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Calcium in PDB 1q9y: Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna

Enzymatic activity of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna

All present enzymatic activity of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna, PDB code: 1q9y was solved by E.Freisinger, A.P.Grollman, H.Miller, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.06 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.822, 118.565, 127.224, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 27.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna (pdb code 1q9y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna, PDB code: 1q9y:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1q9y

Go back to Calcium Binding Sites List in 1q9y
Calcium binding site 1 out of 3 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca939

b:30.8
occ:1.00
 OD2 A:ASP414 1.9 23.6 1.0
OD1 A:ASP626 2.1 30.9 1.0
O2B P:DCP939 2.2 23.1 1.0
O1G P:DCP939 2.3 31.6 1.0
O A:LEU415 2.4 29.3 1.0
O2A P:DCP939 2.6 22.8 1.0
CG A:ASP414 3.1 26.0 1.0
PB P:DCP939 3.2 22.2 1.0
CG A:ASP626 3.3 29.4 1.0
PG P:DCP939 3.4 26.0 1.0
OD1 A:ASP414 3.5 28.6 1.0
O3B P:DCP939 3.6 23.8 1.0
C A:LEU415 3.6 29.9 1.0
PA P:DCP939 3.7 19.7 1.0
O3A P:DCP939 3.7 21.5 1.0
CA A:CA941 3.9 51.8 1.0
O2G P:DCP939 4.1 22.2 1.0
CB A:ASP626 4.1 28.6 1.0
OD2 A:ASP626 4.2 31.9 1.0
C5' P:DCP939 4.2 20.6 1.0
N A:SER417 4.2 28.5 1.0
N A:LEU415 4.2 29.0 1.0
CB A:ASP414 4.3 27.4 1.0
O5' P:DCP939 4.4 19.4 1.0
CA A:LEU415 4.4 29.9 1.0
O1B P:DCP939 4.5 19.9 1.0
N A:THR416 4.5 31.1 1.0
O3G P:DCP939 4.6 27.3 1.0
N A:LEU418 4.7 25.0 1.0
CA A:THR416 4.7 31.5 1.0
C A:THR416 4.7 30.3 1.0
C A:ASP414 4.8 29.2 1.0
O1A P:DCP939 4.9 20.6 1.0
CB A:LEU415 4.9 29.4 1.0
CA A:SER417 5.0 27.2 1.0

Calcium binding site 2 out of 3 in 1q9y

Go back to Calcium Binding Sites List in 1q9y
Calcium binding site 2 out of 3 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca940

b:55.5
occ:1.00
 OE1 A:GLU689 2.7 46.5 1.0
OD1 A:ASP414 3.2 28.6 1.0
OE1 A:GLU719 3.4 45.0 1.0
CD A:GLU689 3.5 44.5 1.0
CD A:GLU719 3.6 43.8 1.0
CG A:GLU719 3.7 40.8 1.0
CG A:GLU689 3.7 38.9 1.0
OE2 A:GLU719 4.3 44.5 1.0
NZ A:LYS489 4.4 26.1 1.0
CG A:ASP414 4.4 26.0 1.0
OE2 A:GLU689 4.7 47.9 1.0
O A:ASP414 4.7 30.1 1.0
CB A:GLU689 4.9 34.8 1.0

Calcium binding site 3 out of 3 in 1q9y

Go back to Calcium Binding Sites List in 1q9y
Calcium binding site 3 out of 3 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with 8-Oxoguanosine Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca941

b:51.8
occ:1.00
 O2A P:DCP939 2.6 22.8 1.0
OD2 A:ASP626 2.9 31.9 1.0
OD1 A:ASP626 3.1 30.9 1.0
OD2 A:ASP414 3.2 23.6 1.0
CG A:ASP626 3.4 29.4 1.0
CG A:ASP414 3.9 26.0 1.0
OG A:SER627 3.9 35.6 1.0
PA P:DCP939 3.9 19.7 1.0
CA A:CA939 3.9 30.8 1.0
CB A:ASP414 4.0 27.4 1.0
O1A P:DCP939 4.2 20.6 1.0
C5' P:DOC938 4.4 28.6 1.0
O1G P:DCP939 4.5 31.6 1.0
C3' P:DOC938 4.6 26.3 1.0
CB A:SER627 4.6 31.0 1.0
OE2 A:GLU689 4.7 47.9 1.0
O5' P:DCP939 4.7 19.4 1.0
OD1 A:ASP414 4.8 28.6 1.0
CB A:ASP626 4.9 28.6 1.0
O5' P:DOC938 4.9 32.2 1.0

Reference:

E.Freisinger, A.P.Grollman, H.Miller, C.Kisker. Lesion (in)Tolerance Reveals Insights Into Dna Replication Fidelity. Embo J. V. 23 1494 2004.
ISSN: ISSN 0261-4189
PubMed: 15057282
DOI: 10.1038/SJ.EMBOJ.7600158
Page generated: Thu Jul 11 14:15:14 2024

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