 34.8 1.0
P D:DDG814 5.0 59.9 1.0

Calcium binding site 2 out of 6 in 3rb4

Go back to Calcium Binding Sites List in 3rb4
Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:30.6
occ:1.00
 O2A A:DGT414 2.2 42.3 1.0
O A:PHE8 2.3 28.1 1.0
OD1 A:ASP7 2.3 32.7 1.0
OD2 A:ASP105 2.3 31.5 1.0
O1B A:DGT414 2.3 34.8 1.0
O1G A:DGT414 2.3 36.1 1.0
PG A:DGT414 3.2 30.9 1.0
PB A:DGT414 3.3 25.0 1.0
PA A:DGT414 3.4 26.6 1.0
CA A:CA415 3.4 43.3 1.0
CG A:ASP7 3.5 31.0 1.0
C A:PHE8 3.5 27.1 1.0
CG A:ASP105 3.5 31.8 1.0
O3A A:DGT414 3.5 27.3 1.0
O3B A:DGT414 3.9 30.2 1.0
OD2 A:ASP7 4.0 34.6 1.0
N A:PHE8 4.1 26.6 1.0
OD1 A:ASP105 4.1 40.5 1.0
C5' A:DGT414 4.2 25.2 1.0
O2G A:DGT414 4.2 30.2 1.0
O3G A:DGT414 4.3 28.5 1.0
CA A:PHE8 4.3 27.1 1.0
C A:ASP7 4.3 27.2 1.0
O5' A:DGT414 4.3 27.7 1.0
N A:TYR10 4.4 25.0 1.0
N A:ASP9 4.4 27.1 1.0
CA A:ASP9 4.5 26.7 1.0
O1A A:DGT414 4.6 28.5 1.0
O2B A:DGT414 4.6 24.5 1.0
CB A:ASP105 4.6 31.8 1.0
CB A:ASP7 4.6 28.2 1.0
O D:HOH501 4.6 23.0 1.0
O A:ASP7 4.7 27.7 1.0
C A:ASP9 4.7 25.8 1.0
CE A:LYS159 4.7 41.3 1.0
NZ A:LYS159 4.8 41.6 1.0
N A:PHE11 4.9 23.8 1.0
O A:HOH502 4.9 26.4 1.0
CA A:ASP7 4.9 28.2 1.0

Calcium binding site 3 out of 6 in 3rb4

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

b:52.6
occ:1.00
 O A:ALA181 2.3 59.1 1.0
O A:HOH516 2.4 23.7 1.0
O A:ILE186 2.5 45.8 1.0
O D:HOH514 2.6 22.0 1.0
O A:HOH512 2.6 36.1 1.0
C A:ALA181 3.5 57.1 1.0
C A:ILE186 3.7 46.5 1.0
CA A:GLY187 4.0 46.5 1.0
CA A:ALA181 4.1 59.1 1.0
CB A:ALA181 4.2 59.1 1.0
N A:GLY187 4.3 46.7 1.0
OP1 D:DG813 4.4 44.8 1.0
OP2 D:DG813 4.5 44.0 1.0
N A:ASP182 4.5 56.2 1.0
C A:GLY187 4.6 49.2 1.0
CA A:ASP182 4.8 52.8 1.0
CA A:ILE186 4.8 47.1 1.0
O A:GLY187 4.9 51.0 1.0
O A:HOH515 4.9 61.2 1.0
P D:DG813 5.0 44.9 1.0

