Manganese in PDB 9icr: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2, PDB code: 9icr 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 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.602, 57.637, 48.459, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2 (pdb code 9icr). 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 (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2, PDB code: 9icr:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2


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 (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.81 O1A A:DCP338 2.3 90.6 0.5 OD1 A:ASP190 2.3 49.6 1.0 O1G A:DCP338 2.7 63.6 0.5 O2B A:DCP338 2.7 86.5 0.5 O3G A:DCP338 3.0 64.9 0.5 O A:ASP190 3.1 36.3 1.0 OD2 A:ASP192 3.1 59.6 1.0 PG A:DCP338 3.2 52.5 0.5 CG A:ASP190 3.2 43.3 1.0 O3B A:DCP338 3.2 76.2 0.5 O A:HOH502 3.3 5.5 1.0 PB A:DCP338 3.4 81.0 0.5 PA A:DCP338 3.4 92.2 0.5 OD2 A:ASP190 3.6 49.4 1.0 O A:HOH549 3.6 8.3 1.0 O3A A:DCP338 3.7 79.5 0.5 CG A:ASP192 3.7 57.8 1.0 O5' A:DCP338 3.8 83.8 0.5 OD1 A:ASP192 3.9 66.0 1.0 C A:ASP190 3.9 24.9 1.0 N A:ASP190 4.2 21.9 1.0 CB A:ASP190 4.3 29.9 1.0 CA A:ASP190 4.4 21.4 1.0 N A:ASP192 4.6 21.9 1.0 O2G A:DCP338 4.6 67.9 0.5 O2A A:DCP338 4.8 96.6 0.5 O1B A:DCP338 4.8 91.9 0.5 N A:MET191 4.8 15.8 1.0 CB A:ASP192 4.9 43.0 1.0 CA A:GLY179 5.0 11.6 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2


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 (E.C.2.7.7.7)/Dna Complex + 2'- Deoxycytidine-5'-Triphosphate, Soaked in the Presence of Dctp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.17 CG A:ASP190 2.9 43.3 1.0 OD1 A:ASP190 3.1 49.6 1.0 CB A:ASP190 3.2 29.9 1.0 OD2 A:ASP190 3.2 49.4 1.0 O A:HOH549 3.3 8.3 1.0 OD2 A:ASP256 3.4 37.0 1.0 OD1 A:ASP256 3.6 36.2 1.0 CG A:ASP256 3.7 35.2 1.0 NH2 A:ARG254 4.0 31.2 1.0 CZ A:ARG254 4.2 28.7 1.0 OD1 A:ASP192 4.2 66.0 1.0 CB A:ARG254 4.3 9.4 1.0 NH1 A:ARG254 4.5 22.4 1.0 CA A:ASP190 4.6 21.4 1.0 NE A:ARG254 4.7 28.2 1.0 O A:ARG254 4.7 1.0 1.0 C A:ARG254 4.8 1.0 1.0 CB A:ASP256 4.9 25.6 1.0 C A:ASP190 4.9 24.9 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