Magnesium in PDB 6jqf: Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila

The structure of Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila, PDB code: 6jqf was solved by M.Zhang, X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.72 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.819, 114.548, 128.073, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.9

The structure of Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila (pdb code 6jqf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila, PDB code: 6jqf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:24.7 occ:1.00 O A:HOH1412 2.0 25.5 1.0 O A:HOH980 2.0 28.8 1.0 O A:HOH976 2.1 22.6 1.0 O A:HOH1074 2.1 24.4 1.0 O A:HOH963 2.1 28.0 1.0 O A:HOH954 2.2 33.4 1.0 OE2 A:GLU59 3.7 52.2 1.0 O A:HOH1010 3.9 30.3 1.0 O A:ASP57 4.1 27.6 1.0 O A:HOH1040 4.1 32.0 1.0 OE1 A:GLN233 4.2 25.3 1.0 O A:SER523 4.2 25.5 1.0 O A:ARG231 4.2 23.5 1.0 O A:LEU528 4.2 22.8 1.0 O A:HIS525 4.3 22.1 1.0 CD A:GLU59 4.4 43.5 1.0 CG A:GLU59 4.4 40.2 1.0 CE1 A:TYR232 4.4 24.2 1.0 O A:ALA56 4.5 22.9 1.0 O A:HOH1144 4.5 35.9 1.0 CD1 A:TYR232 4.6 23.2 1.0 CA A:GLY524 4.6 22.7 1.0 C A:GLY524 4.7 23.6 1.0 O A:GLY524 4.7 28.2 1.0 C A:ASP57 4.8 27.1 1.0 CA A:ASP57 4.9 24.9 1.0

Magnesium binding site 2 out of 2 in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:25.4 occ:1.00 O A:HOH1332 2.0 23.7 1.0 O A:HOH914 2.1 23.2 1.0 O A:HOH1432 2.1 23.5 1.0 O A:HOH1271 2.2 24.4 1.0 O A:HOH1053 2.2 26.5 1.0 NE2 A:HIS597 2.3 25.1 1.0 CE1 A:HIS597 3.2 27.1 1.0 CD2 A:HIS597 3.3 23.9 1.0 O A:HOH1341 3.7 38.9 1.0 O A:HOH1343 4.0 28.7 1.0 OD2 A:ASP666 4.2 27.0 1.0 O A:HOH910 4.3 33.5 1.0 OG A:SER249 4.3 22.3 1.0 O A:HOH967 4.3 24.4 1.0 ND1 A:HIS597 4.3 21.1 1.0 CG A:HIS597 4.4 22.6 1.0 O A:HOH942 4.5 33.5 1.0 O A:HOH1195 4.5 30.1 1.0 CG A:GLU649 4.6 28.3 1.0 OD2 A:ASP253 4.7 29.8 1.0 CL A:CL804 4.7 25.9 1.0 O A:HOH931 5.0 31.9 1.0

X.Chen, M.Li, Y.Wang, R.Tang, M.Zhang. Biochemical Characteristics and Crystallographic Evidence For Substrate-Assisted Catalysis of A Beta-N-Acetylhexosaminidase in Akkermansia Muciniphila. Biochem.Biophys.Res.Commun. V. 517 29 2019.
ISSN: ESSN 1090-2104
PubMed: 31345574
DOI: 10.1016/J.BBRC.2019.06.150