Manganese in PDB 3ac9: Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese

All present enzymatic activity of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese:
3.6.1.13;

The structure of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese, PDB code: 3ac9 was solved by T.Arimori, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.27 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.240, 40.442, 99.418, 90.00, 121.59, 90.00
R / Rfree (%)	19.5 / 23.6

The binding sites of Manganese atom in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese (pdb code 3ac9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese, PDB code: 3ac9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn209 b:41.5 occ:0.41 O1B B:8GD1 2.2 51.0 1.0 OE1 B:GLU112 2.3 39.8 1.0 OE1 B:GLU116 2.4 43.4 1.0 O B:HOH465 2.5 47.3 1.0 MN B:MN2 3.2 40.2 0.6 O B:HOH446 3.3 49.2 1.0 CD B:GLU112 3.3 38.0 1.0 CD B:GLU116 3.4 36.7 1.0 PB B:8GD1 3.5 60.1 1.0 OE1 B:GLU166 3.6 68.3 1.0 O B:ALA96 3.7 31.7 1.0 CG B:GLU116 3.7 31.4 1.0 OE2 B:GLU112 3.8 44.1 1.0 O B:HOH445 3.9 43.4 1.0 O2B B:8GD1 4.0 69.5 1.0 OE2 B:GLU166 4.0 69.1 1.0 CD B:GLU166 4.1 72.2 1.0 O3B B:8GD1 4.1 53.2 1.0 CG B:GLU112 4.5 38.7 1.0 OE2 B:GLU116 4.5 33.6 1.0 O3A B:8GD1 4.6 64.7 1.0 CA B:GLY97 4.7 37.2 1.0 C B:ALA96 4.8 29.4 1.0 O B:HOH455 4.9 27.1 1.0 OE2 B:GLU115 4.9 45.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dgdp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2 b:40.2 occ:0.55 O B:HOH455 2.1 27.1 1.0 OE1 B:GLU116 2.4 43.4 1.0 O B:ALA96 2.5 31.7 1.0 O1B B:8GD1 2.6 51.0 1.0 O B:HOH445 2.6 43.4 1.0 O1A B:8GD1 2.9 47.0 1.0 MN B:MN209 3.2 41.5 0.4 O2A B:8GD1 3.3 60.5 1.0 PA B:8GD1 3.3 71.1 1.0 CD B:GLU116 3.5 36.7 1.0 C B:ALA96 3.7 29.4 1.0 O3A B:8GD1 3.7 64.7 1.0 PB B:8GD1 3.7 60.1 1.0 O B:HOH465 3.8 47.3 1.0 OE2 B:GLU116 3.9 33.6 1.0 NH2 B:ARG84 4.0 30.3 1.0 O B:HOH391 4.1 24.8 1.0 OE1 B:GLN82 4.2 33.5 1.0 OE1 B:GLU112 4.4 39.8 1.0 N B:ALA96 4.4 24.0 1.0 NE2 B:GLN82 4.5 32.3 1.0 CA B:ALA96 4.5 26.3 1.0 N B:GLY97 4.6 33.1 1.0 CA B:GLY97 4.6 37.2 1.0 O2B B:8GD1 4.7 69.5 1.0 O3B B:8GD1 4.8 53.2 1.0 CG B:GLU116 4.8 31.4 1.0 CD B:GLN82 4.8 35.3 1.0 CZ B:ARG84 4.9 31.1 1.0 CB B:ALA96 4.9 23.4 1.0 O5' B:8GD1 4.9 63.4 1.0

T.Arimori, H.Tamaoki, T.Nakamura, H.Kamiya, S.Ikemizu, Y.Takagi, T.Ishibashi, H.Harashima, M.Sekiguchi, Y.Yamagata. Diverse Substrate Recognition and Hydrolysis Mechanisms of Human NUDT5 Nucleic Acids Res. V. 39 8972 2011.
ISSN: ISSN 0305-1048
PubMed: 21768126
DOI: 10.1093/NAR/GKR575