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

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

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

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 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 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

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