Manganese in PDB 4oct: Crystal Structure of Human ALKBH5 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate

The structure of Crystal Structure of Human ALKBH5 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate, PDB code: 4oct was solved by W.Tempel, X.Chao, K.Liu, A.Dong, T.Cerovina, H.He, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.930, 57.234, 78.407, 90.00, 101.07, 90.00
R / Rfree (%)	23.8 / 28.4

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH5 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate (pdb code 4oct). 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 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate, PDB code: 4oct:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human ALKBH5 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate


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 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:47.3 occ:1.00 OD1 A:ASP206 1.9 44.4 1.0 O5 A:AKG502 1.9 44.5 1.0 O1 A:AKG502 1.9 44.8 1.0 NE2 A:HIS266 2.0 41.1 1.0 NE2 A:HIS204 2.1 42.1 1.0 C1 A:AKG502 2.6 47.5 1.0 C2 A:AKG502 2.6 45.6 1.0 CE1 A:HIS266 2.9 40.5 1.0 CE1 A:HIS204 3.0 41.9 1.0 CG A:ASP206 3.0 42.6 1.0 CD2 A:HIS204 3.1 41.5 1.0 CD2 A:HIS266 3.1 40.5 1.0 OD2 A:ASP206 3.6 47.9 1.0 UNK A:UNX511 3.7 42.2 1.0 O2 A:AKG502 3.8 46.0 1.0 C3 A:AKG502 4.1 44.9 1.0 ND1 A:HIS266 4.1 40.7 1.0 ND1 A:HIS204 4.1 42.2 1.0 CG A:HIS204 4.2 40.6 1.0 CG A:HIS266 4.2 40.8 1.0 CB A:ASP206 4.3 41.1 1.0 N A:ASP206 4.5 38.3 1.0 C4 A:AKG502 4.6 45.8 1.0 CA A:ASP206 4.6 38.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human ALKBH5 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate


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 Crystallized in the Presence of Mn^{2+} and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:48.8 occ:1.00 OD1 B:ASP206 1.9 44.3 1.0 O1 B:AKG502 1.9 45.3 1.0 O5 B:AKG502 1.9 45.4 1.0 NE2 B:HIS204 2.1 42.0 1.0 NE2 B:HIS266 2.1 40.2 1.0 C1 B:AKG502 2.5 46.1 1.0 C2 B:AKG502 2.6 44.3 1.0 CE1 B:HIS266 3.0 39.0 1.0 CE1 B:HIS204 3.0 41.1 1.0 CG B:ASP206 3.0 41.3 1.0 CD2 B:HIS204 3.1 40.9 1.0 CD2 B:HIS266 3.2 39.3 1.0 OD2 B:ASP206 3.5 43.9 1.0 O2 B:AKG502 3.7 46.7 1.0 UNK B:UNX516 4.0 37.0 1.0 C3 B:AKG502 4.1 43.9 1.0 ND1 B:HIS204 4.1 41.4 1.0 ND1 B:HIS266 4.1 39.4 1.0 CG B:HIS204 4.2 40.9 1.0 CG B:HIS266 4.2 39.1 1.0 CB B:ASP206 4.3 39.8 1.0 C4 B:AKG502 4.4 44.4 1.0 N B:ASP206 4.5 38.3 1.0 CA B:ASP206 4.6 39.1 1.0

C.Xu, K.Liu, W.Tempel, M.Demetriades, W.Aik, C.J.Schofield, J.Min. Structures of Human ALKBH5 Demethylase Reveal A Unique Binding Mode For Specific Single Stranded M6A Rna Demethylation. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 24778178
DOI: 10.1074/JBC.M114.550350