Manganese in PDB 8ico: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ico 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.687, 57.631, 48.285, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8ico). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ico:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.67 O1A A:AZT338 2.0 80.5 1.0 O1G A:AZT338 2.1 84.8 1.0 OD1 A:ASP190 2.3 48.1 1.0 O2B A:AZT338 2.4 98.3 1.0 O A:HOH653 2.8 40.7 1.0 PA A:AZT338 3.2 83.3 1.0 PB A:AZT338 3.3 96.6 1.0 O3A A:AZT338 3.3 90.6 1.0 O A:ASP190 3.3 35.0 1.0 OD1 A:ASP192 3.3 48.2 1.0 CG A:ASP190 3.4 41.4 1.0 PG A:AZT338 3.4 89.2 1.0 O3B A:AZT338 3.6 96.0 1.0 C5' A:AZT338 3.8 72.2 1.0 O5' A:AZT338 3.9 77.9 1.0 MN A:MN340 3.9 30.0 0.4 OD2 A:ASP190 4.0 53.1 1.0 O A:HOH654 4.1 47.0 1.0 O A:HOH502 4.1 11.5 1.0 N A:ASP190 4.3 32.0 1.0 C A:ASP190 4.3 26.1 1.0 O2G A:AZT338 4.4 92.3 1.0 O2A A:AZT338 4.4 86.2 1.0 O3G A:AZT338 4.4 81.5 1.0 CB A:ASP190 4.6 28.9 1.0 CG A:ASP192 4.6 43.0 1.0 O1B A:AZT338 4.7 0.0 1.0 CA A:ASP190 4.7 26.9 1.0 CA A:GLY179 4.9 22.2 1.0 OG A:SER180 5.0 38.6 1.0

Manganese 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.40 OD2 A:ASP190 2.5 53.1 1.0 OD1 A:ASP192 2.8 48.2 1.0 O3' P:DG7 2.9 63.1 1.0 CG A:ASP192 3.1 43.0 1.0 OD2 A:ASP192 3.2 47.4 1.0 CG A:ASP190 3.3 41.4 1.0 OD2 A:ASP256 3.3 39.2 1.0 OD1 A:ASP190 3.5 48.1 1.0 O1A A:AZT338 3.5 80.5 1.0 O A:HOH656 3.6 38.6 1.0 C3' P:DG7 3.7 57.5 1.0 MN A:MN339 3.9 30.0 0.7 C5' A:AZT338 4.0 72.2 1.0 O A:HOH658 4.2 55.5 1.0 CG A:ASP256 4.3 32.0 1.0 CB A:ASP192 4.4 28.4 1.0 C4' P:DG7 4.5 57.0 1.0 CB A:ASP190 4.6 28.9 1.0 CA A:ASP192 4.6 18.1 1.0 PA A:AZT338 4.7 83.3 1.0 CB A:ASP256 4.7 24.9 1.0 N A:ASP192 4.8 21.5 1.0 O A:HOH663 4.8 53.4 1.0 O5' A:AZT338 4.9 77.9 1.0 O A:ASP190 4.9 35.0 1.0 C4' A:AZT338 5.0 70.8 1.0 C A:MET191 5.0 13.4 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