Atomistry » Calcium » PDB 2w3k-2whk » 2w7o
Atomistry »
  Calcium »
    PDB 2w3k-2whk »
      2w7o »

Calcium in PDB 2w7o: Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct

Enzymatic activity of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct

All present enzymatic activity of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct:
2.7.7.7;

Protein crystallography data

The structure of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct, PDB code: 2w7o was solved by A.Irimia, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 3.16
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.482, 217.629, 117.957, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct (pdb code 2w7o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct, PDB code: 2w7o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2w7o

Go back to Calcium Binding Sites List in 2w7o
Calcium binding site 1 out of 4 in the Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1521

b:60.5
occ:1.00
 OD1 A:ASP325 2.5 90.9 1.0
O A:HOH2003 2.8 56.0 1.0
CG A:ASP325 3.1 88.9 1.0
O1B A:DGT1520 3.2 94.1 1.0
OD2 A:ASP107 3.3 75.0 1.0
O1A A:DGT1520 3.4 0.7 1.0
OD2 A:ASP325 3.5 91.2 1.0
NZ A:LYS328 3.8 75.5 1.0
OG A:SER324 3.8 81.5 1.0
CG A:ASP107 4.1 71.7 1.0
CB A:ASP325 4.2 83.6 1.0
PA A:DGT1520 4.3 0.7 1.0
PB A:DGT1520 4.5 92.5 1.0
OP1 P:DC13 4.5 69.2 1.0
O A:LYS321 4.5 65.8 1.0
O3A A:DGT1520 4.5 97.9 1.0
CE1 A:HIS105 4.6 60.4 1.0
CB A:ASP107 4.6 68.8 1.0
O A:HOH2009 4.8 53.9 1.0
OD1 A:ASP107 4.8 71.1 1.0
CE A:LYS321 4.8 69.2 1.0
N A:ASP325 4.9 77.9 1.0
CG A:LYS321 5.0 66.8 1.0
CA A:ASP325 5.0 78.8 1.0

Calcium binding site 2 out of 4 in 2w7o

Go back to Calcium Binding Sites List in 2w7o
Calcium binding site 2 out of 4 in the Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1522

b:64.0
occ:1.00
 O A:MET108 2.6 65.1 1.0
O1G A:DGT1520 2.7 87.4 1.0
O2B A:DGT1520 2.8 92.7 1.0
OD1 A:ASP107 2.8 71.1 1.0
O A:HOH2009 3.0 53.9 1.0
CG A:ASP198 3.2 85.2 1.0
OD2 A:ASP198 3.2 86.8 1.0
PB A:DGT1520 3.3 92.5 1.0
O3B A:DGT1520 3.4 90.4 1.0
C A:MET108 3.4 65.3 1.0
CB A:ASP198 3.4 81.6 1.0
O1B A:DGT1520 3.5 94.1 1.0
CG A:ASP107 3.6 71.7 1.0
OD1 A:ASP198 3.7 85.8 1.0
OD2 A:ASP107 3.8 75.0 1.0
PG A:DGT1520 3.9 87.1 1.0
N A:MET108 4.0 66.0 1.0
CA A:MET108 4.1 65.1 1.0
CB A:MET108 4.2 66.3 1.0
N A:ASP109 4.3 65.8 1.0
N A:ALA110 4.4 66.3 1.0
C A:ASP107 4.5 66.2 1.0
N A:PHE111 4.5 65.6 1.0
CB A:PHE111 4.5 61.7 1.0
CA A:ASP109 4.6 66.0 1.0
O A:ASP198 4.6 78.3 1.0
O3G A:DGT1520 4.7 85.8 1.0
CA A:ASP198 4.8 77.8 1.0
C A:ASP109 4.8 66.4 1.0
O3A A:DGT1520 4.9 97.9 1.0
O2G A:DGT1520 4.9 87.0 1.0
CB A:ASP107 4.9 68.8 1.0
C A:ASP198 4.9 77.5 1.0
NZ A:LYS328 5.0 75.5 1.0
O A:ASP107 5.0 66.9 1.0
C4' A:DGT1520 5.0 95.6 1.0

