Manganese in PDB 8ict: 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: 8ict 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 (°)	179.889, 57.586, 48.181, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 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 8ict). 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: 8ict:
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:0.47 O1A A:DCP338 1.8 76.7 0.5 OD1 A:ASP190 2.5 58.2 1.0 OD1 A:ASP192 2.5 48.5 1.0 O1G A:DCP338 2.6 7.5 0.5 O2B A:DCP338 2.7 0.0 0.5 PA A:DCP338 3.0 71.1 0.5 CG A:ASP190 3.1 52.2 1.0 PG A:DCP338 3.3 23.1 0.5 O3G A:DCP338 3.3 67.6 0.5 O A:ASP190 3.3 34.2 1.0 PB A:DCP338 3.3 85.9 0.5 O3A A:DCP338 3.4 77.8 0.5 MN A:MN340 3.4 30.0 0.5 O3B A:DCP338 3.5 76.2 0.5 CG A:ASP192 3.5 50.2 1.0 O5' A:DCP338 3.6 78.5 0.5 OD2 A:ASP190 3.6 61.9 1.0 OD2 A:ASP192 3.7 63.8 1.0 O A:HOH502 3.7 1.0 1.0 C A:ASP190 4.2 20.0 1.0 N A:ASP190 4.2 28.4 1.0 O2A A:DCP338 4.2 87.8 0.5 CB A:ASP190 4.3 36.7 1.0 CA A:ASP190 4.5 26.3 1.0 O2G A:DCP338 4.7 65.7 0.5 CB A:ASP192 4.8 33.0 1.0 O1B A:DCP338 4.8 75.6 0.5 N A:ASP192 4.9 2.3 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 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:0.51 OD2 A:ASP192 2.3 63.8 1.0 OD2 A:ASP190 2.4 61.9 1.0 O1A A:DCP338 2.6 76.7 0.5 O3' P:DG7 2.9 79.7 1.0 CG A:ASP190 3.2 52.2 1.0 CG A:ASP192 3.3 50.2 1.0 PA A:DCP338 3.3 71.1 0.5 MN A:MN339 3.4 30.0 0.5 OD1 A:ASP190 3.5 58.2 1.0 O5' A:DCP338 3.5 78.5 0.5 OD1 A:ASP192 3.6 48.5 1.0 OD2 A:ASP256 3.6 25.4 1.0 O2A A:DCP338 3.7 87.8 0.5 C3' P:DG7 3.8 79.4 1.0 C5' A:DCP338 4.3 84.7 0.5 CB A:ASP190 4.4 36.7 1.0 C4' P:DG7 4.6 72.9 1.0 CB A:ASP192 4.6 33.0 1.0 O3A A:DCP338 4.8 77.8 0.5 CG A:ASP256 4.9 28.9 1.0 O5' P:DG7 4.9 56.2 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