Zinc in PDB 9ich: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dgtp (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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ich 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 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.221, 57.678, 48.500, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 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 Dgtp (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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9ich). 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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ich:
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 Dgtp (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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn339 b:30.0 occ:0.37 O1A A:DGT338 1.4 83.1 0.5 OD1 A:ASP190 2.6 45.6 1.0 O1G A:DGT338 2.6 33.0 0.5 O3G A:DGT338 2.7 39.6 0.5 PA A:DGT338 2.8 84.6 0.5 O2B A:DGT338 2.8 76.5 0.5 OD2 A:ASP192 2.9 29.7 1.0 PG A:DGT338 3.1 41.8 0.5 O3A A:DGT338 3.3 79.9 0.5 O5' A:DGT338 3.4 84.0 0.5 PB A:DGT338 3.4 74.9 0.5 O A:ASP190 3.5 35.6 1.0 O3B A:DGT338 3.5 60.3 0.5 CG A:ASP190 3.7 49.9 1.0 O A:HOH522 3.9 50.6 1.0 O2A A:DGT338 4.0 82.1 0.5 O A:HOH656 4.1 76.2 1.0 CG A:ASP192 4.2 34.1 1.0 N A:ASP190 4.2 29.3 1.0 ZN A:ZN340 4.3 30.0 0.4 C A:ASP190 4.3 28.3 1.0 O A:HOH502 4.4 9.8 1.0 OD2 A:ASP190 4.4 58.5 1.0 O2G A:DGT338 4.5 49.5 0.5 CA A:ASP190 4.7 33.3 1.0 CB A:ASP190 4.8 42.9 1.0 O1B A:DGT338 4.9 76.9 0.5 CB A:ASP192 4.9 25.4 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 Dgtp (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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn340 b:30.0 occ:0.37 O3' P:DG7 3.1 0.0 1.0 OD2 A:ASP190 3.1 58.5 1.0 OD2 A:ASP256 3.2 41.3 1.0 OD1 A:ASP192 3.3 44.1 1.0 OD2 A:ASP192 3.3 29.7 1.0 CG A:ASP190 3.5 49.9 1.0 CG A:ASP192 3.6 34.1 1.0 CG A:ASP256 3.7 30.9 1.0 OD1 A:ASP190 3.7 45.6 1.0 O1A A:DGT338 3.8 83.1 0.5 OD1 A:ASP256 4.1 30.0 1.0 CB A:ASP256 4.1 20.9 1.0 C4' P:DG7 4.2 0.0 1.0 C3' P:DG7 4.2 0.0 1.0 ZN A:ZN339 4.3 30.0 0.4 PA A:DGT338 4.4 84.6 0.5 CB A:ASP190 4.5 42.9 1.0 O2A A:DGT338 4.5 82.1 0.5 O5' P:DG7 4.5 0.0 1.0 O5' A:DGT338 4.6 84.0 0.5 O A:HOH657 4.6 59.3 1.0 C5' P:DG7 4.7 0.0 1.0 NH2 A:ARG254 4.8 24.9 1.0 CB A:ASP192 4.8 25.4 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 Dgtp (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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn343 b:30.0 occ:0.74 ND1 A:HIS51 2.4 36.5 1.0 CG A:HIS51 3.1 38.4 1.0 CE1 A:HIS51 3.2 37.1 1.0 CB A:HIS51 3.5 42.6 1.0 CD2 A:HIS51 4.1 37.4 1.0 NE2 A:HIS51 4.1 36.1 1.0 CA A:HIS51 4.2 42.1 1.0 N A:LYS52 4.8 39.2 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