Atomistry » Calcium » PDB 3k5m-3km5 » 3khr
Atomistry »
  Calcium »
    PDB 3k5m-3km5 »
      3khr »

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

Go back to Calcium Binding Sites List in 3khr
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

Go back to Calcium Binding Sites List in 3khr
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

Go back to Calcium Binding Sites List in 3khr
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

Go back to Calcium Binding Sites List in 3khr
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: Sat Jul 13 12:17:40 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy