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Calcium in PDB 3khr: DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion

Enzymatic activity of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion

All present enzymatic activity of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion:
2.7.7.7;

Protein crystallography data

The structure of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion, PDB code: 3khr was solved by O.Rechkoblit, L.Malinina, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.477, 53.019, 99.858, 81.76, 76.76, 70.14
R / Rfree (%) 20.6 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion (pdb code 3khr). 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 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion, PDB code: 3khr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3khr

Go back to Calcium Binding Sites List in 3khr
Calcium binding site 1 out of 6 in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:48.1
occ:1.00
 O A:HOH510 2.3 37.2 1.0
O1A A:TTP414 2.3 32.9 1.0
OD1 A:ASP105 2.5 29.9 1.0
CG A:GLU106 3.2 33.9 1.0
OE2 A:GLU106 3.4 40.4 1.0
CG A:ASP105 3.4 29.0 1.0
C3' D:DDG815 3.5 43.0 1.0
PA A:TTP414 3.5 23.8 1.0
CD A:GLU106 3.5 38.9 1.0
OD2 A:ASP105 3.5 28.1 1.0
OD2 A:ASP7 3.5 28.4 1.0
CA A:CA416 3.6 28.1 1.0
OD1 A:ASP7 3.6 30.0 1.0
CG A:ASP7 3.8 28.5 1.0
O5' D:DDG815 3.9 46.8 1.0
O5' A:TTP414 4.0 20.6 1.0
O2A A:TTP414 4.0 25.3 1.0
C5' D:DDG815 4.1 44.1 1.0
C4' D:DDG815 4.1 42.0 1.0
C5' A:TTP414 4.1 19.1 1.0
OE1 A:GLU106 4.4 44.6 1.0
OG A:SER103 4.5 29.0 1.0
O A:ASP105 4.6 26.4 1.0
CB A:GLU106 4.6 29.1 1.0
C2' D:DDG815 4.7 40.3 1.0
C A:ASP105 4.7 26.9 1.0
NZ A:LYS159 4.8 31.2 1.0
CB A:ASP105 4.8 27.0 1.0
O3A A:TTP414 4.9 21.2 1.0
CB A:ASP7 4.9 23.9 1.0
O A:HOH538 4.9 36.6 1.0
O3G A:TTP414 5.0 19.6 1.0

Calcium binding site 2 out of 6 in 3khr

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Calcium binding site 2 out of 6 in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:28.1
occ:1.00
 OD1 A:ASP7 2.3 30.0 1.0
O A:PHE8 2.3 24.5 1.0
O1B A:TTP414 2.3 22.0 1.0
O1A A:TTP414 2.3 32.9 1.0
OD2 A:ASP105 2.3 28.1 1.0
O3G A:TTP414 2.4 19.6 1.0
PB A:TTP414 3.4 20.0 1.0
CG A:ASP105 3.4 29.0 1.0
CG A:ASP7 3.4 28.5 1.0
C A:PHE8 3.5 23.6 1.0
PA A:TTP414 3.5 23.8 1.0
O A:HOH524 3.6 42.4 1.0
PG A:TTP414 3.6 21.0 1.0
CA A:CA415 3.6 48.1 1.0
O3A A:TTP414 3.7 21.2 1.0
N A:PHE8 3.8 22.3 1.0
O3B A:TTP414 3.9 20.7 1.0
OD1 A:ASP105 3.9 29.9 1.0
OD2 A:ASP7 4.0 28.4 1.0
NZ A:LYS159 4.0 31.2 1.0
C A:ASP7 4.2 22.7 1.0
C5' A:TTP414 4.2 19.1 1.0
O1G A:TTP414 4.2 21.4 1.0
CA A:PHE8 4.2 22.9 1.0
O5' A:TTP414 4.4 20.6 1.0
N A:ASP9 4.5 23.5 1.0
N A:TYR10 4.5 22.8 1.0
CA A:ASP9 4.6 23.8 1.0
CB A:ASP7 4.6 23.9 1.0
O A:ASP7 4.7 22.1 1.0
O2A A:TTP414 4.7 25.3 1.0
CB A:ASP105 4.7 27.0 1.0
O2B A:TTP414 4.7 19.2 1.0
CE A:LYS159 4.7 34.8 1.0
CA A:ASP7 4.7 23.3 1.0
C A:ASP9 4.8 23.0 1.0
N A:PHE11 4.8 22.1 1.0
O2G A:TTP414 4.8 18.9 1.0
O A:HOH510 4.8 37.2 1.0
O A:ASP105 4.9 26.4 1.0
CB A:PHE8 4.9 23.0 1.0
CB A:PHE11 5.0 21.8 1.0

