Manganese in PDB 4npl: Crystal Structure of Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate

The structure of Crystal Structure of Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate, PDB code: 4npl was solved by C.He, W.Chen, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.948, 68.595, 114.909, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.8

The binding sites of Manganese atom in the Crystal Structure of Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate (pdb code 4npl). 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 Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate, PDB code: 4npl:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate


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 Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:86.5 occ:1.00 NE2 A:HIS135 2.1 20.4 1.0 NE2 A:HIS197 2.3 13.2 1.0 O2 A:AKG301 2.3 31.0 1.0 O5 A:AKG301 2.3 40.2 1.0 OD1 A:ASP137 2.4 24.6 1.0 O A:HOH465 2.4 19.0 1.0 CE1 A:HIS135 3.0 18.9 1.0 C2 A:AKG301 3.0 32.8 1.0 C1 A:AKG301 3.0 35.6 1.0 CE1 A:HIS197 3.1 17.9 1.0 CD2 A:HIS135 3.2 17.7 1.0 CG A:ASP137 3.3 22.9 1.0 CD2 A:HIS197 3.3 14.9 1.0 OD2 A:ASP137 3.6 21.4 1.0 ND1 A:HIS135 4.1 13.7 1.0 ND1 A:HIS197 4.2 14.2 1.0 O1 A:AKG301 4.2 33.8 1.0 CG A:HIS135 4.3 13.8 1.0 O A:HOH540 4.3 31.1 1.0 CG A:HIS197 4.4 10.8 1.0 C3 A:AKG301 4.5 28.7 1.0 CB A:ASP137 4.7 15.5 1.0 NH1 A:ARG214 4.8 20.6 1.0 C4 A:AKG301 4.9 25.4 1.0 N A:ASP137 5.0 11.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate


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 Zebrafish ALKBH5 in Complex with Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:21.0 occ:1.00 NE2 B:HIS135 2.2 13.9 1.0 O2 B:AKG301 2.2 22.1 1.0 O B:HOH437 2.2 16.1 1.0 O5 B:AKG301 2.3 22.2 1.0 OD1 B:ASP137 2.3 20.2 1.0 NE2 B:HIS197 2.3 15.5 1.0 C1 B:AKG301 2.9 25.9 1.0 C2 B:AKG301 3.0 21.7 1.0 CD2 B:HIS135 3.1 18.0 1.0 CE1 B:HIS197 3.1 17.9 1.0 CE1 B:HIS135 3.2 18.1 1.0 CG B:ASP137 3.3 20.6 1.0 CD2 B:HIS197 3.4 11.7 1.0 OD2 B:ASP137 3.4 14.9 1.0 O1 B:AKG301 4.1 31.4 1.0 ND1 B:HIS135 4.3 14.7 1.0 O B:HOH541 4.3 28.2 1.0 CG B:HIS135 4.3 14.3 1.0 ND1 B:HIS197 4.3 13.5 1.0 CG B:HIS197 4.4 14.7 1.0 C3 B:AKG301 4.5 25.0 1.0 O B:HOH499 4.5 40.0 1.0 CB B:ASP137 4.7 14.8 1.0 O B:HOH402 4.7 9.0 1.0 C4 B:AKG301 4.9 22.8 1.0 NH1 B:ARG214 5.0 19.1 1.0 N B:ASP137 5.0 9.7 1.0

W.Chen, L.Zhang, G.Zheng, Y.Fu, Q.Ji, F.Liu, H.Chen, C.He. Crystal Structure of the Rna Demethylase ALKBH5 From Zebrafish. Febs Lett. V. 588 892 2014.
ISSN: ISSN 0014-5793
PubMed: 24561204
DOI: 10.1016/J.FEBSLET.2014.02.021