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Calcium in PDB 3khl: DPO4 Post-Extension Ternary Complex with Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion

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

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

Protein crystallography data

The structure of DPO4 Post-Extension Ternary Complex with Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion, PDB code: 3khl 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 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.389, 52.674, 100.103, 82.19, 76.40, 70.07
R / Rfree (%) 20.5 / 26.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3khl

Go back to Calcium Binding Sites List in 3khl
Calcium binding site 1 out of 6 in the DPO4 Post-Extension Ternary Complex with Misinserted A 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 Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:44.9
occ:1.00
 O D:HOH510 2.1 31.2 1.0
O1A A:TTP414 2.3 30.6 1.0
OD1 A:ASP105 2.5 30.4 1.0
OD1 A:ASP7 2.8 27.6 1.0
OE2 A:GLU106 2.8 39.6 1.0
CG A:GLU106 3.2 32.6 1.0
C3' D:DDG815 3.3 56.3 1.0
CD A:GLU106 3.4 36.4 1.0
OD2 A:ASP7 3.4 29.3 1.0
CG A:ASP7 3.4 25.8 1.0
PA A:TTP414 3.4 16.4 1.0
CG A:ASP105 3.4 28.4 1.0
OD2 A:ASP105 3.6 28.0 1.0
CA A:CA416 3.6 28.9 1.0
OP1 D:DDG815 3.7 64.8 1.0
O2A A:TTP414 3.8 21.2 1.0
O5' A:TTP414 3.9 15.6 1.0
C4' D:DDG815 4.1 56.8 1.0
OG A:SER103 4.2 27.7 1.0
C5' A:TTP414 4.2 8.7 1.0
C5' D:DDG815 4.2 58.3 1.0
CB A:GLU106 4.5 27.9 1.0
OE1 A:GLU106 4.5 41.6 1.0
O A:ASP105 4.5 25.5 1.0
NZ A:LYS159 4.6 25.0 1.0
C2' D:DDG815 4.6 54.8 1.0
C A:ASP105 4.7 25.9 1.0
CB A:ASP7 4.7 21.9 1.0
O A:HOH582 4.7 36.0 1.0
O5' D:DDG815 4.8 63.4 1.0
CB A:ASP105 4.8 26.6 1.0
O3A A:TTP414 4.9 17.1 1.0
P D:DDG815 4.9 65.3 1.0
O3G A:TTP414 5.0 12.7 1.0

Calcium binding site 2 out of 6 in 3khl

Go back to Calcium Binding Sites List in 3khl
Calcium binding site 2 out of 6 in the DPO4 Post-Extension Ternary Complex with Misinserted A 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 Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:28.9
occ:1.00
 O1B A:TTP414 2.3 18.6 1.0
OD2 A:ASP105 2.3 28.0 1.0
O A:PHE8 2.3 23.0 1.0
O1A A:TTP414 2.3 30.6 1.0
OD1 A:ASP7 2.3 27.6 1.0
O3G A:TTP414 2.5 12.7 1.0
PB A:TTP414 3.4 13.6 1.0
CG A:ASP105 3.4 28.4 1.0
CG A:ASP7 3.4 25.8 1.0
C A:PHE8 3.5 21.7 1.0
PA A:TTP414 3.5 16.4 1.0
CA A:CA415 3.6 44.9 1.0
PG A:TTP414 3.6 17.1 1.0
O A:HOH544 3.7 37.2 1.0
O3A A:TTP414 3.8 17.1 1.0
OD1 A:ASP105 3.8 30.4 1.0
N A:PHE8 3.8 20.7 1.0
O3B A:TTP414 3.9 13.8 1.0
NZ A:LYS159 4.0 25.0 1.0
OD2 A:ASP7 4.0 29.3 1.0
C A:ASP7 4.2 20.4 1.0
C5' A:TTP414 4.2 8.7 1.0
O1G A:TTP414 4.2 15.3 1.0
CA A:PHE8 4.3 21.2 1.0
O5' A:TTP414 4.4 15.6 1.0
O D:HOH510 4.4 31.2 1.0
N A:ASP9 4.5 22.1 1.0
CB A:ASP7 4.5 21.9 1.0
N A:TYR10 4.5 20.4 1.0
CA A:ASP9 4.5 21.4 1.0
CB A:ASP105 4.6 26.6 1.0
CA A:ASP7 4.7 21.3 1.0
O A:ASP7 4.7 19.1 1.0
C A:ASP9 4.7 20.4 1.0
O2A A:TTP414 4.7 21.2 1.0
O2B A:TTP414 4.7 15.2 1.0
N A:PHE11 4.8 20.4 1.0
O A:ASP105 4.8 25.5 1.0
CE A:LYS159 4.8 30.2 1.0
O2G A:TTP414 4.9 15.4 1.0
CB A:PHE8 4.9 20.7 1.0
CB A:PHE11 4.9 20.8 1.0

