Manganese in PDB 9ics: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2, PDB code: 9ics 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 (°)	178.874, 57.670, 48.476, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp 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',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 (pdb code 9ics). 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',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2, PDB code: 9ics:
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',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp 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',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.58 O1A A:DCT338 1.7 81.2 0.5 OD1 A:ASP190 2.0 46.6 1.0 O1G A:DCT338 2.2 59.9 0.5 O2B A:DCT338 2.3 82.2 0.5 O A:HOH659 2.7 43.3 1.0 PA A:DCT338 2.8 79.8 0.5 CG A:ASP190 2.9 41.9 1.0 O3A A:DCT338 3.0 80.8 0.5 PB A:DCT338 3.1 80.3 0.5 OD2 A:ASP190 3.2 49.0 1.0 PG A:DCT338 3.3 66.4 0.5 O3B A:DCT338 3.5 76.4 0.5 O5' A:DCT338 3.5 79.0 0.5 OD1 A:ASP192 3.8 58.2 1.0 O3G A:DCT338 3.9 71.0 0.5 O A:ASP190 3.9 32.9 1.0 O2A A:DCT338 4.1 79.2 0.5 CB A:ASP190 4.3 23.6 1.0 O A:HOH502 4.4 22.7 1.0 N A:ASP190 4.4 22.8 1.0 C5' A:DCT338 4.5 76.5 0.5 O1B A:DCT338 4.5 81.9 0.5 O2G A:DCT338 4.5 67.4 0.5 C A:ASP190 4.5 24.2 1.0 OG A:SER180 4.6 40.5 1.0 CA A:GLY179 4.7 17.2 1.0 MN A:MN340 4.7 30.0 0.3 CA A:ASP190 4.7 21.4 1.0 CG A:ASP192 4.8 54.0 1.0 N A:SER180 5.0 33.5 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp 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',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.33 OD1 A:ASP192 3.0 58.2 1.0 OD2 A:ASP256 3.6 45.5 1.0 CG A:ASP192 3.6 54.0 1.0 OD1 A:ASP190 3.7 46.6 1.0 CG A:ASP190 3.8 41.9 1.0 O1A A:DCT338 3.8 81.2 0.5 O A:HOH549 3.8 0.0 1.0 OD2 A:ASP192 4.0 55.3 1.0 OD2 A:ASP190 4.0 49.0 1.0 CG A:ASP256 4.1 37.8 1.0 NH1 A:ARG258 4.2 81.1 1.0 CB A:ASP190 4.4 23.6 1.0 PA A:DCT338 4.6 79.8 0.5 CB A:ASP256 4.6 27.2 1.0 O2A A:DCT338 4.7 79.2 0.5 OD1 A:ASP256 4.7 36.7 1.0 MN A:MN339 4.7 30.0 0.6 CB A:ASP192 4.8 40.1 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