Atomistry » Calcium » PDB 2qwd-2rex » 2r8i
Atomistry »
  Calcium »
    PDB 2qwd-2rex »
      2r8i »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy