Manganese in PDB 7wkv: Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna

All present enzymatic activity of Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna:
1.14.11.53;

The structure of Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna, PDB code: 7wkv was solved by S.Kaur, M.A.Mcdonough, C.J.Schofield, W.S.Aik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.26 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	78.364, 78.364, 106.688, 90, 90, 120
R / Rfree (%)	18.8 / 22.8

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna (pdb code 7wkv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna, PDB code: 7wkv:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna


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 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:19.6 occ:1.00 O2 A:AKG302 2.0 31.5 1.0 O5 A:AKG302 2.1 7.4 1.0 OD1 A:ASP206 2.3 28.7 1.0 O A:HOH402 2.4 33.4 1.0 NE2 A:HIS204 2.4 29.3 1.0 NE2 A:HIS266 2.4 33.7 1.0 C1 A:AKG302 2.7 32.0 1.0 C2 A:AKG302 2.8 28.3 1.0 CG A:ASP206 3.1 36.4 1.0 CE1 A:HIS266 3.2 32.6 1.0 CD2 A:HIS204 3.3 29.5 1.0 OD2 A:ASP206 3.3 37.8 1.0 CE1 A:HIS204 3.4 29.4 1.0 NH1 A:ARG283 3.5 43.6 1.0 CD2 A:HIS266 3.5 32.6 1.0 C9 B:6MZ4 4.0 35.7 1.0 O1 A:AKG302 4.0 30.9 1.0 N6 B:6MZ4 4.2 35.6 1.0 C3 A:AKG302 4.2 33.0 1.0 ND1 A:HIS266 4.4 33.3 1.0 CG A:HIS204 4.5 30.2 1.0 ND1 A:HIS204 4.5 34.5 1.0 CB A:ASP206 4.6 29.3 1.0 CG A:HIS266 4.6 33.2 1.0 CZ A:ARG283 4.8 33.3 1.0 C4 A:AKG302 4.9 25.3 1.0 N A:ASP206 4.9 32.9 1.0 CA A:ASP206 5.0 29.8 1.0 C6 B:6MZ4 5.0 36.0 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna


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 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:42.2 occ:1.00 OD1 C:ASP206 1.9 43.8 1.0 O1 C:AKG302 2.0 45.0 1.0 NE2 C:HIS266 2.2 43.8 1.0 O C:HOH404 2.2 34.3 1.0 O5 C:AKG302 2.2 28.7 1.0 NE2 C:HIS204 2.6 40.4 1.0 CG C:ASP206 2.7 43.6 1.0 C1 C:AKG302 2.8 35.4 1.0 CE1 C:HIS266 2.8 44.2 1.0 C2 C:AKG302 2.8 30.4 1.0 OD2 C:ASP206 2.9 43.0 1.0 CD2 C:HIS204 3.3 40.5 1.0 CD2 C:HIS266 3.4 44.1 1.0 CE1 C:HIS204 3.6 40.5 1.0 O2 C:AKG302 4.0 39.9 1.0 ND1 C:HIS266 4.0 46.8 1.0 CB C:ASP206 4.1 44.1 1.0 C9 D:6MZ4 4.2 45.2 1.0 N6 D:6MZ4 4.2 46.1 1.0 NH1 C:ARG283 4.2 42.4 1.0 C3 C:AKG302 4.3 37.4 1.0 CG C:HIS266 4.3 44.6 1.0 CG C:HIS204 4.5 40.8 1.0 N C:ASP206 4.5 45.4 1.0 CA C:ASP206 4.6 44.8 1.0 ND1 C:HIS204 4.6 40.8 1.0 C4 C:AKG302 4.8 36.0 1.0 C6 D:6MZ4 5.0 46.8 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human ALKBH5 in Complex with 2-Oxoglutarate (2OG) and M6A-Containing Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:46.0 occ:1.00 O1 E:AKG302 2.0 50.8 1.0 O5 E:AKG302 2.0 42.6 1.0 O E:HOH402 2.3 42.1 1.0 NE2 E:HIS204 2.3 44.1 1.0 OD1 E:ASP206 2.3 43.6 1.0 NE2 E:HIS266 2.4 43.9 1.0 C2 E:AKG302 2.6 41.7 1.0 C1 E:AKG302 2.6 47.5 1.0 CD2 E:HIS204 3.2 44.4 1.0 CD2 E:HIS266 3.3 44.2 1.0 CE1 E:HIS204 3.3 44.4 1.0 CG E:ASP206 3.3 46.3 1.0 CE1 E:HIS266 3.4 44.2 1.0 OD2 E:ASP206 3.6 54.5 1.0 O2 E:AKG302 3.9 52.5 1.0 C3 E:AKG302 4.0 50.5 1.0 C9 F:6MZ4 4.1 50.1 1.0 N6 F:6MZ4 4.3 50.3 1.0 CG E:HIS204 4.3 44.9 1.0 ND1 E:HIS204 4.3 44.9 1.0 CG E:HIS266 4.4 51.0 1.0 ND1 E:HIS266 4.5 52.7 1.0 NH1 E:ARG283 4.5 43.1 1.0 C4 E:AKG302 4.7 42.5 1.0 CB E:ASP206 4.7 44.7 1.0 N E:ASP206 4.9 44.5 1.0 CA E:ASP206 5.0 48.3 1.0

S.Kaur, N.Y.Tam, M.A.Mcdonough, C.J.Schofield, W.S.Aik. Mechanisms of Substrate Recognition and N6-Methyladenosine Demethylation Revealed By Crystal Structures of ALKBH5-Rna Complexes. Nucleic Acids Res. V. 50 4148 2022.
ISSN: ESSN 1362-4962
PubMed: 35333330
DOI: 10.1093/NAR/GKAC195