Manganese in PDB 6uom: Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp

All present enzymatic activity of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp:
2.7.7.7;

The structure of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp, PDB code: 6uom was solved by M.R.Smith, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%)	19.4 / 24.4

The structure of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Manganese atom in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp (pdb code 6uom). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp, PDB code: 6uom:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:23.0 occ:1.00 OD1 A:ASP190 2.1 20.5 1.0 OD2 A:ASP192 2.1 23.9 1.0 O2A A:8GT407 2.1 27.0 1.0 O1B A:8GT407 2.2 23.4 1.0 O A:HOH533 2.4 16.8 1.0 O1G A:8GT407 2.4 28.6 1.0 CG A:ASP192 3.0 18.7 1.0 H5'1 A:8GT407 3.1 40.9 1.0 CG A:ASP190 3.2 24.8 1.0 PB A:8GT407 3.2 26.7 1.0 OD1 A:ASP192 3.2 26.7 1.0 PA A:8GT407 3.3 27.9 1.0 O3A A:8GT407 3.5 33.0 1.0 PG A:8GT407 3.6 27.8 1.0 OD2 A:ASP190 3.6 27.5 1.0 MN A:MN404 3.6 42.1 0.8 O3B A:8GT407 3.7 27.6 1.0 C5' A:8GT407 3.9 33.9 1.0 O A:ASP190 4.0 20.9 1.0 O5' A:8GT407 4.1 30.3 1.0 O A:HOH560 4.2 20.5 1.0 OG A:SER180 4.2 20.1 1.0 C A:ASP190 4.2 19.6 1.0 H5'2 A:8GT407 4.3 40.9 1.0 O3G A:8GT407 4.3 21.2 1.0 CB A:ASP192 4.4 23.5 1.0 N A:ASP190 4.4 19.0 1.0 N A:SER180 4.4 23.0 1.0 CA A:GLY179 4.4 21.3 1.0 CB A:ASP190 4.4 19.5 1.0 O1A A:8GT407 4.5 30.2 1.0 CA A:ASP190 4.6 18.9 1.0 O2B A:8GT407 4.6 28.7 1.0 N A:ASP192 4.7 18.6 1.0 O2G A:8GT407 4.8 35.1 1.0 N A:MET191 4.8 18.5 1.0 C A:MET191 5.0 20.2 1.0 O A:HOH648 5.0 31.9 1.0

Manganese binding site 2 out of 2 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:42.1 occ:0.80 OD1 A:ASP192 2.0 26.7 1.0 O P:HOH207 2.0 33.3 1.0 OD2 A:ASP190 2.5 27.5 1.0 O2A A:8GT407 2.8 27.0 1.0 H5'2 A:8GT407 2.9 40.9 1.0 OD2 A:ASP256 3.0 28.4 1.0 CG A:ASP192 3.1 18.7 1.0 O5' A:8GT407 3.2 30.3 1.0 C5' A:8GT407 3.3 33.9 1.0 CG A:ASP190 3.3 24.8 1.0 H5'1 A:8GT407 3.3 40.9 1.0 OD1 A:ASP190 3.4 20.5 1.0 PA A:8GT407 3.5 27.9 1.0 OD2 A:ASP192 3.6 23.9 1.0 MN A:MN403 3.6 23.0 1.0 CG A:ASP256 3.8 24.4 1.0 C5' P:DOC101 4.1 35.0 1.0 C3' P:DOC101 4.3 41.0 1.0 O1A A:8GT407 4.3 30.2 1.0 CB A:ASP256 4.3 20.9 1.0 CB A:ASP192 4.3 23.5 1.0 C4' P:DOC101 4.5 35.3 1.0 O P:HOH205 4.6 31.2 1.0 OP2 P:DOC101 4.6 27.6 1.0 CB A:ASP190 4.7 19.5 1.0 OD1 A:ASP256 4.7 23.9 1.0 C4' A:8GT407 4.8 26.2 1.0 O A:MET191 4.9 20.3 1.0 O3A A:8GT407 4.9 33.0 1.0 CA A:ASP192 4.9 17.6 1.0

M.R.Smith, K.S.Alnajjar, N.M.Hoitsma, J.B.Sweasy, B.D.Freudenthal. Molecular Characterization of Oxidized Ribonucleotide Insertion By Human Dna Polymerase Beta J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X