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

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

All present enzymatic activity of DPO4 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 Extension Ternary Complex with Misinserted A Opposite the 2- Aminofluorene-Guanine [Af]G Lesion, PDB code: 3khg 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 / 2.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.811, 110.948, 100.772, 90.00, 101.38, 90.00
R / Rfree (%) 20.5 / 28.2

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3khg

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Calcium binding site 1 out of 6 in the DPO4 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 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:38.6
occ:1.00
 OE2 A:GLU106 2.3 31.4 1.0
O2A A:DGT414 2.3 28.4 1.0
OD2 A:ASP7 2.3 32.1 1.0
OD1 A:ASP105 2.7 17.0 1.0
OD2 A:ASP105 3.1 22.5 1.0
CD A:GLU106 3.1 21.9 1.0
CG A:ASP7 3.2 18.8 1.0
CA A:CA416 3.2 29.5 1.0
CG A:ASP105 3.2 15.6 1.0
OD1 A:ASP7 3.7 27.0 1.0
PA A:DGT414 3.7 14.6 1.0
OP1 D:2DA814 3.8 71.1 1.0
OE1 A:GLU106 3.8 23.5 1.0
CB A:GLU106 3.8 15.2 1.0
CG A:GLU106 4.0 18.4 1.0
O1A A:DGT414 4.0 18.5 1.0
CB A:ASP7 4.2 14.1 1.0
C5' A:DGT414 4.4 20.0 1.0
O5' A:DGT414 4.5 18.9 1.0
OG A:SER103 4.6 11.1 1.0
O A:ASP105 4.6 13.7 1.0
C A:ASP105 4.6 13.9 1.0
CB A:ASP105 4.7 14.4 1.0
N A:GLU106 4.7 14.2 1.0
O1B A:DGT414 4.8 6.2 1.0
CA A:ASP7 4.8 13.1 1.0
O3A A:DGT414 4.9 8.8 1.0
O1G A:DGT414 4.9 2.0 1.0
CA A:GLU106 4.9 14.7 1.0
C7 E:AF926 4.9 53.3 1.0
P D:2DA814 4.9 68.9 1.0

Calcium binding site 2 out of 6 in 3khg

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Calcium binding site 2 out of 6 in the DPO4 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 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:29.5
occ:1.00
 O1B A:DGT414 2.3 6.2 1.0
OD2 A:ASP105 2.3 22.5 1.0
O A:PHE8 2.3 17.1 1.0
O2A A:DGT414 2.3 28.4 1.0
OD1 A:ASP7 2.3 27.0 1.0
O1G A:DGT414 3.0 2.0 1.0
CG A:ASP7 3.1 18.8 1.0
OD2 A:ASP7 3.2 32.1 1.0
CA A:CA415 3.2 38.6 1.0
PA A:DGT414 3.4 14.6 1.0
PB A:DGT414 3.4 2.1 1.0
C A:PHE8 3.5 13.6 1.0
CG A:ASP105 3.5 15.6 1.0
PG A:DGT414 3.6 2.0 1.0
O3A A:DGT414 3.6 8.8 1.0
N A:PHE8 3.9 13.4 1.0
C5' A:DGT414 3.9 20.0 1.0
OD1 A:ASP105 4.0 17.0 1.0
O5' A:DGT414 4.1 18.9 1.0
O3B A:DGT414 4.1 2.3 1.0
C A:ASP7 4.2 13.1 1.0
CA A:PHE8 4.2 13.4 1.0
CB A:ASP7 4.4 14.1 1.0
NZ A:LYS159 4.4 6.7 1.0
N A:ASP9 4.5 13.2 1.0
O2B A:DGT414 4.6 2.2 1.0
CB A:ASP105 4.6 14.4 1.0
O A:ASP7 4.6 12.8 1.0
O3G A:DGT414 4.7 2.0 1.0
O1A A:DGT414 4.7 18.5 1.0
CA A:ASP9 4.7 12.2 1.0
CA A:ASP7 4.7 13.1 1.0
O2G A:DGT414 4.7 2.0 1.0
N A:TYR10 4.7 10.9 1.0
CB A:PHE8 4.8 13.0 1.0
O A:ASP105 4.9 13.7 1.0
C A:ASP9 5.0 11.8 1.0

Calcium binding site 3 out of 6 in 3khg

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Calcium binding site 3 out of 6 in the DPO4 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 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:38.9
occ:1.00
 O A:HOH513 2.2 2.0 1.0
O A:ILE186 2.3 28.4 1.0
O A:ALA181 2.3 27.9 1.0
O A:HOH516 2.5 33.4 1.0
O D:HOH3 2.5 2.0 1.0
O D:HOH515 2.7 29.0 1.0
C A:ALA181 3.4 24.2 1.0
C A:ILE186 3.5 25.1 1.0
CA A:GLY187 4.2 25.7 1.0
CA A:ALA181 4.2 24.0 1.0
N A:GLY187 4.3 25.8 1.0
N A:ASP182 4.3 23.5 1.0
CA A:ASP182 4.3 22.5 1.0
OP1 D:DG813 4.4 22.6 1.0
CB A:ALA181 4.5 24.0 1.0
CA A:ILE186 4.6 24.1 1.0
OP2 D:DG813 4.6 22.6 1.0
N A:ILE186 4.8 22.9 1.0
CB A:ILE186 4.8 23.8 1.0
C A:ASP182 4.8 21.8 1.0
C A:GLY187 4.8 26.0 1.0
O A:VAL183 4.9 20.6 1.0
N A:VAL183 5.0 20.9 1.0
O A:GLY187 5.0 26.1 1.0
OD1 A:ASP182 5.0 25.6 1.0

