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Calcium in PDB 2c28: Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4

Enzymatic activity of Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4

All present enzymatic activity of Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4:
2.7.7.7;

Protein crystallography data

The structure of Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4, PDB code: 2c28 was solved by A.Irimia, L.V.Loukachevitch, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.96 / 2.27
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.355, 102.030, 52.826, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4 (pdb code 2c28). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4, PDB code: 2c28:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2c28

Go back to Calcium Binding Sites List in 2c28
Calcium binding site 1 out of 3 in the Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1343

b:79.3
occ:1.00
 OD1 A:ASP7 2.5 43.8 1.0
OE2 A:GLU106 2.8 53.0 1.0
CG A:ASP7 3.0 40.6 1.0
OD2 A:ASP7 3.0 42.6 1.0
OD2 A:ASP105 3.2 38.5 1.0
O5' A:DG1342 3.3 79.9 1.0
CA A:CA1344 3.3 40.8 1.0
CG A:GLU106 3.4 45.8 1.0
CD A:GLU106 3.5 48.7 1.0
O A:HOH2037 3.6 69.8 1.0
OD1 A:ASP105 3.8 38.1 1.0
CG A:ASP105 3.9 40.7 1.0
NZ A:LYS159 3.9 51.7 1.0
O A:HOH2044 4.2 41.5 1.0
CB A:ASP7 4.3 39.9 1.0
C5' A:DG1342 4.4 77.2 1.0
OE1 A:GLU106 4.6 49.5 1.0
O A:ASP105 4.8 32.5 1.0
CB A:GLU106 4.9 41.8 1.0

Calcium binding site 2 out of 3 in 2c28

Go back to Calcium Binding Sites List in 2c28
Calcium binding site 2 out of 3 in the Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1344

b:40.8
occ:1.00
 O A:HOH2044 2.3 41.5 1.0
OD2 A:ASP105 2.4 38.5 1.0
O A:PHE8 2.4 30.3 1.0
OD2 A:ASP7 2.5 42.6 1.0
CA A:CA1343 3.3 79.3 1.0
C A:PHE8 3.5 32.8 1.0
CG A:ASP7 3.6 40.6 1.0
CG A:ASP105 3.6 40.7 1.0
O A:HOH2005 3.9 34.6 1.0
O A:HOH2019 3.9 50.4 1.0
OD1 A:ASP7 4.0 43.8 1.0
O5' A:DG1342 4.0 79.9 1.0
C5' A:DG1342 4.1 77.2 1.0
N A:TYR10 4.2 29.5 1.0
N A:PHE8 4.2 34.0 1.0
NZ A:LYS159 4.3 51.7 1.0
CA A:ASP9 4.4 32.8 1.0
CA A:PHE8 4.4 34.4 1.0
N A:ASP9 4.4 32.7 1.0
CB A:ASP105 4.5 37.6 1.0
C A:ASP9 4.5 30.5 1.0
C A:ASP7 4.5 36.7 1.0
OD1 A:ASP105 4.5 38.1 1.0
N A:PHE11 4.6 31.9 1.0
O A:ASP7 4.8 37.0 1.0
O A:ASP105 4.8 32.5 1.0
CB A:ASP7 4.9 39.9 1.0
CB A:PHE11 4.9 29.4 1.0
CA A:TYR10 4.9 31.6 1.0

Calcium binding site 3 out of 3 in 2c28

Go back to Calcium Binding Sites List in 2c28
Calcium binding site 3 out of 3 in the Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1345

b:73.4
occ:1.00
 O A:ALA181 2.6 48.3 1.0
O P:HOH2012 2.7 80.6 1.0
O A:HOH2049 2.7 65.5 1.0
O A:HOH2046 2.8 48.9 1.0
O A:HOH2048 2.9 51.0 1.0
O A:ILE186 3.1 43.9 1.0
C A:ALA181 3.5 46.9 1.0
CA A:ALA181 4.3 47.0 1.0
C A:ILE186 4.3 46.9 1.0
CB A:ALA181 4.3 47.2 1.0
N A:ASP182 4.4 46.5 1.0
CA A:ASP182 4.5 47.1 1.0
CA A:GLY187 4.7 49.8 1.0
OP2 P:DC13 4.8 55.1 1.0
OP1 P:DC13 4.8 55.7 1.0
OD1 A:ASP182 4.9 55.4 1.0
C A:GLY187 5.0 50.9 1.0

Reference:

H.Zang, A.Irimia, J.-Y.Choi, K.C.Angel, L.V.Loukachevitch, M.Egli, F.P Guengerich. Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus Solfataricus Dna Polymerase DPO4 J.Biol.Chem. V. 281 2358 2006.
ISSN: ISSN 0021-9258
PubMed: 16306039
DOI: 10.1074/JBC.M510889200
Page generated: Fri Jul 12 09:18:35 2024

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