Chlorine 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:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila, PDB code: 6jqf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl804 b:25.9 occ:1.00 O A:HOH1343 2.9 28.7 1.0 O A:HOH1195 3.0 30.1 1.0 O A:HOH1432 3.2 23.5 1.0 N A:TYR550 3.3 22.8 1.0 CB A:TYR550 3.5 20.2 1.0 CD A:PRO549 3.9 26.3 1.0 CB A:PRO549 4.0 23.4 1.0 CA A:TYR550 4.0 20.6 1.0 CB A:ALA548 4.0 19.4 1.0 N A:PRO549 4.1 27.9 1.0 CG A:PRO549 4.2 24.4 1.0 OD1 A:ASP666 4.2 27.8 1.0 O A:HOH914 4.2 23.2 1.0 C A:PRO549 4.3 22.2 1.0 CA A:PRO549 4.4 21.1 1.0 CG1 A:ILE734 4.5 23.7 1.0 O A:HOH967 4.7 24.4 1.0 MG A:MG802 4.7 25.4 1.0 O A:HOH1271 4.8 24.4 1.0 C A:ALA548 4.8 22.1 1.0 CG A:TYR550 4.9 23.8 1.0 O A:HOH1145 4.9 28.2 1.0 CA A:ALA548 4.9 20.1 1.0

Chlorine binding site 2 out of 3 in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl805 b:43.6 occ:1.00 NH1 A:ARG502 3.1 27.0 1.0 CD A:ARG502 3.5 27.7 1.0 CZ A:ARG502 4.1 29.4 1.0 NE A:ARG502 4.2 26.7 1.0 O A:HOH1102 4.2 38.5 1.0 CB A:ARG499 4.3 22.4 1.0 CG A:ARG499 4.6 24.9 1.0 CG A:ARG502 4.7 26.6 1.0 CB A:ARG502 4.7 26.2 1.0 O A:HOH1513 5.0 45.8 1.0

Chlorine binding site 3 out of 3 in the Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystallization Analysis of A Beta-N-Acetylhexosaminidase (AM2136) From Akkermansia Muciniphila within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl806 b:47.9 occ:1.00 N A:MSE98 3.1 36.0 1.0 O A:HOH990 3.2 49.5 1.0 N A:VAL34 3.3 42.1 1.0 CA A:ILE97 3.5 34.7 1.0 CB A:ILE97 3.7 35.3 1.0 CA A:PRO33 3.7 54.5 1.0 C A:ILE97 3.8 36.5 1.0 C A:PRO33 4.1 51.6 1.0 CB A:VAL34 4.1 41.1 1.0 CA A:MSE98 4.2 32.9 1.0 O A:MSE98 4.2 41.9 1.0 CA A:VAL34 4.3 45.7 1.0 CB A:PRO33 4.3 55.1 1.0 CB A:MSE98 4.3 41.1 1.0 CG2 A:VAL34 4.3 48.2 1.0 CG2 A:ILE97 4.3 34.6 1.0 C A:MSE98 4.6 37.6 1.0 O A:VAL34 4.6 39.9 1.0 O A:HOH933 4.7 38.2 1.0 O A:GLU96 4.7 38.9 1.0 O A:PRO32 4.8 48.0 1.0 N A:ILE97 4.8 29.7 1.0 N A:PRO33 4.9 54.4 1.0 C A:VAL34 5.0 42.0 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