Calcium binding site 4 out of 6 in 3rb4

Go back to Calcium Binding Sites List in 3rb4
Calcium binding site 4 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:63.5
occ:1.00
 O2A B:DGT1414 2.3 0.3 1.0
OD1 B:ASP1007 2.6 75.7 1.0
OE2 B:GLU1106 3.1 82.7 1.0
OD1 B:ASP1105 3.1 80.1 1.0
CG B:GLU1106 3.1 78.7 1.0
OP1 H:DDG1814 3.3 0.9 1.0
CD B:GLU1106 3.3 81.8 1.0
OD2 B:ASP1105 3.4 87.4 1.0
CG B:ASP1007 3.4 77.9 1.0
CA B:CA1416 3.4 50.7 1.0
PA B:DGT1414 3.5 0.2 1.0
CG B:ASP1105 3.6 78.0 1.0
OD2 B:ASP1007 3.6 77.2 1.0
O1A B:DGT1414 3.7 0.9 1.0
O5' B:DGT1414 4.1 0.1 1.0
C5' B:DGT1414 4.1 0.8 1.0
C3' H:DDG1814 4.3 0.5 0.5
O5' H:DDG1814 4.3 0.5 1.0
OE1 B:GLU1106 4.3 83.0 1.0
P H:DDG1814 4.4 0.7 1.0
C4' H:DDG1814 4.5 0.5 0.5
CB B:GLU1106 4.6 78.8 1.0
O1B B:DGT1414 4.7 0.5 1.0
CB B:ASP1007 4.8 81.0 1.0
O3A B:DGT1414 4.8 0.4 1.0
OG B:SER1103 4.8 73.7 1.0
C5' H:DDG1814 4.9 0.8 0.5
O B:ASP1105 4.9 78.5 1.0
C B:ASP1105 4.9 77.3 1.0

Calcium binding site 5 out of 6 in 3rb4

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

b:50.7
occ:1.00
 OD2 B:ASP1105 2.3 87.4 1.0
O B:PHE1008 2.3 85.3 1.0
O2A B:DGT1414 2.3 0.3 1.0
O1B B:DGT1414 2.3 0.5 1.0
OD2 B:ASP1007 2.9 77.2 1.0
OD1 B:ASP1007 3.1 75.7 1.0
O3B B:DGT1414 3.2 0.5 1.0
O B:HOH55 3.2 6.7 1.0
PB B:DGT1414 3.2 1.0 1.0
CG B:ASP1007 3.3 77.9 1.0
CA B:CA1415 3.4 63.5 1.0
C B:PHE1008 3.5 82.1 1.0
CG B:ASP1105 3.5 78.0 1.0
PA B:DGT1414 3.5 0.2 1.0
O3A B:DGT1414 3.8 0.4 1.0
O3G B:DGT1414 3.8 0.4 1.0
N B:PHE1008 4.0 81.1 1.0
OD1 B:ASP1105 4.1 80.1 1.0
C5' B:DGT1414 4.2 0.8 1.0
CA B:PHE1008 4.3 82.2 1.0
O5' B:DGT1414 4.4 0.1 1.0
PG B:DGT1414 4.5 0.6 1.0
N B:ASP1009 4.5 82.8 1.0
O2B B:DGT1414 4.5 0.4 1.0
C B:ASP1007 4.6 82.1 1.0
CB B:ASP1105 4.6 75.8 1.0
CB B:ASP1007 4.6 81.0 1.0
N B:TYR1010 4.7 77.2 1.0
O1A B:DGT1414 4.7 0.9 1.0
CA B:ASP1009 4.7 81.9 1.0
CB B:PHE1008 4.9 80.2 1.0
N B:PHE1011 4.9 70.5 1.0
C B:ASP1009 4.9 79.2 1.0

Calcium binding site 6 out of 6 in 3rb4

Go back to Calcium Binding Sites List in 3rb4
Calcium binding site 6 out of 6 in the DPO4 Extension Ternary Complex with 3'-Terminal Primer G 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 G Base Opposite the 3-Methylcytosine (M3C) Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:64.7
occ:1.00
 O B:ALA1181 2.3 0.3 1.0
O B:HOH1512 2.4 2.0 1.0
O B:HOH1514 2.7 2.0 1.0
O B:ILE1186 2.9 96.2 1.0
O H:HOH1516 3.3 5.0 1.0
C B:ALA1181 3.5 0.9 1.0
C B:ILE1186 4.1 97.5 1.0
O B:HOH1511 4.3 16.9 1.0
CA B:ASP1182 4.4 0.7 1.0
N B:ASP1182 4.4 0.3 1.0
CA B:ALA1181 4.5 0.1 1.0
CA B:GLY1187 4.5 97.9 1.0
N B:VAL1183 4.6 1.0 1.0
O B:VAL1183 4.7 0.0 1.0
CB B:ALA1181 4.7 0.4 1.0
N B:GLY1187 4.8 98.2 1.0
C B:ASP1182 4.9 0.6 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 17:56:54 2024

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