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

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

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

Protein crystallography data

The structure of DPO4 Extension Ternary Complex with A C Base Opposite the 2- Aminofluorene-Guanine [Af]G Lesion, PDB code: 3khh 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.746, 98.799, 98.638, 90.00, 99.08, 90.00
R / Rfree (%) 19.2 / 25.2

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3khh

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

b:62.0
occ:1.00
 O2A A:DGT414 2.3 60.2 1.0
OD1 A:ASP105 2.7 36.2 1.0
O2B A:DGT414 2.7 48.7 1.0
OD2 A:ASP105 2.7 36.4 1.0
OE2 A:GLU106 2.7 35.3 1.0
O A:HOH543 2.9 25.8 1.0
O3A A:DGT414 3.0 53.1 1.0
CG A:ASP105 3.0 32.8 1.0
O3' A:DGT414 3.1 63.2 1.0
PA A:DGT414 3.1 57.4 1.0
PB A:DGT414 3.4 49.1 1.0
C4' A:DGT414 3.6 63.0 1.0
CD A:GLU106 3.6 34.8 1.0
CG A:GLU106 3.7 32.2 1.0
CA A:CA416 3.9 37.5 1.0
C3' A:DGT414 3.9 63.7 1.0
O5' A:DGT414 4.1 59.1 1.0
OG A:SER103 4.2 31.8 1.0
O3B A:DGT414 4.2 42.7 1.0
O1A A:DGT414 4.3 58.3 1.0
C5' A:DGT414 4.4 61.3 1.0
O4' A:DGT414 4.5 64.1 1.0
CB A:ASP105 4.5 30.7 1.0
OD1 A:ASP7 4.6 35.6 1.0
PG A:DGT414 4.6 44.3 1.0
O1B A:DGT414 4.7 49.1 1.0
OE1 A:GLU106 4.7 35.1 1.0
OD2 A:ASP7 4.9 33.8 1.0

Calcium binding site 2 out of 6 in 3khh

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Calcium binding site 2 out of 6 in the DPO4 Extension Ternary Complex with A C Base 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 A C Base Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca416

b:37.5
occ:1.00
 OD1 A:ASP7 2.3 35.6 1.0
O3B A:DGT414 2.3 42.7 1.0
OD2 A:ASP105 2.3 36.4 1.0
O A:PHE8 2.3 32.6 1.0
O2B A:DGT414 2.7 48.7 1.0
PB A:DGT414 3.0 49.1 1.0
PG A:DGT414 3.3 44.3 1.0
O A:HOH515 3.4 29.3 1.0
CG A:ASP7 3.4 32.1 1.0
C A:PHE8 3.4 30.6 1.0
CG A:ASP105 3.5 32.8 1.0
O1G A:DGT414 3.6 44.1 1.0
OD2 A:ASP7 3.9 33.8 1.0
CA A:CA415 3.9 62.0 1.0
O3G A:DGT414 3.9 43.4 1.0
N A:PHE8 4.0 30.4 1.0
O3A A:DGT414 4.1 53.1 1.0
O1B A:DGT414 4.1 49.1 1.0
CB A:ASP105 4.2 30.7 1.0
CA A:PHE8 4.3 30.6 1.0
N A:TYR10 4.4 28.2 1.0
N A:ASP9 4.4 30.0 1.0
C A:ASP7 4.4 30.0 1.0
O3' A:DGT414 4.4 63.2 1.0
OD1 A:ASP105 4.5 36.2 1.0
CA A:ASP9 4.5 29.4 1.0
O A:ASP105 4.6 30.5 1.0
O2G A:DGT414 4.7 45.1 1.0
CB A:ASP7 4.7 30.4 1.0
C A:ASP9 4.7 28.8 1.0
N A:PHE11 4.8 26.0 1.0
O A:ASP7 4.9 30.1 1.0
CB A:PHE8 4.9 30.2 1.0
CA A:ASP7 4.9 29.9 1.0
CE A:LYS159 4.9 30.1 1.0

Calcium binding site 3 out of 6 in 3khh

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Calcium binding site 3 out of 6 in the DPO4 Extension Ternary Complex with A C Base 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 A C Base Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:43.5
occ:1.00
 O A:ALA181 2.3 38.9 1.0
O A:ILE186 2.3 38.9 1.0
O A:HOH512 2.4 24.6 1.0
O D:HOH515 2.4 25.4 1.0
O A:HOH513 2.4 35.4 1.0
O A:HOH514 2.5 11.4 1.0
C A:ALA181 3.4 37.1 1.0
C A:ILE186 3.5 36.9 1.0
OP2 D:DOC814 4.1 20.3 1.0
CA A:GLY187 4.2 37.2 1.0
N A:GLY187 4.3 37.1 1.0
CA A:ALA181 4.3 37.0 1.0
N A:ASP182 4.3 36.8 1.0
CA A:ASP182 4.4 35.9 1.0
O A:VAL183 4.4 34.0 1.0
OP1 D:DOC814 4.5 19.9 1.0
CB A:ALA181 4.6 36.9 1.0
CA A:ILE186 4.6 36.1 1.0
P D:DOC814 4.8 19.5 1.0
C A:GLY187 4.8 37.3 1.0
C A:ASP182 4.9 35.2 1.0
CB A:ILE186 4.9 35.9 1.0
N A:ILE186 4.9 35.3 1.0
N A:VAL183 5.0 34.7 1.0

