Zinc in PDB 9icf: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2

Protein crystallography data

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2, PDB code: 9icf was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.962, 57.615, 48.380, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / n/a

Other elements in 9icf:

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 (pdb code 9icf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2, PDB code: 9icf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 9icf

Go back to Zinc Binding Sites List in 9icf
Zinc binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn339

b:30.0
occ:0.67
OD2 A:ASP192 2.0 44.0 1.0
O3G A:DTP338 2.0 73.8 0.5
OP2 P:DA8 2.4 0.0 1.0
OD1 A:ASP190 2.4 41.9 1.0
CG A:ASP192 3.0 40.9 1.0
PG A:DTP338 3.1 20.2 0.5
O1G A:DTP338 3.2 1.0 0.5
O1A A:DTP338 3.2 90.7 0.5
OD1 A:ASP192 3.3 47.1 1.0
P P:DA8 3.3 0.0 1.0
OP1 P:DA8 3.3 0.0 1.0
CG A:ASP190 3.5 41.1 1.0
O A:ASP190 3.6 26.6 1.0
O3B A:DTP338 3.6 68.5 0.5
O3A A:DTP338 3.8 82.6 0.5
PA A:DTP338 4.0 87.9 0.5
OD2 A:ASP190 4.2 47.8 1.0
C A:ASP190 4.3 19.2 1.0
N A:ASP190 4.3 25.7 1.0
CB A:ASP192 4.4 28.0 1.0
O2G A:DTP338 4.4 76.4 0.5
O5' P:DA8 4.4 96.5 1.0
O3' P:DG7 4.5 0.0 1.0
O2A A:DTP338 4.5 93.3 0.5
PB A:DTP338 4.5 70.2 0.5
CB A:ASP190 4.5 30.5 1.0
CA A:ASP190 4.5 23.3 1.0
O A:HOH502 4.7 1.0 1.0
C5' P:DA8 4.7 91.3 0.5
N A:ASP192 4.9 18.6 1.0
O2B A:DTP338 5.0 86.2 0.5

Zinc binding site 2 out of 2 in 9icf

Go back to Zinc Binding Sites List in 9icf
Zinc binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn343

b:30.0
occ:0.81
ND1 A:HIS51 2.1 36.6 1.0
CE1 A:HIS51 2.9 35.6 1.0
CG A:HIS51 3.1 37.9 1.0
CB A:HIS51 3.6 35.8 1.0
NE2 A:HIS51 4.0 37.6 1.0
CD2 A:HIS51 4.1 37.7 1.0
CA A:HIS51 4.1 29.0 1.0
O A:PRO50 4.6 56.2 1.0
N A:LYS52 4.7 21.2 1.0
C A:HIS51 4.8 22.1 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566
Page generated: Wed Dec 16 14:05:20 2020

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