Zinc in PDB 9icg: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9icg 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 (°)	179.890, 57.600, 48.430, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9icg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9icg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn339 b:30.0 occ:0.51 O1A A:DCP338 1.8 79.9 0.5 OD1 A:ASP190 2.3 52.4 1.0 O1G A:DCP338 2.5 9.9 0.5 OD1 A:ASP192 2.9 44.9 1.0 O2B A:DCP338 3.1 0.0 0.5 PA A:DCP338 3.2 59.9 0.5 O3G A:DCP338 3.3 68.0 0.5 PG A:DCP338 3.4 35.5 0.5 O A:ASP190 3.4 22.3 1.0 CG A:ASP190 3.5 55.1 1.0 O3A A:DCP338 3.7 83.3 0.5 O3B A:DCP338 3.7 76.0 0.5 PB A:DCP338 3.7 94.0 0.5 ZN A:ZN340 3.8 30.0 0.4 O5' A:DCP338 3.9 64.6 0.5 CG A:ASP192 4.1 41.7 1.0 C A:ASP190 4.2 17.3 1.0 N A:ASP190 4.2 29.5 1.0 O A:HOH502 4.2 1.0 1.0 O2A A:DCP338 4.4 81.9 0.5 O A:HOH654 4.4 50.4 1.0 OD2 A:ASP190 4.4 66.9 1.0 CB A:ASP190 4.5 42.7 1.0 CA A:ASP190 4.5 29.8 1.0 O A:HOH522 4.7 56.5 1.0 O2G A:DCP338 4.8 75.7 0.5 OD2 A:ASP192 4.9 47.9 1.0

Zinc binding site 2 out of 3 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn340 b:30.0 occ:0.41 OD1 A:ASP190 3.1 52.4 1.0 CG A:ASP190 3.2 55.1 1.0 OD2 A:ASP190 3.2 66.9 1.0 OD1 A:ASP192 3.2 44.9 1.0 OD2 A:ASP192 3.3 47.9 1.0 O3' P:DG7 3.4 0.0 1.0 CG A:ASP192 3.5 41.7 1.0 OD2 A:ASP256 3.6 33.7 1.0 O1A A:DCP338 3.7 79.9 0.5 ZN A:ZN339 3.8 30.0 0.5 CG A:ASP256 4.0 27.8 1.0 CB A:ASP190 4.1 42.7 1.0 C4' P:DG7 4.1 0.0 1.0 C3' P:DG7 4.3 0.0 1.0 OD1 A:ASP256 4.5 28.5 1.0 C5' P:DG7 4.5 0.0 1.0 O5' P:DG7 4.5 0.0 1.0 CB A:ASP256 4.6 15.3 1.0 PA A:DCP338 4.7 59.9 0.5 O A:MET191 4.8 18.5 1.0 CB A:ASP192 4.8 30.5 1.0

Zinc binding site 3 out of 3 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn343 b:30.0 occ:0.85 ND1 A:HIS51 1.8 33.4 1.0 CE1 A:HIS51 2.8 33.0 1.0 CG A:HIS51 2.9 36.6 1.0 CB A:HIS51 3.3 33.7 1.0 CA A:HIS51 3.9 30.3 1.0 NE2 A:HIS51 4.0 33.6 1.0 CD2 A:HIS51 4.0 35.4 1.0 C A:HIS51 4.6 23.0 1.0 N A:LYS52 4.7 20.2 1.0 O A:PRO50 4.7 55.1 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I