Calcium binding site 3 out of 4 in 2w7o

Go back to Calcium Binding Sites List in 2w7o
Calcium binding site 3 out of 4 in the Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1521

b:0.3
occ:1.00
 O1A B:DGT1520 2.8 0.5 1.0
OD1 B:ASP325 2.9 0.7 1.0
OD2 B:ASP325 3.1 0.8 1.0
CG B:ASP325 3.4 0.8 1.0
O1B B:DGT1520 3.5 1.0 1.0
OP1 E:DC13 3.5 99.6 1.0
OE2 B:GLU199 3.5 95.9 0.5
NZ B:LYS321 3.5 78.6 1.0
OD1 B:ASP107 3.8 0.2 1.0
CE1 B:HIS105 4.0 88.0 1.0
CG B:ASP107 4.0 0.3 1.0
CE B:LYS321 4.3 77.8 1.0
OD2 B:ASP107 4.4 0.6 1.0
PA B:DGT1520 4.4 0.3 1.0
CB B:ASP107 4.4 0.5 1.0
CD B:GLU199 4.4 97.2 0.5
OG B:SER324 4.6 92.0 1.0
O5' B:DGT1520 4.6 0.6 1.0
P E:DC13 4.7 100.0 1.0
CG B:LYS321 4.7 77.2 1.0
C5' B:DGT1520 4.7 0.8 1.0
O B:LYS321 4.8 82.1 1.0
NE2 B:HIS105 4.8 86.6 1.0
O5' E:DC13 4.8 0.8 1.0
OE1 B:GLU199 4.8 96.4 0.5
ND1 B:HIS105 4.8 87.3 1.0
CB B:ASP325 4.8 0.1 1.0
PB B:DGT1520 4.9 0.8 1.0

Calcium binding site 4 out of 4 in 2w7o

Go back to Calcium Binding Sites List in 2w7o
Calcium binding site 4 out of 4 in the Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure and Activity of Bypass Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxodeoxyguanosine Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1522

b:95.9
occ:1.00
 OD1 B:ASP198 2.7 0.1 1.0
O2B B:DGT1520 2.7 0.8 1.0
O B:MET108 2.8 0.8 1.0
OD1 B:ASP107 2.9 0.2 1.0
OD2 B:ASP198 2.9 0.8 1.0
OD2 B:ASP107 3.0 0.6 1.0
CG B:ASP107 3.0 0.3 1.0
CG B:ASP198 3.0 0.6 1.0
O1G B:DGT1520 3.1 0.8 1.0
C B:MET108 3.3 0.5 1.0
O B:ASP107 3.4 0.7 1.0
C B:ASP107 3.4 0.3 1.0
PB B:DGT1520 3.5 0.8 1.0
O1B B:DGT1520 3.7 1.0 1.0
O B:ASP198 3.7 0.2 1.0
N B:MET108 3.7 0.3 1.0
CA B:ASP107 4.0 0.7 1.0
O3B B:DGT1520 4.0 0.7 1.0
N B:ASP109 4.0 0.2 1.0
CA B:MET108 4.1 0.8 1.0
CB B:ASP107 4.1 0.5 1.0
PG B:DGT1520 4.2 0.7 1.0
C B:ASP109 4.3 0.9 1.0
CA B:ASP109 4.3 0.8 1.0
CB B:ASP198 4.3 0.6 1.0
N B:ALA110 4.3 0.8 1.0
O B:ALA110 4.4 0.6 1.0
O3G B:DGT1520 4.4 0.3 1.0
C B:ASP198 4.5 0.0 1.0
CB B:PHE111 4.5 0.6 1.0
CA B:ASP198 4.5 0.3 1.0
C B:ALA110 4.6 0.1 1.0
O B:ASP109 4.8 0.4 1.0
NZ B:LYS328 4.9 87.5 0.5
CB B:MET108 4.9 0.2 1.0

Reference:

A.Irimia, R.L.Eoff, F.P.Guengerich, M.Egli. Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis By Human Dna Polymerase Kappa Opposite the 7,8-Dihydro-8- Oxo-2'-Deoxyguanosine Adduct. J.Biol.Chem. V. 284 22467 2009.
ISSN: ISSN 0021-9258
PubMed: 19542228
DOI: 10.1074/JBC.M109.003905
Page generated: Fri Jul 12 18:32:22 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