Manganese in PDB 4npm: Crystal Structure of Zebrafish ALKBH5 in Complex with Succinic Acid

The structure of Crystal Structure of Zebrafish ALKBH5 in Complex with Succinic Acid, PDB code: 4npm 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)	47.98 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.067, 69.792, 115.050, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.2

The binding sites of Manganese atom in the Crystal Structure of Zebrafish ALKBH5 in Complex with Succinic Acid (pdb code 4npm). 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 Succinic Acid, PDB code: 4npm:
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 Succinic Acid


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 Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:18.8 occ:1.00 O A:HOH414 2.1 20.0 1.0 O A:HOH634 2.1 24.7 1.0 O1 A:SIN301 2.2 22.9 1.0 OD1 A:ASP137 2.2 17.2 1.0 NE2 A:HIS135 2.2 19.2 1.0 NE2 A:HIS197 2.3 19.5 1.0 C1 A:SIN301 3.1 33.8 1.0 CE1 A:HIS135 3.1 22.0 1.0 CE1 A:HIS197 3.1 20.3 1.0 CG A:ASP137 3.2 22.4 1.0 CD2 A:HIS135 3.2 20.3 1.0 CD2 A:HIS197 3.3 18.4 1.0 O2 A:SIN301 3.4 33.6 1.0 OD2 A:ASP137 3.4 17.8 1.0 O A:HOH529 4.2 42.0 1.0 ND1 A:HIS135 4.3 18.6 1.0 ND1 A:HIS197 4.3 16.6 1.0 CG A:HIS135 4.3 19.2 1.0 CG A:HIS197 4.4 17.1 1.0 O A:HOH440 4.4 30.1 1.0 C2 A:SIN301 4.5 32.3 1.0 CB A:ASP137 4.6 19.9 1.0 NH1 A:ARG214 4.6 23.9 1.0 C3 A:SIN301 4.7 32.7 1.0 N A:ASP137 4.9 16.0 1.0 CA A:ASP137 4.9 15.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Zebrafish ALKBH5 in Complex with Succinic Acid


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 Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:20.1 occ:1.00 O B:HOH417 2.1 21.7 1.0 O B:HOH632 2.2 23.2 1.0 OD1 B:ASP137 2.2 20.9 1.0 NE2 B:HIS197 2.2 16.1 1.0 NE2 B:HIS135 2.2 19.4 1.0 O1 B:SIN301 2.3 23.9 1.0 CE1 B:HIS197 3.0 22.8 1.0 CE1 B:HIS135 3.1 21.1 1.0 CG B:ASP137 3.2 22.1 1.0 C1 B:SIN301 3.2 35.7 1.0 CD2 B:HIS135 3.3 18.0 1.0 CD2 B:HIS197 3.4 19.0 1.0 OD2 B:ASP137 3.4 20.2 1.0 O2 B:SIN301 3.6 34.6 1.0 ND1 B:HIS197 4.2 22.0 1.0 O B:HOH491 4.3 30.0 1.0 ND1 B:HIS135 4.3 20.5 1.0 CG B:HIS135 4.4 18.8 1.0 CG B:HIS197 4.4 18.6 1.0 CB B:ASP137 4.6 19.2 1.0 C2 B:SIN301 4.6 30.5 1.0 O B:HOH583 4.6 38.0 1.0 NH1 B:ARG214 4.7 25.6 1.0 C3 B:SIN301 4.8 33.5 1.0 N B:ASP137 4.9 18.6 1.0 O B:HOH424 4.9 23.2 1.0 CA B:ASP137 4.9 17.9 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