Manganese in PDB 7v4g: Crystal Structure of Human ALKBH5 in Complex with M6A-Containing Ssrna

All present enzymatic activity of Crystal Structure of Human ALKBH5 in Complex with M6A-Containing Ssrna:
1.14.11.53;

The structure of Crystal Structure of Human ALKBH5 in Complex with M6A-Containing Ssrna, PDB code: 7v4g 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)	41.46 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	76.474, 76.474, 106.347, 90, 90, 120
R / Rfree (%)	18.5 / 22.4

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH5 in Complex with M6A-Containing Ssrna (pdb code 7v4g). 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 M6A-Containing Ssrna, PDB code: 7v4g:
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 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 M6A-Containing Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:26.9 occ:1.00 NE2 A:HIS266 2.1 22.1 1.0 O1 A:SO4303 2.2 25.0 1.0 OD1 A:ASP206 2.2 21.1 1.0 O A:HOH473 2.3 25.9 1.0 NE2 A:HIS204 2.5 20.8 1.0 CE1 A:HIS266 2.8 19.4 1.0 CG A:ASP206 3.1 20.6 1.0 OD2 A:ASP206 3.3 23.6 1.0 CD2 A:HIS266 3.3 20.1 1.0 CD2 A:HIS204 3.3 20.3 1.0 S A:SO4303 3.5 23.6 1.0 CE1 A:HIS204 3.5 18.2 1.0 O2 A:SO4303 3.8 22.7 1.0 ND1 A:HIS266 4.0 19.9 1.0 C9 D:6MZ4 4.1 16.8 1.0 N6 D:6MZ4 4.2 19.3 1.0 O3 A:SO4303 4.2 26.5 1.0 CG A:HIS266 4.2 19.0 1.0 NH1 A:ARG283 4.4 19.8 1.0 CB A:ASP206 4.4 17.1 1.0 O4 A:SO4303 4.5 24.2 1.0 CG A:HIS204 4.5 18.6 1.0 ND1 A:HIS204 4.6 17.7 1.0 N A:ASP206 4.8 20.8 1.0 CA A:ASP206 4.8 17.9 1.0 O A:HOH502 4.9 30.1 1.0 C6 D:6MZ4 5.0 18.0 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Human ALKBH5 in Complex with 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 M6A-Containing Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:26.9 occ:1.00 O4 B:SO4303 1.9 23.6 1.0 NE2 B:HIS266 2.2 22.1 1.0 NE2 B:HIS204 2.3 19.2 1.0 O B:HOH410 2.4 26.6 1.0 OD1 B:ASP206 2.5 20.6 1.0 S B:SO4303 2.9 28.7 1.0 CE1 B:HIS266 3.0 18.4 1.0 O3 B:SO4303 3.0 24.1 1.0 CD2 B:HIS204 3.2 17.1 1.0 CD2 B:HIS266 3.3 19.1 1.0 CE1 B:HIS204 3.3 18.3 1.0 CG B:ASP206 3.5 18.8 1.0 O1 B:SO4303 3.7 27.9 1.0 OD2 B:ASP206 3.8 19.4 1.0 C9 E:6MZ4 4.1 19.8 1.0 ND1 B:HIS266 4.1 18.3 1.0 O2 B:SO4303 4.1 25.9 1.0 N6 E:6MZ4 4.2 19.5 1.0 NH1 B:ARG283 4.3 18.7 1.0 CG B:HIS266 4.3 18.8 1.0 CG B:HIS204 4.4 18.1 1.0 ND1 B:HIS204 4.4 18.1 1.0 O B:HOH457 4.7 25.3 1.0 CB B:ASP206 4.8 18.0 1.0 CD1 B:ILE281 5.0 22.6 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human ALKBH5 in Complex with 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 M6A-Containing Ssrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:48.0 occ:1.00 NE2 C:HIS266 2.4 35.3 1.0 OD1 C:ASP206 2.5 33.0 1.0 NE2 C:HIS204 2.6 33.3 1.0 CE1 C:HIS266 3.1 34.4 1.0 O1 C:SO4302 3.1 40.1 1.0 O4 C:SO4302 3.4 41.0 1.0 CD2 C:HIS204 3.4 34.1 1.0 CG C:ASP206 3.4 31.4 1.0 CE1 C:HIS204 3.5 33.4 1.0 CD2 C:HIS266 3.5 35.9 1.0 OD2 C:ASP206 3.6 31.6 1.0 S C:SO4302 3.6 40.6 1.0 O2 C:SO4302 3.9 40.4 1.0 NH1 C:ARG283 4.1 33.3 1.0 C9 F:6MZ4 4.2 33.7 1.0 N6 F:6MZ4 4.3 33.7 1.0 ND1 C:HIS266 4.3 34.8 1.0 CG C:HIS266 4.5 33.9 1.0 ND1 C:HIS204 4.5 36.0 1.0 CG C:HIS204 4.6 35.9 1.0 CB C:ASP206 4.8 31.6 1.0 C6 F:6MZ4 5.0 33.3 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