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Calcium in PDB 2c2r: 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: 2c2r 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) 42.99 / 2.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.200, 100.150, 52.000, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 31

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 2c2r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 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: 2c2r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2c2r

Go back to Calcium Binding Sites List in 2c2r
Calcium binding site 1 out of 4 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:50.6
occ:1.00
 OE2 A:GLU106 2.4 49.9 1.0
OP2 P:DOC14 2.6 33.1 1.0
OD2 A:ASP105 2.6 20.5 1.0
OD2 A:ASP7 2.7 51.9 1.0
OD1 A:ASP105 2.8 32.0 1.0
O1A A:DCT1342 3.0 72.3 1.0
CG A:ASP105 3.0 27.3 1.0
CA A:CA1344 3.1 41.8 1.0
CD A:GLU106 3.2 51.0 1.0
CG A:GLU106 3.2 46.8 1.0
CG A:ASP7 3.7 49.0 1.0
P P:DOC14 3.8 35.8 1.0
O A:HOH2067 4.0 47.9 1.0
O3A A:DCT1342 4.0 74.5 1.0
PA A:DCT1342 4.1 71.2 1.0
O A:ASP105 4.1 28.1 1.0
OP1 P:DOC14 4.2 33.4 1.0
C5' A:DCT1342 4.2 64.2 1.0
OD1 A:ASP7 4.3 49.2 1.0
OE1 A:GLU106 4.4 53.7 1.0
O2G A:DCT1342 4.4 65.7 1.0
C A:ASP105 4.4 32.5 1.0
O A:HOH2022 4.5 24.3 1.0
CB A:ASP105 4.5 26.4 1.0
CB A:GLU106 4.5 41.6 1.0
O5' P:DOC14 4.5 38.5 1.0
O5' A:DCT1342 4.7 68.7 1.0
OG A:SER103 4.7 40.6 1.0
CB A:ASP7 4.7 47.8 1.0
N A:GLU106 4.8 35.8 1.0
NZ A:LYS152 4.9 34.6 1.0
CA A:GLU106 4.9 39.8 1.0
O A:HOH2002 4.9 25.6 1.0

Calcium binding site 2 out of 4 in 2c2r

Go back to Calcium Binding Sites List in 2c2r
Calcium binding site 2 out of 4 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:41.8
occ:1.00
 O2G A:DCT1342 2.1 65.7 1.0
OD2 A:ASP105 2.3 20.5 1.0
O A:PHE8 2.4 30.3 1.0
OD1 A:ASP7 2.8 49.2 1.0
CA A:CA1343 3.1 50.6 1.0
O3A A:DCT1342 3.1 74.5 1.0
OD2 A:ASP7 3.2 51.9 1.0
CG A:ASP7 3.3 49.0 1.0
CG A:ASP105 3.5 27.3 1.0
PG A:DCT1342 3.6 66.4 1.0
C A:PHE8 3.6 34.0 1.0
O2B A:DCT1342 3.7 73.8 1.0
PB A:DCT1342 3.8 77.8 1.0
O3B A:DCT1342 3.8 71.8 1.0
O A:HOH2022 3.9 24.3 1.0
O1A A:DCT1342 4.2 72.3 1.0
N A:PHE8 4.2 38.4 1.0
OD1 A:ASP105 4.3 32.0 1.0
PA A:DCT1342 4.3 71.2 1.0
CB A:ASP105 4.4 26.4 1.0
O3G A:DCT1342 4.4 69.4 1.0
O A:HOH2067 4.4 47.9 1.0
CA A:PHE8 4.5 35.0 1.0
N A:TYR10 4.5 35.0 1.0
N A:ASP9 4.5 35.1 1.0
O1G A:DCT1342 4.5 67.7 1.0
CA A:ASP9 4.5 36.3 1.0
N A:PHE11 4.6 35.2 1.0
C A:ASP9 4.6 36.4 1.0
O A:ASP105 4.6 28.1 1.0
C A:ASP7 4.6 42.3 1.0
CB A:PHE11 4.6 35.8 1.0
CB A:ASP7 4.7 47.8 1.0
CB A:PHE8 4.9 34.3 1.0

Calcium binding site 3 out of 4 in 2c2r

Go back to Calcium Binding Sites List in 2c2r
Calcium binding site 3 out of 4 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:72.6
occ:1.00
 O A:ILE186 2.5 39.4 1.0
O A:ALA181 2.5 49.4 1.0
O P:HOH2019 3.1 62.3 1.0
C A:ILE186 3.7 38.5 1.0
C A:ALA181 3.7 49.2 1.0
CA A:GLY187 4.2 40.7 1.0
C A:GLY187 4.2 41.6 1.0
O A:GLY187 4.3 40.6 1.0
N A:GLY187 4.4 40.8 1.0
CA A:ALA181 4.4 50.2 1.0
OP2 P:DC13 4.6 30.5 1.0
CB A:ILE186 4.7 37.2 1.0
CB A:ALA181 4.7 50.4 1.0
N A:ASN188 4.7 41.0 1.0
N A:ASP182 4.7 47.8 1.0
CA A:ILE186 4.8 36.5 1.0
CG2 A:ILE186 4.8 34.0 1.0
CA A:ASP182 4.9 44.7 1.0

Calcium binding site 4 out of 4 in 2c2r

Go back to Calcium Binding Sites List in 2c2r
Calcium binding site 4 out of 4 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 4 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:Ca1346

b:65.0
occ:1.00
 OP1 P:DOC14 2.5 33.4 1.0
O A:HOH2067 2.8 47.9 1.0
O1A A:DCT1342 3.1 72.3 1.0
O2A A:DCT1342 3.2 70.4 1.0
PA A:DCT1342 3.7 71.2 1.0
O P:HOH2018 3.8 47.5 1.0
P P:DOC14 3.8 35.8 1.0
C3' P:DC13 4.3 31.7 1.0
O3' P:DC13 4.3 35.6 1.0
O A:HOH2030 4.5 64.1 1.0
OP2 P:DOC14 4.6 33.1 1.0
C2' P:DC13 4.7 32.1 1.0
O5' A:DCT1342 4.8 68.7 1.0
O3A A:DCT1342 4.9 74.5 1.0
NZ A:LYS152 4.9 34.6 1.0
O5' P:DOC14 4.9 38.5 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 09:19:56 2024

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