Manganese in PDB 9icq: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 9icq 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 (°)	178.676, 57.705, 48.482, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of Datp (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 Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 9icq). 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 Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 9icq:
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 Six Base Pairs of Dna; Soaked in the Presence of Datp (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 Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.54 O1A A:DTP338 2.0 88.0 0.5 O1G A:DTP338 2.7 82.0 0.5 OD1 A:ASP190 2.7 49.0 1.0 O2B A:DTP338 2.7 91.7 0.5 O3G A:DTP338 2.9 85.1 0.5 OD2 A:ASP192 2.9 67.1 1.0 PA A:DTP338 3.1 90.7 0.5 PG A:DTP338 3.2 85.5 0.5 O3A A:DTP338 3.2 91.9 0.5 PB A:DTP338 3.3 91.2 0.5 O3B A:DTP338 3.3 88.8 0.5 CG A:ASP190 3.4 44.7 1.0 O A:ASP190 3.5 33.7 1.0 O5' A:DTP338 3.8 88.2 0.5 OD2 A:ASP190 3.8 50.4 1.0 N A:ASP190 3.9 22.6 1.0 O A:HOH502 4.0 13.5 1.0 CG A:ASP192 4.2 64.0 1.0 C A:ASP190 4.3 25.2 1.0 O2A A:DTP338 4.4 92.3 0.5 CB A:ASP190 4.5 31.4 1.0 CA A:ASP190 4.5 25.2 1.0 O2G A:DTP338 4.7 84.8 0.5 N A:GLY189 4.7 26.6 1.0 O1B A:DTP338 4.8 90.1 0.5 CA A:GLY179 4.8 13.6 1.0 O A:HOH660 4.8 58.3 1.0 CB A:ASP192 4.9 49.1 1.0 C A:GLY189 4.9 26.8 1.0 CA A:GLY189 5.0 27.8 1.0 CB A:SER188 5.0 34.4 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of Datp (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 Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.24 OD2 A:ASP256 2.9 30.5 1.0 OD1 A:ASP190 3.2 49.0 1.0 CG A:ASP190 3.3 44.7 1.0 O A:HOH660 3.4 58.3 1.0 CG A:ASP256 3.5 30.2 1.0 OD1 A:ASP256 3.6 32.7 1.0 OD2 A:ASP190 3.7 50.4 1.0 CB A:ASP190 3.7 31.4 1.0 NH2 A:ARG254 4.0 35.2 1.0 OD1 A:ASP192 4.0 69.1 1.0 CB A:ASP256 4.6 25.4 1.0 CZ A:ARG254 4.6 32.6 1.0 CG A:ASP192 4.7 64.0 1.0 OD2 A:ASP192 4.7 67.1 1.0 O1A A:DTP338 4.9 88.0 0.5

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