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Calcium in PDB 2r8i: 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: 2r8i 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 / 2.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.200, 101.900, 52.700, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.6

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 2r8i). 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: 2r8i:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2r8i

Go back to Calcium Binding Sites List in 2r8i
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:69.9
occ:1.00
 O A:HOH9531 2.7 51.1 1.0
O A:HOH9105 2.7 64.8 1.0
O A:ALA181 2.7 57.8 1.0
O A:ILE186 2.8 47.4 1.0
O A:HOH9104 2.9 0.8 1.0
O P:HOH9604 3.0 61.2 1.0
C A:ALA181 3.8 57.5 1.0
C A:ILE186 4.0 47.6 1.0
OP2 P:DC513 4.3 52.7 1.0
CA A:GLY187 4.4 48.3 1.0
OP1 P:DC513 4.5 50.4 1.0
CA A:ALA181 4.6 57.1 1.0
N A:GLY187 4.7 48.7 1.0
N A:ASP182 4.7 57.4 1.0
CA A:ASP182 4.7 57.1 1.0
CB A:ALA181 4.8 55.8 1.0
O A:VAL183 4.8 52.8 1.0
C A:GLY187 4.8 50.1 1.0
P P:DC513 5.0 51.4 1.0

Calcium binding site 2 out of 3 in 2r8i

Go back to Calcium Binding Sites List in 2r8i
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:77.5
occ:1.00
 O2A A:DTP7000 2.7 53.0 0.2
OD2 A:ASP7 2.8 53.1 1.0
O A:HOH9525 2.8 55.2 1.0
O A:HOH9605 2.9 76.0 1.0
OE1 A:GLU106 2.9 60.7 1.0
OD1 A:ASP105 2.9 46.6 1.0
OD2 A:ASP105 3.2 49.4 1.0
CG A:GLU106 3.2 55.8 1.0
CA A:CA8003 3.3 49.8 1.0
CD A:GLU106 3.4 57.1 1.0
CG A:ASP105 3.4 47.8 1.0
CG A:ASP7 3.4 49.6 1.0
PA A:DTP7000 3.5 53.2 0.9
OD1 A:ASP7 3.7 50.8 1.0
O1A A:DTP7000 3.7 52.9 0.8
O5' A:DTP7000 4.3 52.0 1.0
O3G A:DTP7000 4.4 55.0 0.9
C5' A:DTP7000 4.5 49.7 1.0
O A:ASP105 4.5 44.8 1.0
CB A:GLU106 4.6 50.6 1.0
OE2 A:GLU106 4.6 60.9 1.0
O2B A:DTP7000 4.6 50.6 0.8
CB A:ASP7 4.7 47.0 1.0
O A:HOH9526 4.7 85.0 1.0
OG A:SER103 4.8 43.3 1.0
C A:ASP105 4.8 46.1 1.0
NZ A:LYS159 4.8 57.8 1.0
CB A:ASP105 4.9 43.7 1.0
NZ A:LYS152 4.9 56.2 1.0

Calcium binding site 3 out of 3 in 2r8i

Go back to Calcium Binding Sites List in 2r8i
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:49.8
occ:1.00
 O2B A:DTP7000 2.3 50.6 0.8
O A:PHE8 2.4 43.4 1.0
O2A A:DTP7000 2.4 53.0 0.2
OD1 A:ASP7 2.4 50.8 1.0
OD2 A:ASP105 2.4 49.4 1.0
O3G A:DTP7000 2.5 55.0 0.9
PA A:DTP7000 3.3 53.2 0.9
CA A:CA8002 3.3 77.5 1.0
CG A:ASP7 3.4 49.6 1.0
C A:PHE8 3.5 43.7 1.0
CG A:ASP105 3.6 47.8 1.0
PG A:DTP7000 3.6 53.9 0.6
PB A:DTP7000 3.6 50.7 1.0
OD2 A:ASP7 3.7 53.1 1.0
O1G A:DTP7000 3.9 53.7 1.0
O3A A:DTP7000 3.9 50.7 1.0
N A:PHE8 4.0 44.2 1.0
O3B A:DTP7000 4.1 52.4 0.8
C5' A:DTP7000 4.2 49.7 1.0
C A:ASP7 4.2 44.6 1.0
O5' A:DTP7000 4.3 52.0 1.0
NZ A:LYS159 4.3 57.8 1.0
OD1 A:ASP105 4.3 46.6 1.0
CA A:PHE8 4.3 44.8 1.0
N A:ASP9 4.4 42.7 1.0
N A:TYR10 4.5 41.7 1.0
CA A:ASP9 4.5 43.5 1.0
O A:ASP7 4.5 42.2 1.0
O1A A:DTP7000 4.6 52.9 0.8
CB A:ASP7 4.6 47.0 1.0
CB A:ASP105 4.6 43.7 1.0
C A:ASP9 4.7 43.8 1.0
CA A:ASP7 4.8 45.1 1.0
O A:ASP105 4.8 44.8 1.0
N A:PHE11 4.9 42.7 1.0
CE A:LYS159 4.9 59.7 1.0
O1B A:DTP7000 4.9 51.8 0.6
CB A:PHE8 5.0 44.2 1.0
O2G A:DTP7000 5.0 54.6 0.7

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 15:46:29 2024

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