Zinc in PDB 6sj4: Amidohydrolase, Ahs with Substrate Analog

The structure of Amidohydrolase, Ahs with Substrate Analog, PDB code: 6sj4 was solved by J.H.Naismith, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.08 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.320, 54.337, 139.844, 90.00, 111.45, 90.00
R / Rfree (%)	18.2 / 21

The binding sites of Zinc atom in the Amidohydrolase, Ahs with Substrate Analog (pdb code 6sj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Amidohydrolase, Ahs with Substrate Analog, PDB code: 6sj4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Amidohydrolase, Ahs with Substrate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Amidohydrolase, Ahs with Substrate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:34.0 occ:1.00 NE2 A:HIS77 2.0 34.4 1.0 NE2 A:HIS75 2.0 33.3 1.0 NE2 A:HIS253 2.0 38.4 1.0 OD1 A:ASP345 2.2 37.3 1.0 CE1 A:HIS253 2.9 39.5 1.0 CE1 A:HIS75 2.9 34.1 1.0 CD2 A:HIS77 3.0 33.5 1.0 CE1 A:HIS77 3.0 35.7 1.0 CD2 A:HIS75 3.0 33.9 1.0 CD2 A:HIS253 3.0 38.1 1.0 CG A:ASP345 3.2 36.6 1.0 O8 A:LFK501 3.2 53.5 1.0 C7 A:LFK501 3.4 52.4 1.0 O3 A:LFK501 3.5 52.1 1.0 OD2 A:ASP345 3.6 36.7 1.0 ND1 A:HIS253 4.1 39.8 1.0 ND1 A:HIS75 4.1 33.3 1.0 ND1 A:HIS77 4.1 35.4 1.0 CG A:HIS77 4.1 33.6 1.0 CG A:HIS75 4.1 33.0 1.0 CG A:HIS253 4.1 37.9 1.0 C3 A:LFK501 4.2 51.1 1.0 NE2 A:HIS290 4.3 37.6 1.0 CB A:ASP345 4.3 35.3 1.0 C21 A:LFK501 4.4 52.5 1.0 CA A:ASP345 4.4 34.9 1.0 C4 A:LFK501 4.5 52.2 1.0 O A:HOH649 4.7 46.1 1.0 C A:ASP345 4.9 36.0 1.0 N A:ALA346 5.0 34.6 1.0 CE1 A:HIS290 5.0 38.3 1.0

Zinc binding site 2 out of 2 in the Amidohydrolase, Ahs with Substrate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Amidohydrolase, Ahs with Substrate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:25.9 occ:1.00 NE2 B:HIS253 2.0 27.5 1.0 NE2 B:HIS75 2.0 25.7 1.0 OD1 B:ASP345 2.0 34.8 1.0 NE2 B:HIS77 2.1 25.6 1.0 O8 B:LFK501 2.7 43.6 1.0 CE1 B:HIS253 2.9 29.7 1.0 CE1 B:HIS75 2.9 27.9 1.0 CG B:ASP345 3.0 33.3 1.0 CD2 B:HIS77 3.0 24.3 1.0 CD2 B:HIS253 3.1 26.2 1.0 CD2 B:HIS75 3.1 26.1 1.0 CE1 B:HIS77 3.1 26.6 1.0 C7 B:LFK501 3.3 42.8 1.0 OD2 B:ASP345 3.4 37.1 1.0 O3 B:LFK501 3.6 41.7 1.0 ND1 B:HIS253 4.0 29.8 1.0 ND1 B:HIS75 4.0 27.6 1.0 NE2 B:HIS290 4.1 27.7 1.0 CG B:HIS253 4.1 26.3 1.0 CG B:HIS75 4.2 24.4 1.0 CG B:HIS77 4.2 24.3 1.0 ND1 B:HIS77 4.2 25.6 1.0 CB B:ASP345 4.2 32.3 1.0 C3 B:LFK501 4.3 39.8 1.0 C21 B:LFK501 4.3 39.2 1.0 CA B:ASP345 4.4 30.6 1.0 C4 B:LFK501 4.6 39.6 1.0 O B:HOH759 4.6 37.0 1.0 CE1 B:HIS290 4.9 28.9 1.0 N B:ALA346 4.9 32.4 1.0 CD2 B:HIS290 4.9 28.7 1.0 C31 B:LFK501 5.0 39.0 1.0 C B:ASP345 5.0 31.7 1.0

H.Song, C.Rao, Z.Deng, Y.Yi, J.H.Naismith. The Biosynthetic Pathway of the Benzoxazole in Nataxazole Proceeds Via An Unstable Ester and Has Synthetic Utility. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 31903677
DOI: 10.1002/ANIE.201915685