Calcium binding site 3 out of 6 in 3khl

Go back to Calcium Binding Sites List in 3khl
Calcium binding site 3 out of 6 in the DPO4 Post-Extension Ternary Complex with Misinserted A 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 Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:51.6
occ:1.00
 O A:HOH512 2.1 42.6 1.0
O A:ILE186 2.3 46.3 1.0
O A:ALA181 2.3 43.6 1.0
O A:HOH514 2.4 33.7 1.0
O A:HOH513 2.4 66.9 1.0
O A:HOH515 2.8 50.3 1.0
OP1 D:DA814 3.0 39.9 1.0
C A:ILE186 3.5 44.0 1.0
C A:ALA181 3.5 40.2 1.0
CA A:GLY187 4.0 44.2 1.0
N A:GLY187 4.2 44.2 1.0
P D:DA814 4.2 39.5 1.0
O A:VAL183 4.4 36.2 1.0
CA A:ALA181 4.4 39.9 1.0
OP2 D:DA814 4.5 40.8 1.0
N A:ASP182 4.5 39.5 1.0
CA A:ILE186 4.6 42.9 1.0
CA A:ASP182 4.7 38.6 1.0
N A:ILE186 4.7 41.5 1.0
CB A:ALA181 4.8 39.6 1.0
C A:GLY187 4.8 44.2 1.0

Calcium binding site 4 out of 6 in 3khl

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Calcium binding site 4 out of 6 in the DPO4 Post-Extension Ternary Complex with Misinserted A 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 Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1415

b:54.5
occ:1.00
 O B:HOH1519 2.3 24.7 1.0
OE2 B:GLU1106 2.3 49.0 1.0
O B:HOH161 2.4 49.8 1.0
OD2 B:ASP1007 2.7 32.1 1.0
OP1 H:DDG1815 2.8 62.5 1.0
O1A B:TTP1414 3.2 13.2 1.0
CG B:ASP1007 3.4 27.6 1.0
CD B:GLU1106 3.5 38.3 1.0
OD1 B:ASP1007 3.5 29.5 1.0
NZ B:LYS1159 3.7 35.4 1.0
P H:DDG1815 3.9 62.2 1.0
O2A B:TTP1414 4.0 17.8 1.0
CG B:GLU1106 4.0 32.3 1.0
O5' H:DDG1815 4.0 60.7 1.0
PA B:TTP1414 4.2 13.7 1.0
C5' H:DDG1815 4.4 56.2 1.0
C3' H:DDG1815 4.4 53.3 1.0
CA B:CA1416 4.4 27.7 1.0
OE1 B:GLU1106 4.5 42.9 1.0
OP2 H:DDG1815 4.5 61.8 1.0
NZ B:LYS1152 4.5 39.5 1.0
CE B:LYS1152 4.6 35.0 1.0
OD1 B:ASP1105 4.7 28.0 1.0
CB B:ASP1007 4.7 23.1 1.0
O3G B:TTP1414 4.7 10.6 1.0
C4' H:DDG1815 5.0 54.8 1.0
CZ B:PHE1005 5.0 25.5 1.0