Calcium binding site 4 out of 6 in 3khg

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Calcium binding site 4 out of 6 in the DPO4 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 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:63.8
occ:1.00
 O2A B:DGT1414 2.3 61.1 1.0
OE2 B:GLU1106 2.3 59.0 1.0
OD1 B:ASP1105 2.3 58.8 1.0
OD2 B:ASP1007 2.3 58.8 1.0
OD2 B:ASP1105 2.9 53.8 1.0
CD B:GLU1106 3.0 54.0 1.0
CG B:ASP1105 3.0 51.3 1.0
CG B:GLU1106 3.1 51.7 1.0
CG B:ASP1007 3.5 50.9 1.0
PA B:DGT1414 3.5 59.6 1.0
CA B:CA1416 3.6 57.8 1.0
O1A B:DGT1414 3.7 59.3 1.0
C5' B:DGT1414 3.8 60.8 1.0
OD1 B:ASP1007 4.0 54.8 1.0
O5' B:DGT1414 4.0 60.2 1.0
OG B:SER1103 4.0 49.8 1.0
OE1 B:GLU1106 4.1 55.1 1.0
O1B B:DGT1414 4.3 55.8 1.0
CB B:ASP1105 4.4 50.1 1.0
CB B:GLU1106 4.5 50.3 1.0
CB B:ASP1007 4.7 48.7 1.0
C B:ASP1105 4.7 49.6 1.0
O B:ASP1105 4.8 49.3 1.0
O3A B:DGT1414 4.8 57.3 1.0

Calcium binding site 5 out of 6 in 3khg

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Calcium binding site 5 out of 6 in the DPO4 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 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:57.8
occ:1.00
 OD2 B:ASP1105 2.3 53.8 1.0
O1B B:DGT1414 2.3 55.8 1.0
OD1 B:ASP1007 2.3 54.8 1.0
O B:PHE1008 2.3 50.9 1.0
O2A B:DGT1414 2.4 61.1 1.0
CG B:ASP1007 3.1 50.9 1.0
PB B:DGT1414 3.2 55.3 1.0
O3B B:DGT1414 3.3 54.2 1.0
OD2 B:ASP1007 3.3 58.8 1.0
PG B:DGT1414 3.3 53.0 1.0
CG B:ASP1105 3.5 51.3 1.0
C B:PHE1008 3.5 48.8 1.0
PA B:DGT1414 3.6 59.6 1.0
O3A B:DGT1414 3.6 57.3 1.0
O2G B:DGT1414 3.6 52.8 1.0
CA B:CA1415 3.6 63.8 1.0
N B:PHE1008 4.0 48.5 1.0
OD1 B:ASP1105 4.1 58.8 1.0
C B:ASP1007 4.2 48.4 1.0
O B:TYR1010 4.2 46.6 1.0
CA B:PHE1008 4.3 48.7 1.0
CB B:ASP1007 4.4 48.7 1.0
O1G B:DGT1414 4.4 52.3 1.0
CB B:ASP1105 4.4 50.1 1.0
O B:ASP1007 4.5 48.4 1.0
N B:ASP1009 4.5 48.3 1.0
O2B B:DGT1414 4.6 53.9 1.0
O1A B:DGT1414 4.6 59.3 1.0
N B:TYR1010 4.6 46.7 1.0
O5' B:DGT1414 4.6 60.2 1.0
O3G B:DGT1414 4.7 52.5 1.0
CA B:ASP1009 4.7 47.9 1.0
CA B:ASP1007 4.7 48.2 1.0
C5' B:DGT1414 4.8 60.8 1.0
C B:ASP1009 4.8 47.3 1.0
C B:TYR1010 4.9 45.8 1.0
CA B:TYR1010 5.0 46.5 1.0

Calcium binding site 6 out of 6 in 3khg

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Calcium binding site 6 out of 6 in the DPO4 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 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:64.0
occ:1.00
 O B:ALA1181 2.3 56.7 1.0
O B:ILE1186 2.3 59.0 1.0
O B:HOH1514 2.4 13.6 1.0
O B:HOH1511 2.5 21.4 1.0
O B:HOH1516 2.6 13.7 1.0
O B:HOH1515 2.8 30.1 1.0
C B:ILE1186 3.5 57.5 1.0
C B:ALA1181 3.5 54.6 1.0
O B:VAL1183 3.6 52.5 1.0
OP1 H:DG1813 3.7 45.9 1.0
CA B:GLY1187 4.2 58.8 1.0
N B:GLY1187 4.3 58.3 1.0
OP2 H:DG1813 4.3 45.9 1.0
CA B:ASP1182 4.3 53.6 1.0
N B:ASP1182 4.3 54.2 1.0
N B:VAL1183 4.4 52.9 1.0
CA B:ALA1181 4.5 54.5 1.0
C B:VAL1183 4.5 52.6 1.0
C B:ASP1182 4.5 53.3 1.0
P H:DG1813 4.5 45.5 1.0
CA B:ILE1186 4.5 56.7 1.0
N B:ILE1186 4.6 55.9 1.0
CB B:ILE1186 4.9 56.8 1.0
CB B:ALA1181 4.9 54.5 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 13:49:17 2025

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