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Calcium in PDB 2w7p: 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: 2w7p 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) 44.65 / 3.71
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 167.829, 220.847, 119.208, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 27.3

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 2w7p). 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: 2w7p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2w7p

Go back to Calcium Binding Sites List in 2w7p
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:Ca1522

b:64.1
occ:1.00
 OD1 A:ASP325 2.8 70.2 1.0
OD2 A:ASP325 2.9 69.8 1.0
OD2 A:ASP107 2.9 73.7 1.0
O1B A:DTP1521 3.1 0.8 1.0
CG A:ASP325 3.2 69.2 1.0
OP1 P:DC13 3.7 69.0 1.0
O3A A:DTP1521 3.8 0.5 1.0
PB A:DTP1521 3.8 0.7 1.0
OE1 A:GLU199 3.9 87.8 1.0
O2B A:DTP1521 3.9 0.8 1.0
CG A:ASP107 4.0 72.3 1.0
CE A:LYS321 4.0 65.4 1.0
O2A A:DTP1521 4.2 0.3 1.0
CD A:LYS321 4.4 64.3 1.0
PA A:DTP1521 4.4 0.6 1.0
OG A:SER324 4.6 64.3 1.0
OD1 A:ASP107 4.7 74.3 1.0
CB A:ASP325 4.7 66.3 1.0
O1A A:DTP1521 4.8 0.5 1.0
O A:LYS321 4.8 56.3 1.0
CD A:GLU199 4.8 87.5 1.0
P P:DC13 4.9 70.6 1.0
CE1 A:HIS105 4.9 55.1 1.0
CB A:ASP107 4.9 68.7 1.0

Calcium binding site 2 out of 4 in 2w7p

Go back to Calcium Binding Sites List in 2w7p
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:Ca1523

b:67.5
occ:1.00
 O A:MET108 2.7 60.2 1.0
OD2 A:ASP198 2.7 82.4 1.0
O3B A:DTP1521 2.9 96.0 1.0
O2B A:DTP1521 2.9 0.8 1.0
O3' A:DTP1521 3.1 1.0 1.0
OD1 A:ASP107 3.3 74.3 1.0
C A:MET108 3.4 60.5 1.0
O2G A:DTP1521 3.4 91.6 1.0
CG A:ASP198 3.5 82.2 1.0
PB A:DTP1521 3.5 0.7 1.0
CB A:ASP198 3.5 80.0 1.0
PG A:DTP1521 3.7 91.8 1.0
N A:ALA110 3.7 57.4 1.0
N A:PHE111 3.8 61.6 1.0
C3' A:DTP1521 4.0 0.0 1.0
C4' A:DTP1521 4.0 0.5 1.0
N A:ASP109 4.1 59.7 1.0
CA A:MET108 4.1 60.8 1.0
O3G A:DTP1521 4.2 91.6 1.0
CB A:MET108 4.2 61.3 1.0
CB A:PHE111 4.2 63.5 1.0
CA A:ASP109 4.2 58.6 1.0
N A:MET108 4.3 61.2 1.0
C A:ASP109 4.3 56.9 1.0
CA A:ALA110 4.4 58.8 1.0
CG A:ASP107 4.4 72.3 1.0
O3A A:DTP1521 4.5 0.5 1.0
O1B A:DTP1521 4.5 0.8 1.0
OD1 A:ASP198 4.6 83.5 1.0
CA A:PHE111 4.6 62.9 1.0
C A:ALA110 4.6 60.1 1.0
C A:ASP107 4.7 62.8 1.0
O A:ASP198 4.8 76.8 1.0
O4' A:DTP1521 4.9 0.1 1.0
CA A:ASP198 4.9 77.5 1.0
OD2 A:ASP107 4.9 73.7 1.0
C5' A:DTP1521 5.0 0.7 1.0

Calcium binding site 3 out of 4 in 2w7p

Go back to Calcium Binding Sites List in 2w7p
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:Ca1522

b:88.5
occ:1.00
 O2A B:DTP1521 2.8 0.2 1.0
OD1 B:ASP325 2.9 87.5 1.0
OD2 B:ASP325 3.3 89.6 1.0
CG B:ASP325 3.5 87.5 1.0
OD2 B:ASP107 3.5 87.9 1.0
CE B:LYS321 3.7 72.4 1.0
NZ B:LYS321 3.8 73.0 1.0
OP1 E:DC13 3.9 98.7 1.0
PA B:DTP1521 4.0 0.2 1.0
CG B:ASP107 4.0 88.6 1.0
CE1 B:HIS105 4.1 91.6 1.0
OG B:SER324 4.1 79.3 1.0
O3A B:DTP1521 4.1 0.5 1.0
CB B:ASP107 4.2 89.2 1.0
OE1 B:GLU199 4.4 0.3 1.0
CD B:LYS321 4.5 71.5 1.0
O B:LYS321 4.6 73.7 1.0
O5' B:DTP1521 4.9 0.9 1.0
OD1 B:ASP107 4.9 88.2 1.0
CE B:LYS328 4.9 0.8 1.0
NE2 B:HIS105 4.9 90.7 1.0
CB B:ASP325 4.9 85.3 1.0
ND1 B:HIS105 4.9 91.6 1.0
CG B:LYS321 5.0 71.9 1.0
O1B B:DTP1521 5.0 0.4 1.0

Calcium binding site 4 out of 4 in 2w7p

Go back to Calcium Binding Sites List in 2w7p
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:Ca1523

b:94.3
occ:1.00
 OD1 B:ASP107 2.6 88.2 1.0
O B:MET108 2.7 92.5 1.0
O2G B:DTP1521 2.8 0.9 1.0
O2B B:DTP1521 2.8 0.8 1.0
OD2 B:ASP198 2.8 0.4 1.0
O3A B:DTP1521 3.1 0.5 1.0
CG B:ASP107 3.3 88.6 1.0
OD2 B:ASP107 3.3 87.9 1.0
PB B:DTP1521 3.4 0.9 1.0
CG B:ASP198 3.5 0.6 1.0
C3' B:DTP1521 3.5 0.6 1.0
O3' B:DTP1521 3.6 0.3 1.0
C4' B:DTP1521 3.6 0.1 1.0
PG B:DTP1521 3.7 0.7 1.0
O3B B:DTP1521 3.8 0.3 1.0
C B:MET108 3.8 91.6 1.0
C5' B:DTP1521 3.8 0.2 1.0
CB B:ASP198 3.9 0.8 1.0
N B:ALA110 4.1 96.9 1.0
O5' B:DTP1521 4.2 0.9 1.0
NZ B:LYS328 4.2 0.8 1.0
O1G B:DTP1521 4.4 0.9 1.0
OD1 B:ASP198 4.4 0.2 1.0
PA B:DTP1521 4.4 0.2 1.0
O B:ALA110 4.4 98.9 1.0
N B:MET108 4.4 89.2 1.0
C B:ALA110 4.5 98.6 1.0
C B:ASP109 4.6 96.2 1.0
CA B:ALA110 4.6 97.5 1.0
CA B:MET108 4.6 89.7 1.0
O B:ASP198 4.7 0.3 1.0
N B:ASP109 4.7 93.4 1.0
CA B:ASP109 4.7 95.4 1.0
CB B:ASP107 4.7 89.2 1.0
C B:ASP107 4.7 89.3 1.0
CB B:PHE111 4.8 0.1 1.0
O1B B:DTP1521 4.8 0.4 1.0
CE B:LYS328 4.9 0.8 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 18:32:24 2024

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