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Calcium in PDB 2r8g: 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: 2r8g 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 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.500, 103.300, 52.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.8

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 2r8g). 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: 2r8g:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2r8g

Go back to Calcium Binding Sites List in 2r8g
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:90.9
occ:1.00
O A:HOH9083 2.4 42.7 1.0
O A:ILE186 2.4 50.1 1.0
O P:HOH9610 2.5 57.8 1.0
O A:ALA181 2.7 67.4 1.0
O A:HOH9208 2.8 54.9 1.0
OP1 P:DT513 3.1 52.8 1.0
O A:VAL183 3.3 53.8 1.0
C A:ILE186 3.6 50.2 1.0
O A:HOH8812 3.8 0.8 1.0
C A:ALA181 3.9 66.9 1.0
C A:VAL183 3.9 55.2 1.0
OP2 P:DT513 4.0 55.6 1.0
P P:DT513 4.0 55.3 1.0
N A:ILE186 4.1 50.7 1.0
N A:VAL183 4.1 60.8 1.0
CA A:ILE186 4.3 49.6 1.0
C A:ASP182 4.3 64.1 1.0
CA A:ASP182 4.3 65.5 1.0
CB A:ILE186 4.4 48.8 1.0
N A:PRO184 4.5 54.0 1.0
CA A:PRO184 4.5 52.5 1.0
N A:GLY185 4.5 50.0 1.0
N A:ASP182 4.6 66.4 1.0
N A:GLY187 4.6 50.7 1.0
CA A:VAL183 4.7 57.1 1.0
CA A:GLY187 4.8 52.5 1.0
C A:PRO184 4.8 51.2 1.0
O A:ASP182 4.9 64.3 1.0
CA A:ALA181 5.0 67.3 1.0
O A:HOH9202 5.0 85.2 1.0

Calcium binding site 2 out of 3 in 2r8g

Go back to Calcium Binding Sites List in 2r8g
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
O A:PHE8 2.5 49.6 1.0
O3G A:DGT7000 2.5 71.1 0.5
O2A A:DGT7000 2.6 60.8 0.8
O2G A:DGT7000 2.7 70.5 0.5
OD2 A:ASP105 2.7 64.9 1.0
OD2 A:ASP7 2.7 66.4 1.0
O2B A:DGT7000 2.9 62.1 0.8
CG A:ASP7 3.2 61.8 1.0
PG A:DGT7000 3.2 71.7 0.5
C A:PHE8 3.5 48.7 1.0
OD1 A:ASP7 3.5 65.2 1.0
CG A:ASP105 3.7 62.5 1.0
N A:PHE8 3.8 50.6 1.0
PA A:DGT7000 3.8 60.9 1.0
C A:ASP7 3.9 53.7 1.0
PB A:DGT7000 4.0 59.7 1.0
CA A:CA8003 4.0 0.1 1.0
O3B A:DGT7000 4.1 65.3 1.0
CB A:ASP7 4.1 58.2 1.0
CA A:PHE8 4.2 48.9 1.0
O A:ASP7 4.2 55.5 1.0
C5' A:DGT7000 4.2 49.1 1.0
OD1 A:ASP105 4.3 62.9 1.0
CA A:ASP7 4.3 54.6 1.0
N A:ASP9 4.4 49.6 1.0
O1G A:DGT7000 4.4 71.2 0.5
O3A A:DGT7000 4.4 62.3 0.8
NZ A:LYS159 4.5 72.0 1.0
O A:ASP105 4.5 56.5 1.0
O5' A:DGT7000 4.5 57.3 1.0
CA A:ASP9 4.5 51.1 1.0
N A:TYR10 4.7 50.3 1.0
CB A:ASP105 4.8 60.2 1.0
C A:ASP9 4.9 51.0 1.0
CB A:PHE8 4.9 47.3 1.0

Calcium binding site 3 out of 3 in 2r8g

Go back to Calcium Binding Sites List in 2r8g
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:0.1
occ:1.00
O2A A:DGT7000 3.0 60.8 0.8
OD1 A:ASP7 3.0 65.2 1.0
OD2 A:ASP7 3.3 66.4 1.0
O2G A:DGT7000 3.3 70.5 0.5
OE2 A:GLU106 3.3 75.3 1.0
CG A:ASP7 3.5 61.8 1.0
O1A A:DGT7000 3.7 61.3 1.0
PA A:DGT7000 3.7 60.9 1.0
CD A:GLU106 3.7 71.7 1.0
O A:HOH8602 3.8 60.0 1.0
CA A:CA8002 4.0 77.5 1.0
CG A:GLU106 4.1 69.1 1.0
O A:HOH8801 4.1 79.2 1.0
NZ A:LYS159 4.1 72.0 1.0
OE1 A:GLU106 4.4 72.3 1.0
O5' A:DGT7000 4.5 57.3 1.0
O3' P:DT513 4.8 61.4 1.0
OD1 A:ASP105 4.9 62.9 1.0
PG A:DGT7000 4.9 71.7 0.5

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: Sat Dec 12 03:51:44 2020

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