Manganese in PDB 9icl: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2, PDB code: 9icl 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 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.634, 57.763, 48.491, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate 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, Soaked in the Presence of Pyrophosphate and MNCL2 (pdb code 9icl). 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, Soaked in the Presence of Pyrophosphate and MNCL2, PDB code: 9icl:
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, Soaked in the Presence of Pyrophosphate 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, Soaked in the Presence of Pyrophosphate and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.31 OD1 A:ASP190 2.7 40.5 1.0 OD1 A:ASP192 3.5 47.5 1.0 CG A:ASP190 3.7 36.9 1.0 O A:HOH660 3.9 64.7 1.0 OD2 A:ASP190 4.1 49.6 1.0 CG A:ASP192 4.1 43.3 1.0 O A:ASP190 4.4 36.7 1.0 O A:HOH664 4.5 50.6 1.0 O A:HOH502 4.5 18.6 1.0 O A:HOH668 4.6 26.8 1.0 CB A:ASP192 4.7 37.0 1.0 O A:HOH587 4.7 81.0 1.0 OD2 A:ASP192 4.8 44.8 1.0 CA A:GLY179 4.9 27.0 1.0 CB A:ASP190 5.0 23.2 1.0 C A:ASP190 5.0 27.6 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate 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, Soaked in the Presence of Pyrophosphate and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.25 OD2 A:ASP190 2.7 49.6 1.0 O A:HOH660 3.3 64.7 1.0 CG A:ASP190 3.5 36.9 1.0 OD2 A:ASP256 3.5 38.1 1.0 NH2 A:ARG254 3.8 18.5 1.0 CB A:ASP190 3.8 23.2 1.0 OD1 A:ASP256 3.8 35.4 1.0 CG A:ASP256 3.9 31.3 1.0 O A:HOH534 4.1 70.4 1.0 CZ A:ARG254 4.2 23.9 1.0 OD1 A:ASP190 4.3 40.5 1.0 NE A:ARG254 4.6 27.7 1.0 CB A:ARG254 4.6 9.6 1.0 NH1 A:ARG254 4.7 25.1 1.0 OD1 A:ASP192 4.7 47.5 1.0 O3' P:DG6 4.8 40.3 1.0 O A:HOH548 4.8 63.2 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