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Calcium in PDB 2r8h: Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase

Enzymatic activity of Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase

All present enzymatic activity of Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase:
2.7.7.7;

Protein crystallography data

The structure of Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase, PDB code: 2r8h was solved by Y.Wang, S.Saleh, L.J.Marnette, M.Egli, M.P.Stone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.400, 103.000, 52.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase (pdb code 2r8h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase, PDB code: 2r8h:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2r8h

Go back to Calcium Binding Sites List in 2r8h
Calcium binding site 1 out of 3 in the Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8001

b:90.7
occ:1.00
 O A:HOH9107 2.2 22.5 1.0
O A:HOH9042 2.2 86.7 1.0
O A:HOH9037 2.3 75.4 1.0
O P:HOH9108 2.5 68.5 1.0
O A:ALA181 2.5 65.1 1.0
O A:HOH9312 2.6 56.6 1.0
O P:HOH9106 3.0 73.5 1.0
O A:HOH9311 3.0 78.0 1.0
O A:ILE186 3.0 48.5 1.0
O P:HOH9036 3.1 76.1 1.0
C A:ALA181 3.7 65.0 1.0
O A:HOH9041 3.9 84.1 1.0
C A:ILE186 4.0 47.3 1.0
OP1 P:DC513 4.1 49.8 1.0
OP2 P:DC513 4.2 48.7 1.0
CA A:ASP182 4.3 62.0 1.0
N A:ASP182 4.5 63.1 1.0
O A:VAL183 4.5 54.2 1.0
C A:ASP182 4.7 59.6 1.0
P P:DC513 4.7 48.5 1.0
N A:ILE186 4.7 45.2 1.0
CA A:ALA181 4.7 66.8 1.0
N A:VAL183 4.8 56.2 1.0
CA A:ILE186 4.8 45.7 1.0
N A:GLY187 4.8 47.8 1.0
CB A:ILE186 4.8 43.9 1.0
CA A:GLY187 4.9 48.2 1.0

Calcium binding site 2 out of 3 in 2r8h

Go back to Calcium Binding Sites List in 2r8h
Calcium binding site 2 out of 3 in the Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8002

b:0.9
occ:1.00
 O2A A:DGT7000 2.9 45.2 0.8
OD1 A:ASP7 3.0 61.5 1.0
OE1 A:GLU106 3.2 62.4 1.0
OD2 A:ASP7 3.2 64.8 1.0
CG A:ASP7 3.4 60.9 1.0
CG A:GLU106 3.5 60.4 1.0
CA A:CA8003 3.6 68.1 1.0
CD A:GLU106 3.8 63.5 1.0
OD2 A:ASP105 3.8 60.9 1.0
OD1 A:ASP105 4.1 58.3 1.0
PA A:DGT7000 4.1 47.7 0.8
O5' A:DGT7000 4.1 48.5 1.0
CG A:ASP105 4.3 59.0 1.0
O1A A:DGT7000 4.5 48.9 0.7
O3' P:DC513 4.5 60.1 1.0
O3B A:DGT7000 4.7 46.6 0.7
O3G A:DGT7000 4.7 48.3 0.8
C5' A:DGT7000 4.7 45.3 1.0
CB A:ASP7 4.8 55.5 1.0
OE2 A:GLU106 5.0 64.8 1.0
NZ A:LYS159 5.0 76.0 1.0
CB A:GLU106 5.0 56.3 1.0

Calcium binding site 3 out of 3 in 2r8h

Go back to Calcium Binding Sites List in 2r8h
Calcium binding site 3 out of 3 in the Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2- Propanodeoxyguanosine (Pdg) By the Sulfolobus Solfataricus Dna Polymerase DPO4 Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8003

b:68.1
occ:1.00
 OD2 A:ASP105 2.7 60.9 1.0
O3B A:DGT7000 2.7 46.6 0.7
O A:PHE8 2.7 49.5 1.0
OD2 A:ASP7 2.8 64.8 1.0
O2A A:DGT7000 3.0 45.2 0.8
O5' A:DGT7000 3.1 48.5 1.0
O2B A:DGT7000 3.1 42.8 0.6
O A:HOH9128 3.2 71.7 1.0
O3G A:DGT7000 3.3 48.3 0.8
CG A:ASP7 3.4 60.9 1.0
OD1 A:ASP7 3.4 61.5 1.0
PG A:DGT7000 3.5 47.0 0.3
PB A:DGT7000 3.5 44.2 0.9
CA A:CA8002 3.6 0.9 1.0
C A:PHE8 3.8 47.4 1.0
PA A:DGT7000 3.8 47.7 0.8
CG A:ASP105 3.9 59.0 1.0
O1G A:DGT7000 3.9 49.3 1.0
C5' A:DGT7000 4.1 45.3 1.0
O3A A:DGT7000 4.2 47.7 0.7
N A:TYR10 4.5 43.8 1.0
C A:ASP7 4.5 50.3 1.0
CA A:ASP9 4.5 47.0 1.0
N A:PHE8 4.5 48.5 1.0
OD1 A:ASP105 4.6 58.3 1.0
O A:ASP7 4.6 51.2 1.0
N A:ASP9 4.6 46.7 1.0
CB A:ASP7 4.6 55.5 1.0
CA A:PHE8 4.7 47.7 1.0
C A:ASP9 4.7 45.1 1.0
O1B A:DGT7000 4.8 45.7 0.4
O2G A:DGT7000 4.9 48.0 0.9
CB A:ASP105 4.9 55.5 1.0
N A:PHE11 4.9 40.0 1.0

Reference:

Y.Wang, S.K.Musser, S.Saleh, L.J.Marnett, M.Egli, M.P.Stone. Insertion of Dntps Opposite the 1,N2-Propanodeoxyguanosine Adduct By Sulfolobus Solfataricus P2 Dna Polymerase IV Biochemistry V. 47 7322 2008.
ISSN: ISSN 0006-2960
PubMed: 18563918
DOI: 10.1021/BI800152J
Page generated: Fri Jul 12 15:46:07 2024

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