Calcium binding site 5 out of 6 in 3khl

Go back to Calcium Binding Sites List in 3khl
Calcium binding site 5 out of 6 in the DPO4 Post-Extension Ternary Complex with Misinserted A 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 Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:27.7
occ:1.00
 O B:PHE1008 2.3 24.0 1.0
OD1 B:ASP1007 2.3 29.5 1.0
OD2 B:ASP1105 2.3 25.7 1.0
O1B B:TTP1414 2.3 18.4 1.0
O1A B:TTP1414 2.4 13.2 1.0
O3G B:TTP1414 2.4 10.6 1.0
CG B:ASP1007 3.4 27.6 1.0
CG B:ASP1105 3.4 26.1 1.0
C B:PHE1008 3.5 22.2 1.0
PB B:TTP1414 3.5 14.2 1.0
O B:HOH1519 3.5 24.7 1.0
PA B:TTP1414 3.6 13.7 1.0
PG B:TTP1414 3.6 15.5 1.0
N B:PHE1008 3.8 21.7 1.0
O B:HOH25 3.8 40.5 1.0
O3A B:TTP1414 3.9 14.8 1.0
OD2 B:ASP1007 3.9 32.1 1.0
OD1 B:ASP1105 3.9 28.0 1.0
O3B B:TTP1414 4.0 11.9 1.0
C B:ASP1007 4.2 21.8 1.0
C5' B:TTP1414 4.2 12.6 1.0
CA B:PHE1008 4.2 21.9 1.0
O1G B:TTP1414 4.2 13.2 1.0
NZ B:LYS1159 4.3 35.4 1.0
O5' B:TTP1414 4.4 14.0 1.0
CA B:CA1415 4.4 54.5 1.0
N B:ASP1009 4.5 22.4 1.0
CB B:ASP1007 4.5 23.1 1.0
N B:TYR1010 4.5 19.7 1.0
CB B:ASP1105 4.6 24.5 1.0
CA B:ASP1009 4.6 21.4 1.0
CA B:ASP1007 4.7 22.8 1.0
O B:ASP1007 4.7 21.7 1.0
C B:ASP1009 4.8 20.2 1.0
O B:ASP1105 4.8 23.4 1.0
O2B B:TTP1414 4.8 13.3 1.0
N B:PHE1011 4.8 18.7 1.0
O2G B:TTP1414 4.8 15.5 1.0
O2A B:TTP1414 4.8 17.8 1.0
CB B:PHE1011 4.9 17.9 1.0
CB B:PHE1008 4.9 21.4 1.0
O B:HOH161 4.9 49.8 1.0

Calcium binding site 6 out of 6 in 3khl

Go back to Calcium Binding Sites List in 3khl
Calcium binding site 6 out of 6 in the DPO4 Post-Extension Ternary Complex with Misinserted A 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 Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1417

b:54.9
occ:1.00
 O B:HOH1512 2.2 37.7 1.0
O B:ALA1181 2.3 44.7 1.0
O H:HOH1511 2.4 37.6 1.0
O B:ILE1186 2.8 34.7 1.0
C B:ALA1181 3.5 40.3 1.0
O B:HOH1513 3.8 49.7 1.0
C B:ILE1186 4.0 34.4 1.0
OP2 H:DA1814 4.2 32.2 1.0
CA B:ALA1181 4.2 40.1 1.0
CA B:GLY1187 4.2 35.1 1.0
OP1 H:DA1814 4.3 34.8 1.0
CB B:ALA1181 4.5 40.1 1.0
N B:ASP1182 4.6 39.0 1.0
N B:GLY1187 4.6 34.8 1.0
O B:HOH1516 4.6 62.6 1.0
C B:GLY1187 4.8 35.4 1.0
CA B:ASP1182 4.8 37.5 1.0
P H:DA1814 4.8 31.9 1.0
O B:VAL1183 4.9 32.5 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 13:50:12 2025

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