Manganese in PDB 4nj4: Crystal Structure of Human ALKBH5

The structure of Crystal Structure of Human ALKBH5, PDB code: 4nj4 was solved by W.S.Aik, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.99 / 2.02
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.100, 82.660, 89.171, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.8

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH5 (pdb code 4nj4). 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 ALKBH5, PDB code: 4nj4:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human ALKBH5


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 ALKBH5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:28.5 occ:1.00 O A:HOH416 2.2 27.2 1.0 OD1 A:ASP206 2.2 26.2 1.0 O A:HOH405 2.2 24.4 1.0 NE2 A:HIS204 2.3 27.4 1.0 O A:HOH439 2.3 24.9 1.0 NE2 A:HIS266 2.3 23.6 1.0 CG A:ASP206 3.2 25.9 1.0 CE1 A:HIS204 3.2 21.4 1.0 CE1 A:HIS266 3.2 19.2 1.0 CD2 A:HIS204 3.3 28.3 1.0 CD2 A:HIS266 3.3 22.2 1.0 OD2 A:ASP206 3.4 30.8 1.0 O A:HOH515 3.8 61.0 1.0 O A:HOH532 3.9 42.5 1.0 O A:HOH478 4.0 36.3 1.0 ND1 A:HIS204 4.4 31.4 1.0 ND1 A:HIS266 4.4 18.0 1.0 CG A:HIS204 4.4 23.5 1.0 CG A:HIS266 4.4 26.1 1.0 CB A:ASP206 4.6 23.9 1.0 C3 A:GOL304 4.7 94.1 1.0 NH1 A:ARG283 4.8 26.7 1.0 N A:ASP206 4.9 22.9 1.0 CD1 A:ILE281 4.9 62.1 1.0 CA A:ASP206 4.9 27.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human ALKBH5


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 ALKBH5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:46.7 occ:1.00 O B:HOH434 2.2 44.9 1.0 O B:HOH431 2.2 53.3 1.0 O B:HOH422 2.2 38.8 1.0 OD1 B:ASP206 2.2 43.5 1.0 NE2 B:HIS204 2.2 36.4 1.0 NE2 B:HIS266 2.4 34.5 1.0 CE1 B:HIS204 3.2 38.2 1.0 CD2 B:HIS204 3.2 35.2 1.0 CE1 B:HIS266 3.3 32.0 1.0 CG B:ASP206 3.3 46.4 1.0 CD2 B:HIS266 3.4 34.9 1.0 OD2 B:ASP206 3.6 49.3 1.0 O B:HOH479 4.0 61.4 1.0 ND1 B:HIS204 4.3 31.2 1.0 CG B:HIS204 4.3 31.6 1.0 ND1 B:HIS266 4.4 33.3 1.0 CG B:HIS266 4.5 35.2 1.0 CB B:ASP206 4.7 41.6 1.0 NH1 B:ARG283 4.9 41.1 1.0 N B:ASP206 4.9 35.4 1.0 CA B:ASP206 4.9 40.0 1.0

W.Aik, J.S.Scotti, H.Choi, L.Gong, M.Demetriades, C.J.Schofield, M.A.Mcdonough. Structure of Human Rna N6-Methyladenine Demethylase ALKBH5 Provides Insights Into Its Mechanisms of Nucleic Acid Recognition and Demethylation. Nucleic Acids Res. V. 42 4741 2014.
ISSN: ISSN 0305-1048
PubMed: 24489119
DOI: 10.1093/NAR/GKU085