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Calcium in PDB 2c2d: 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: 2c2d 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) 43.99 / 2.57
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.507, 102.017, 53.093, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 28

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 2c2d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 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: 2c2d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2c2d

Go back to Calcium Binding Sites List in 2c2d
Calcium binding site 1 out of 5 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:Ca2001

b:60.4
occ:1.00
 O1A A:DTP1001 2.3 88.5 1.0
O1A A:DTP1002 2.3 0.2 1.0
O A:HOH2057 2.7 46.2 1.0
OE2 A:GLU106 2.8 64.8 1.0
OD1 A:ASP105 2.8 55.6 1.0
OD2 A:ASP105 3.0 55.7 1.0
CG A:GLU106 3.1 60.7 1.0
OD2 A:ASP7 3.1 55.3 1.0
CD A:GLU106 3.2 62.9 1.0
CG A:ASP105 3.3 52.2 1.0
OD1 A:ASP7 3.3 55.8 1.0
CG A:ASP7 3.5 53.2 1.0
PA A:DTP1002 3.5 0.1 1.0
CA A:CA2002 3.6 53.3 1.0
O3A A:DTP1002 3.6 0.9 1.0
PA A:DTP1001 3.7 89.2 1.0
O5' A:DTP1001 3.8 88.4 1.0
O2A A:DTP1002 4.2 0.7 1.0
OE1 A:GLU106 4.3 67.6 1.0
O5' A:DTP1002 4.4 0.1 1.0
O2G A:DTP1002 4.4 0.0 0.7
O A:ASP105 4.4 50.7 1.0
O2B A:DTP1002 4.4 0.8 0.7
O3A A:DTP1001 4.5 87.9 1.0
CB A:GLU106 4.5 54.9 1.0
O2A A:DTP1001 4.5 90.2 1.0
O A:HOH2059 4.6 78.7 1.0
C5' A:DTP1002 4.7 0.1 1.0
CB A:ASP105 4.7 52.0 1.0
C A:ASP105 4.7 50.2 1.0
CB A:ASP7 4.8 52.8 1.0
OG A:SER103 4.8 55.4 1.0
PB A:DTP1002 4.9 0.7 0.7
NZ A:LYS152 4.9 51.4 1.0

Calcium binding site 2 out of 5 in 2c2d

Go back to Calcium Binding Sites List in 2c2d
Calcium binding site 2 out of 5 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:Ca2002

b:53.3
occ:1.00
 O A:PHE8 2.5 46.9 1.0
OD2 A:ASP7 2.5 55.3 1.0
OD2 A:ASP105 2.6 55.7 1.0
O3A A:DTP1001 2.6 87.9 1.0
O3G A:DTP1001 2.7 85.4 1.0
O1A A:DTP1001 2.8 88.5 1.0
CG A:ASP7 3.1 53.2 1.0
OD1 A:ASP7 3.2 55.8 1.0
PA A:DTP1001 3.3 89.2 1.0
O2B A:DTP1001 3.5 82.6 1.0
C A:PHE8 3.6 48.0 1.0
CA A:CA2001 3.6 60.4 1.0
PB A:DTP1001 3.7 82.9 1.0
CG A:ASP105 3.8 52.2 1.0
PG A:DTP1001 3.8 87.0 1.0
O5' A:DTP1001 4.0 88.4 1.0
O3B A:DTP1001 4.1 86.7 1.0
N A:PHE8 4.2 50.3 1.0
C A:ASP7 4.3 52.4 1.0
O1G A:DTP1001 4.3 89.5 1.0
CB A:ASP7 4.3 52.8 1.0
CA A:ASP9 4.4 54.3 1.0
N A:ASP9 4.4 49.9 1.0
NZ A:LYS159 4.4 80.2 1.0
CA A:PHE8 4.5 47.8 1.0
OD1 A:ASP105 4.5 55.6 1.0
N A:TYR10 4.5 51.7 1.0
O A:ASP7 4.6 52.2 1.0
O A:HOH2057 4.6 46.2 1.0
CB A:ASP105 4.7 52.0 1.0
O A:ASP105 4.7 50.7 1.0
O2A A:DTP1001 4.7 90.2 1.0
C A:ASP9 4.7 53.3 1.0
CA A:ASP7 4.8 52.9 1.0

Calcium binding site 3 out of 5 in 2c2d

Go back to Calcium Binding Sites List in 2c2d
Calcium binding site 3 out of 5 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:Ca2003

b:88.2
occ:0.80
 O A:ALA181 2.5 78.0 1.0
O P:HOH2018 3.1 73.5 1.0
C A:ALA181 3.5 76.6 1.0
O A:ILE186 3.8 67.0 1.0
CA A:ASP182 3.9 73.8 1.0
OD1 A:ASP182 3.9 79.1 1.0
N A:ASP182 4.1 75.5 1.0
C A:ASP182 4.5 70.8 1.0
CA A:ALA181 4.6 76.6 1.0
CB A:ALA181 4.8 75.5 1.0
CG A:ASP182 4.9 78.7 1.0
O A:VAL183 4.9 61.4 1.0
N A:VAL183 4.9 67.6 1.0
CB A:ASP182 5.0 76.5 1.0

Calcium binding site 4 out of 5 in 2c2d

Go back to Calcium Binding Sites List in 2c2d
Calcium binding site 4 out of 5 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:Ca2004

b:1.0
occ:0.70
 O1G A:DTP1002 2.7 0.4 0.7
O3G A:DTP1002 2.8 0.4 0.7
O2A A:DTP1001 3.1 90.2 1.0
PG A:DTP1002 3.2 0.3 0.7
O2G A:DTP1002 3.4 0.0 0.7
CA A:CA2005 3.5 0.7 0.7
O1B A:DTP1001 4.1 83.1 1.0
PA A:DTP1001 4.5 89.2 1.0
O3B A:DTP1002 4.8 0.8 0.7
O3A A:DTP1001 4.8 87.9 1.0
NZ A:LYS159 4.9 80.2 1.0
PB A:DTP1001 5.0 82.9 1.0

Calcium binding site 5 out of 5 in 2c2d

Go back to Calcium Binding Sites List in 2c2d
Calcium binding site 5 out of 5 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 5 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:Ca2005

b:0.7
occ:0.70
 O A:HOH2058 2.3 76.5 1.0
O3G A:DTP1002 2.5 0.4 0.7
O2A A:DTP1001 2.6 90.2 1.0
C5' A:DTP1001 3.1 92.0 1.0
O1G A:DTP1001 3.4 89.5 1.0
O5' A:DTP1001 3.5 88.4 1.0
CA A:CA2004 3.5 1.0 0.7
PA A:DTP1001 3.6 89.2 1.0
PG A:DTP1002 3.7 0.3 0.7
O2G A:DTP1002 3.7 0.0 0.7
C4' A:DTP1001 4.4 92.0 1.0
O4' A:DTP1001 4.6 91.7 1.0
C8 A:DTP1001 4.6 89.3 1.0
O1G A:DTP1002 4.6 0.4 0.7
O1A A:DTP1001 4.7 88.5 1.0
O3B A:DTP1002 4.7 0.8 0.7
O3A A:DTP1001 4.8 87.9 1.0
PG A:DTP1001 4.9 87.0 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: Fri Jul 12 09:18:39 2024

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