Manganese in PDB 9ica: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2, PDB code: 9ica 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 (°)	178.479, 57.751, 48.511, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / n/a

The binding sites of Manganese atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2 (pdb code 9ica). 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'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2, PDB code: 9ica:
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'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S 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'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.41 S1A A:STP338 1.9 79.2 0.5 O1G A:STP338 2.6 59.0 0.5 OD1 A:ASP190 2.8 40.0 1.0 O2B A:STP338 2.9 75.2 0.5 O3G A:STP338 3.0 62.8 0.5 OD2 A:ASP192 3.0 38.2 1.0 PA A:STP338 3.0 80.4 0.5 O A:ASP190 3.1 24.7 1.0 PG A:STP338 3.2 62.6 0.5 O3A A:STP338 3.4 80.1 0.5 PB A:STP338 3.5 74.9 0.5 O3B A:STP338 3.5 68.1 0.5 O5' A:STP338 3.7 81.2 0.5 O A:HOH502 3.8 7.2 1.0 CG A:ASP190 4.0 43.2 1.0 C A:ASP190 4.1 20.6 1.0 N A:ASP190 4.2 20.5 1.0 O A:HOH654 4.3 30.7 1.0 O2A A:STP338 4.3 82.9 0.5 CG A:ASP192 4.4 40.8 1.0 O A:HOH522 4.4 54.8 1.0 MN A:MN340 4.4 30.0 0.4 CA A:ASP190 4.6 23.2 1.0 O2G A:STP338 4.7 63.5 0.5 OD2 A:ASP190 4.8 50.6 1.0 CB A:ASP190 4.9 35.4 1.0 O1B A:STP338 4.9 74.9 0.5

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S 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'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.38 O3' P:DG7 2.6 0.0 1.0 OD2 A:ASP256 3.1 39.1 1.0 OD2 A:ASP190 3.3 50.6 1.0 OD2 A:ASP192 3.3 38.2 1.0 OD1 A:ASP192 3.5 50.9 1.0 OD1 A:ASP190 3.5 40.0 1.0 S1A A:STP338 3.5 79.2 0.5 C4' P:DG7 3.5 0.0 1.0 C3' P:DG7 3.6 0.0 1.0 CG A:ASP190 3.6 43.2 1.0 CG A:ASP192 3.6 40.8 1.0 CG A:ASP256 3.8 30.6 1.0 C5' P:DG7 4.3 0.0 1.0 CB A:ASP256 4.3 15.4 1.0 MN A:MN339 4.4 30.0 0.4 OD1 A:ASP256 4.4 33.0 1.0 PA A:STP338 4.4 80.4 0.5 O5' P:DG7 4.5 0.0 1.0 O2A A:STP338 4.6 82.9 0.5 C2' P:DG7 4.7 0.0 1.0 O4' P:DG7 4.7 0.0 1.0 O A:MET191 4.7 20.2 1.0 O5' A:STP338 4.8 81.2 0.5 CB A:ASP190 4.8 35.4 1.0 CB A:ASP192 4.9 29.9 1.0 NH1 A:ARG258 5.0 78.7 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I