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Calcium in PDB 2c2e: 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: 2c2e 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) 44.49 / 2.61
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.030, 100.390, 52.410, 90.00, 90.00, 90.00
R / Rfree (%) 26.7 / 31.5

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 2c2e). 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: 2c2e:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2c2e

Go back to Calcium Binding Sites List in 2c2e
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:51.0
occ:1.00
 O1A A:DCP1342 2.4 62.5 1.0
OD2 A:ASP7 2.5 46.2 1.0
OE2 A:GLU106 2.7 59.0 1.0
OD2 A:ASP105 2.8 41.0 1.0
CG A:GLU106 3.0 51.3 1.0
OP2 P:DC14 3.0 44.4 1.0
OD1 A:ASP105 3.1 41.5 1.0
CD A:GLU106 3.1 56.3 1.0
CG A:ASP105 3.3 39.8 1.0
OP1 P:DC14 3.3 46.1 1.0
O A:HOH2061 3.4 52.2 1.0
CA A:CA1344 3.4 41.0 1.0
CG A:ASP7 3.4 44.0 1.0
P P:DC14 3.6 46.2 1.0
PA A:DCP1342 3.7 60.5 1.0
O A:HOH2017 3.7 31.7 1.0
O A:ASP105 3.8 36.9 1.0
OD1 A:ASP7 3.9 42.4 1.0
O3A A:DCP1342 4.0 62.9 1.0
OE1 A:GLU106 4.2 61.0 1.0
C5' A:DCP1342 4.4 55.2 1.0
CB A:GLU106 4.4 44.8 1.0
C A:ASP105 4.4 37.8 1.0
O5' A:DCP1342 4.6 60.0 1.0
CB A:ASP7 4.6 44.8 1.0
O5' P:DC14 4.6 47.4 1.0
CB A:ASP105 4.6 39.4 1.0
OG A:SER103 4.6 34.7 0.5
NZ A:LYS152 4.7 31.0 1.0
O2A A:DCP1342 4.8 61.3 1.0
O3' P:DC13 4.9 44.7 1.0

Calcium binding site 2 out of 3 in 2c2e

Go back to Calcium Binding Sites List in 2c2e
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:41.0
occ:1.00
 O3A A:DCP1342 2.4 62.9 1.0
OD1 A:ASP7 2.5 42.4 1.0
O A:PHE8 2.5 35.0 1.0
OD2 A:ASP105 2.6 41.0 1.0
O A:HOH2061 3.0 52.2 1.0
O3B A:DCP1342 3.1 61.1 1.0
O1G A:DCP1342 3.1 57.3 1.0
CG A:ASP7 3.3 44.0 1.0
PB A:DCP1342 3.3 64.6 1.0
CA A:CA1343 3.4 51.0 1.0
OD2 A:ASP7 3.4 46.2 1.0
O1A A:DCP1342 3.5 62.5 1.0
PA A:DCP1342 3.6 60.5 1.0
C A:PHE8 3.7 34.8 1.0
O2B A:DCP1342 3.7 63.6 1.0
PG A:DCP1342 3.7 57.1 1.0
CG A:ASP105 3.8 39.8 1.0
O2G A:DCP1342 4.2 57.9 1.0
N A:PHE8 4.2 38.4 1.0
O5' A:DCP1342 4.4 60.0 1.0
CA A:PHE8 4.4 34.4 1.0
C A:ASP7 4.5 41.5 1.0
O1B A:DCP1342 4.6 65.6 1.0
N A:ASP9 4.6 36.6 1.0
C5' A:DCP1342 4.6 55.2 1.0
N A:TYR10 4.6 35.5 1.0
O A:ASP105 4.6 36.9 1.0
CB A:ASP7 4.6 44.8 1.0
CA A:ASP9 4.6 38.3 1.0
OD1 A:ASP105 4.7 41.5 1.0
O2A A:DCP1342 4.7 61.3 1.0
CB A:ASP105 4.7 39.4 1.0
C A:ASP9 4.7 36.9 1.0
O A:ASP7 4.8 42.5 1.0
CB A:PHE8 4.9 30.5 1.0
N A:PHE11 4.9 35.1 1.0
CA A:ASP7 5.0 41.6 1.0

Calcium binding site 3 out of 3 in 2c2e

Go back to Calcium Binding Sites List in 2c2e
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:63.0
occ:1.00
 O A:ALA181 2.6 63.0 1.0
O A:HOH2029 2.8 95.0 1.0
O A:ILE186 2.8 50.1 1.0
O P:HOH2022 3.0 41.0 1.0
C A:ALA181 3.2 62.1 1.0
N A:ASP182 3.9 60.0 1.0
CA A:ASP182 3.9 57.2 1.0
C A:ILE186 4.0 48.9 1.0
CA A:ALA181 4.1 62.9 1.0
CB A:ALA181 4.4 64.3 1.0
C A:ASP182 4.5 55.7 1.0
N A:VAL183 4.6 54.3 1.0
OD1 A:ASP182 4.7 57.3 1.0
O A:VAL183 4.7 49.8 1.0
CB A:ILE186 4.7 45.7 1.0
CA A:GLY187 4.8 52.1 1.0
N A:GLY187 4.9 50.3 1.0
CA A:ILE186 4.9 47.7 1.0
CG2 A:ILE186 5.0 44.0 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: Sat Dec 12 03:33:25 2020

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