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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: Tue Jul 8 08:58:47 2025

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