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

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp and MNCL2, PDB code: 9ict 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 (°)	178.541, 57.719, 48.510, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp 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'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp and MNCL2 (pdb code 9ict). 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'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp and MNCL2, PDB code: 9ict:
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'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp 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'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.52 O1A A:DGT338 2.0 89.3 0.5 OD1 A:ASP190 2.2 31.9 1.0 O1G A:DGT338 2.6 67.5 0.5 O2B A:DGT338 2.7 0.0 0.5 O3G A:DGT338 3.1 80.0 0.5 CG A:ASP190 3.1 27.9 1.0 PA A:DGT338 3.2 0.0 0.5 PG A:DGT338 3.2 80.7 0.5 O3A A:DGT338 3.4 99.6 0.5 O A:ASP190 3.4 17.2 1.0 PB A:DGT338 3.4 98.6 0.5 OD2 A:ASP190 3.4 39.0 1.0 O3B A:DGT338 3.5 90.3 0.5 O A:HOH502 3.6 11.0 1.0 O5' A:DGT338 3.7 76.0 0.5 OD2 A:ASP192 3.8 56.8 1.0 N A:ASP190 4.1 15.7 1.0 C A:ASP190 4.2 10.9 1.0 CG A:ASP192 4.3 52.7 1.0 CB A:ASP190 4.3 7.7 1.0 OD1 A:ASP192 4.4 63.6 1.0 CA A:ASP190 4.5 8.1 1.0 O2A A:DGT338 4.5 0.0 0.5 MN A:MN340 4.5 30.0 0.4 CA A:GLY179 4.6 11.7 1.0 N A:GLY189 4.7 13.3 1.0 O2G A:DGT338 4.7 94.3 0.5 O1B A:DGT338 4.9 99.4 0.5 CB A:SER188 5.0 35.7 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp 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'- Deoxyguanosine-5'-Triphosphate, Soaked in the Presence of Dgtp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.42 OD1 A:ASP192 2.6 63.6 1.0 OD1 A:ASP190 3.1 31.9 1.0 O1A A:DGT338 3.3 89.3 0.5 CG A:ASP192 3.5 52.7 1.0 CG A:ASP190 3.5 27.9 1.0 O A:HOH549 3.7 76.6 1.0 OD2 A:ASP192 3.7 56.8 1.0 OD2 A:ASP256 3.8 28.7 1.0 OD2 A:ASP190 3.9 39.0 1.0 O2A A:DGT338 4.0 0.0 0.5 PA A:DGT338 4.0 0.0 0.5 CB A:ASP190 4.4 7.7 1.0 MN A:MN339 4.5 30.0 0.5 CG A:ASP256 4.6 23.8 1.0 O5' A:DGT338 4.7 76.0 0.5 CB A:ASP192 4.9 31.2 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