Calcium binding site 3 out of 6 in 3khr

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Calcium binding site 3 out of 6 in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:40.5
occ:1.00
 O A:HOH513 2.0 42.7 1.0
O A:HOH585 2.2 46.1 1.0
O A:ALA181 2.3 34.6 1.0
O A:ILE186 2.3 35.6 1.0
O D:HOH514 2.3 25.7 1.0
C A:ALA181 3.5 32.0 1.0
C A:ILE186 3.5 33.9 1.0
OP2 D:DC814 4.0 29.4 1.0
CA A:GLY187 4.1 34.5 1.0
CA A:ALA181 4.3 32.1 1.0
N A:GLY187 4.3 33.8 1.0
OP1 D:DC814 4.3 23.8 1.0
N A:ASP182 4.5 31.2 1.0
CB A:ALA181 4.6 31.6 1.0
CA A:ASP182 4.6 31.4 1.0
O A:VAL183 4.6 27.2 1.0
CA A:ILE186 4.7 32.9 1.0
P D:DC814 4.7 27.2 1.0
C A:GLY187 4.8 35.2 1.0
CB A:ILE186 4.9 33.1 1.0
N A:ILE186 4.9 31.8 1.0

Calcium binding site 4 out of 6 in 3khr

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Calcium binding site 4 out of 6 in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:56.7
occ:1.00
 OE2 B:GLU1106 2.3 50.7 1.0
OD2 B:ASP1007 2.7 27.8 1.0
O B:HOH1519 3.0 64.9 1.0
CD B:GLU1106 3.1 40.8 1.0
O B:HOH140 3.3 38.6 1.0
CG B:GLU1106 3.5 31.7 1.0
NZ B:LYS1152 3.5 32.8 1.0
CG B:ASP1007 3.6 27.4 1.0
O5' H:DDG1815 3.7 40.3 1.0
O1A B:TTP1414 3.8 21.7 1.0
O B:HOH76 3.9 32.4 1.0
OP2 H:DDG1815 4.0 39.4 1.0
OE1 B:GLU1106 4.0 45.7 1.0
OD1 B:ASP1007 4.1 28.6 1.0
CZ B:PHE1005 4.2 21.5 1.0
NZ B:LYS1159 4.2 34.7 1.0
C3' H:DDG1815 4.4 39.3 1.0
CE B:LYS1152 4.4 29.6 1.0
C5' H:DDG1815 4.4 41.2 1.0
P H:DDG1815 4.4 39.9 1.0
CB B:ASP1007 4.6 22.1 1.0
CE2 B:PHE1005 4.7 21.1 1.0
CA B:CA1416 4.7 27.4 1.0
CB B:GLU1106 4.8 25.2 1.0
OD1 B:ASP1105 4.8 28.1 1.0
O2A B:TTP1414 4.8 22.4 1.0
C4' H:DDG1815 4.9 38.3 1.0
PA B:TTP1414 4.9 20.8 1.0

