Zinc in PDB 9ici: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dttp (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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ici 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.932, 57.542, 48.216, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 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 Dttp (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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9ici). 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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dttp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ici:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Dttp (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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn340 b:30.0 occ:0.59 OP1 P:DT8 1.9 0.0 1.0 OD1 A:ASP192 2.3 48.4 1.0 OD2 A:ASP190 2.3 56.3 1.0 CG A:ASP192 2.8 43.9 1.0 OD2 A:ASP256 2.9 32.6 1.0 CG A:ASP190 3.0 48.5 1.0 O A:HOH658 3.1 28.6 1.0 OD2 A:ASP192 3.1 45.3 1.0 P P:DT8 3.4 99.6 1.0 OD1 A:ASP190 3.4 46.1 1.0 O A:ASP190 3.9 31.3 1.0 CB A:ASP192 4.0 34.8 1.0 CB A:ASP190 4.1 40.6 1.0 CG A:ASP256 4.1 24.3 1.0 O3' P:DG7 4.1 93.9 1.0 OP2 P:DT8 4.2 0.0 1.0 O5' P:DT8 4.3 0.0 1.0 CA A:ASP192 4.3 19.1 1.0 C A:ASP190 4.4 27.0 1.0 N A:ASP192 4.4 11.6 1.0 O A:MET191 4.5 9.0 1.0 C A:MET191 4.5 8.4 1.0 CB A:ASP256 4.5 14.1 1.0 O P:HOH655 4.5 48.9 1.0 CA A:ASP190 4.9 33.9 1.0 C3' P:DG7 4.9 90.6 1.0

Zinc binding site 2 out of 2 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 Dttp (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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn343 b:30.0 occ:0.90 ND1 A:HIS51 2.2 45.0 1.0 CG A:HIS51 3.1 50.4 1.0 CE1 A:HIS51 3.2 45.8 1.0 CB A:HIS51 3.3 47.8 1.0 CA A:HIS51 3.7 38.7 1.0 O A:PRO50 4.0 68.2 1.0 CD2 A:HIS51 4.2 49.8 1.0 NE2 A:HIS51 4.2 48.3 1.0 N A:LYS52 4.5 20.5 1.0 C A:HIS51 4.5 29.5 1.0 N A:HIS51 4.7 46.0 1.0 C A:PRO50 4.8 57.6 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