Calcium binding site 4 out of 6 in 3khh

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

b:42.9
occ:1.00
 OE2 B:GLU1106 2.3 40.6 1.0
OD1 B:ASP1105 2.6 29.5 1.0
O B:HOH103 2.6 22.2 1.0
OD2 B:ASP1105 2.7 29.1 1.0
O2B B:DGT1414 2.9 34.0 1.0
O B:HOH10 3.0 15.2 1.0
CG B:ASP1105 3.0 28.3 1.0
CD B:GLU1106 3.5 35.6 1.0
O2G B:DGT1414 3.6 35.3 1.0
C5' B:DGT1414 4.0 40.1 1.0
OG B:SER1103 4.0 28.6 1.0
O3' B:DGT1414 4.2 40.8 1.0
CG B:GLU1106 4.2 31.5 1.0
CA B:CA1416 4.2 29.8 1.0
O2A B:DGT1414 4.3 37.6 1.0
PB B:DGT1414 4.4 37.5 1.0
C4' B:DGT1414 4.4 40.0 1.0
O5' B:DGT1414 4.4 39.3 1.0
CB B:ASP1105 4.5 27.6 1.0
OE1 B:GLU1106 4.5 35.8 1.0
C3' B:DGT1414 4.8 39.9 1.0
O1B B:DGT1414 4.9 32.2 1.0
PA B:DGT1414 4.9 37.0 1.0
PG B:DGT1414 4.9 34.7 1.0

Calcium binding site 5 out of 6 in 3khh

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Calcium binding site 5 out of 6 in the DPO4 Extension Ternary Complex with A C Base 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 A C Base Opposite the 2- Aminofluorene-Guanine [Af]G Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1416

b:29.8
occ:1.00
 OD1 B:ASP1007 2.3 27.5 1.0
O B:PHE1008 2.3 24.6 1.0
O1B B:DGT1414 2.3 32.2 1.0
OD2 B:ASP1105 2.3 29.1 1.0
O3G B:DGT1414 2.4 33.8 1.0
O B:HOH103 2.8 22.2 1.0
PB B:DGT1414 3.2 37.5 1.0
O2B B:DGT1414 3.2 34.0 1.0
PG B:DGT1414 3.4 34.7 1.0
CG B:ASP1007 3.4 23.1 1.0
CG B:ASP1105 3.5 28.3 1.0
C B:PHE1008 3.5 22.5 1.0
O2G B:DGT1414 3.6 35.3 1.0
NZ B:LYS1159 3.6 31.6 1.0
O3B B:DGT1414 3.8 36.1 1.0
OD2 B:ASP1007 3.8 24.6 1.0
O B:HOH35 4.0 25.9 1.0
CB B:ASP1105 4.1 27.6 1.0
N B:PHE1008 4.1 21.4 1.0
CA B:CA1415 4.2 42.9 1.0
CA B:PHE1008 4.4 22.1 1.0
N B:ASP1009 4.4 22.6 1.0
OD1 B:ASP1105 4.5 29.5 1.0
CA B:ASP1009 4.5 22.2 1.0
N B:TYR1010 4.6 21.7 1.0
C B:ASP1007 4.6 21.1 1.0
O3A B:DGT1414 4.6 37.5 1.0
CB B:ASP1007 4.7 21.4 1.0
C B:ASP1009 4.7 21.9 1.0
O1G B:DGT1414 4.7 34.8 1.0
N B:PHE1011 4.9 21.4 1.0
OE2 B:GLU1106 4.9 40.6 1.0
CB B:PHE1008 5.0 21.9 1.0

Calcium binding site 6 out of 6 in 3khh

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

b:45.1
occ:1.00
 O B:ALA1181 2.3 40.7 1.0
O B:ILE1186 2.3 41.5 1.0
O B:HOH4 2.3 39.7 1.0
OP2 H:DOC1814 2.7 21.3 1.0
O H:HOH2 2.9 29.1 1.0
O B:VAL1183 3.2 35.4 1.0
OP1 H:DOC1814 3.4 21.0 1.0
C B:ILE1186 3.5 39.8 1.0
C B:ALA1181 3.5 38.9 1.0
P H:DOC1814 3.5 22.0 1.0
C B:VAL1183 4.1 35.3 1.0
CA B:ASP1182 4.2 37.1 1.0
C B:ASP1182 4.3 36.5 1.0
N B:VAL1183 4.3 35.9 1.0
CA B:GLY1187 4.3 39.5 1.0
N B:ASP1182 4.3 38.1 1.0
N B:GLY1187 4.3 39.8 1.0
N B:ILE1186 4.4 38.2 1.0
CA B:ILE1186 4.5 39.2 1.0
O3' H:DG1813 4.6 20.8 1.0
CA B:ALA1181 4.6 39.2 1.0
O B:ASP1182 4.8 36.3 1.0
O5' H:DOC1814 4.8 23.9 1.0
O B:HOH5 4.8 45.3 1.0
N B:PRO1184 4.9 35.2 1.0
CA B:VAL1183 4.9 35.3 1.0
CB B:ILE1186 5.0 39.1 1.0
CA B:PRO1184 5.0 35.3 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: Sat Jul 13 12:15:44 2024

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