Calcium binding site 5 out of 6 in 3khr

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Calcium binding site 5 out of 6 in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:27.4
occ:1.00
 OD1 B:ASP1007 2.3 28.6 1.0
O B:PHE1008 2.3 24.2 1.0
O1B B:TTP1414 2.3 21.0 1.0
OD2 B:ASP1105 2.3 26.3 1.0
O1A B:TTP1414 2.4 21.7 1.0
O3G B:TTP1414 2.4 19.0 1.0
O B:HOH1519 2.8 64.9 1.0
PB B:TTP1414 3.4 16.9 1.0
CG B:ASP1007 3.4 27.4 1.0
CG B:ASP1105 3.5 26.1 1.0
C B:PHE1008 3.5 22.1 1.0
PG B:TTP1414 3.5 19.7 1.0
PA B:TTP1414 3.6 20.8 1.0
O3A B:TTP1414 3.8 20.4 1.0
O3B B:TTP1414 3.8 18.7 1.0
N B:PHE1008 3.8 20.7 1.0
O B:HOH25 3.9 41.4 1.0
OD1 B:ASP1105 4.0 28.1 1.0
OD2 B:ASP1007 4.0 27.8 1.0
C5' B:TTP1414 4.2 19.9 1.0
NZ B:LYS1159 4.2 34.7 1.0
C B:ASP1007 4.2 21.1 1.0
O1G B:TTP1414 4.2 20.5 1.0
CA B:PHE1008 4.2 21.5 1.0
O5' B:TTP1414 4.4 20.8 1.0
N B:ASP1009 4.5 21.3 1.0
N B:TYR1010 4.6 20.6 1.0
CA B:ASP1009 4.6 21.3 1.0
O B:ASP1007 4.6 20.2 1.0
CB B:ASP1007 4.6 22.1 1.0
CA B:ASP1007 4.7 21.3 1.0
CB B:ASP1105 4.7 22.8 1.0
O2B B:TTP1414 4.7 16.6 1.0
CA B:CA1415 4.7 56.7 1.0
O2G B:TTP1414 4.8 18.8 1.0
O B:ASP1105 4.8 22.8 1.0
O2A B:TTP1414 4.8 22.4 1.0
C B:ASP1009 4.8 20.5 1.0
N B:PHE1011 4.9 19.1 1.0
CB B:PHE1008 4.9 21.3 1.0

Calcium binding site 6 out of 6 in 3khr

Go back to Calcium Binding Sites List in 3khr
Calcium binding site 6 out of 6 in the DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of DPO4 Post-Extension Ternary Complex with the Correct C Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:43.5
occ:1.00
 O B:HOH344 2.1 32.1 1.0
O B:HOH1513 2.2 48.1 1.0
O B:ALA1181 2.3 34.1 1.0
O H:HOH331 2.3 25.9 1.0
O B:HOH1511 2.4 24.2 1.0
O B:HOH1512 2.4 36.4 1.0
O B:ILE1186 2.6 25.5 1.0
C B:ALA1181 3.5 30.3 1.0
C B:ILE1186 3.8 25.3 1.0
O B:HOH425 3.9 54.4 1.0
CA B:ALA1181 4.2 30.3 1.0
OP2 H:DC1814 4.2 22.5 1.0
CA B:GLY1187 4.2 26.0 1.0
CB B:ALA1181 4.4 29.7 1.0
N B:GLY1187 4.5 24.9 1.0
N B:ASP1182 4.5 29.4 1.0
O B:HOH359 4.5 40.3 1.0
OP1 H:DC1814 4.6 18.4 1.0
CA B:ASP1182 4.7 28.7 1.0
O B:VAL1183 4.7 24.5 1.0
C B:GLY1187 4.8 26.7 1.0
CA B:ILE1186 4.9 25.6 1.0
P H:DC1814 5.0 20.6 1.0

Reference:

O.Rechkoblit, A.Kolbanovskiy, L.Malinina, N.E.Geacintov, S.Broyde, D.J.Patel. Mechanism of Error-Free and Semitargeted Mutagenic Bypass of An Aromatic Amine Lesion By Y-Family Polymerase DPO4. Nat.Struct.Mol.Biol. V. 17 379 2010.
ISSN: ISSN 1545-9993
PubMed: 20154704
DOI: 10.1038/NSMB.1771
Page generated: Tue Jul 8 13:50:33 2025

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