Manganese in PDB 8ics: 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 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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ics 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 (°)	178.792, 57.623, 48.419, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 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 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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8ics). 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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ics:
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 Dctp (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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.48 O1A A:DCP338 1.6 78.1 0.5 O1G A:DCP338 2.6 46.1 0.5 OD1 A:ASP190 2.7 65.4 1.0 OD2 A:ASP192 2.8 50.8 1.0 O2B A:DCP338 3.0 0.0 0.5 O3G A:DCP338 3.0 45.5 0.5 PA A:DCP338 3.0 65.5 0.5 O A:ASP190 3.1 37.0 1.0 PG A:DCP338 3.2 41.9 0.5 O3A A:DCP338 3.5 69.8 0.5 O3B A:DCP338 3.5 79.0 0.5 PB A:DCP338 3.5 81.5 0.5 O5' A:DCP338 3.8 60.4 0.5 CG A:ASP190 3.8 62.3 1.0 CG A:ASP192 4.1 46.9 1.0 C A:ASP190 4.1 26.9 1.0 O2A A:DCP338 4.1 76.2 0.5 N A:ASP190 4.2 32.9 1.0 MN A:MN340 4.2 30.0 0.4 O A:HOH502 4.4 9.4 1.0 OD2 A:ASP190 4.6 72.8 1.0 CA A:ASP190 4.6 32.3 1.0 O2G A:DCP338 4.7 83.0 0.5 OD1 A:ASP192 4.7 55.6 1.0 O A:HOH522 4.7 66.2 1.0 CB A:ASP190 4.9 44.6 1.0 N A:GLY189 5.0 31.5 1.0 O1B A:DCP338 5.0 88.8 0.5

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 Dctp (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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.41 O3' P:DG7 2.3 0.0 1.0 OD1 A:ASP192 2.7 55.6 1.0 OD2 A:ASP190 3.1 72.8 1.0 OD2 A:ASP256 3.3 30.9 1.0 CG A:ASP192 3.3 46.9 1.0 C3' P:DG7 3.4 0.0 1.0 OD2 A:ASP192 3.4 50.8 1.0 C4' P:DG7 3.6 0.0 1.0 CG A:ASP190 3.7 62.3 1.0 O1A A:DCP338 3.7 78.1 0.5 OD1 A:ASP190 3.7 65.4 1.0 CG A:ASP256 3.9 31.9 1.0 MN A:MN339 4.2 30.0 0.5 C5' P:DG7 4.5 0.0 1.0 CB A:ASP256 4.5 22.8 1.0 O5' P:DG7 4.5 0.0 1.0 PA A:DCP338 4.5 65.5 0.5 OD1 A:ASP256 4.5 38.6 1.0 O2A A:DCP338 4.6 76.2 0.5 C2' P:DG7 4.7 0.0 1.0 CB A:ASP192 4.7 33.1 1.0 O5' A:DCP338 4.8 60.4 0.5 CB A:ASP190 4.8 44.6 1.0 O4' P:DG7 4.9 0.0 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