Zinc in PDB 8h98: Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1

All present enzymatic activity of Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1:
6.1.1.3;

The structure of Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1, PDB code: 8h98 was solved by H.Qiao, M.Xia, J.Wang, P.Fang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.28 / 2.50
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.75, 105.91, 134.7, 90, 90, 90
R / Rfree (%)	19.1 / 23

The binding sites of Zinc atom in the Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1 (pdb code 8h98). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1, PDB code: 8h98:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:36.9 occ:1.00 O7 B:X5V701 2.0 39.6 1.0 O1 B:X5V701 2.2 38.7 1.0 NE2 B:HIS385 2.2 32.3 1.0 ND1 B:HIS511 2.2 37.9 1.0 SG B:CYS334 2.3 35.2 1.0 C16 B:X5V701 2.9 38.2 1.0 C6 B:X5V701 2.9 35.2 1.0 CG B:HIS511 3.2 37.1 1.0 CD2 B:HIS385 3.2 38.0 1.0 CE1 B:HIS385 3.2 34.5 1.0 CB B:CYS334 3.2 33.6 1.0 CE1 B:HIS511 3.2 40.8 1.0 CB B:HIS511 3.4 37.7 1.0 CA B:CYS334 4.1 35.0 1.0 C4 B:X5V701 4.2 37.9 1.0 C1 B:X5V701 4.3 36.1 1.0 ND1 B:HIS385 4.3 35.8 1.0 NE2 B:HIS511 4.3 41.6 1.0 CG B:HIS385 4.3 37.8 1.0 CD2 B:HIS511 4.3 39.2 1.0 O B:HOH832 4.3 37.6 1.0 N B:CYS334 4.3 36.6 1.0 CA B:HIS511 4.5 33.6 1.0 N1 B:X5V701 4.5 38.0 1.0 OD2 B:ASP383 4.5 41.2 1.0 OD1 B:ASP383 4.7 38.3 1.0 O2 B:X5V701 4.8 45.9 1.0 C5 B:X5V701 4.9 38.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Chemically Modified E. Coli Thrs Catalytic Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:35.4 occ:1.00 O7 A:X5V701 2.0 37.3 1.0 O1 A:X5V701 2.1 37.3 1.0 ND1 A:HIS511 2.3 34.6 1.0 NE2 A:HIS385 2.3 29.7 1.0 SG A:CYS334 2.3 30.7 1.0 C16 A:X5V701 2.8 35.2 1.0 C6 A:X5V701 2.9 33.9 1.0 CD2 A:HIS385 3.2 34.4 1.0 CE1 A:HIS511 3.2 36.5 1.0 CB A:CYS334 3.3 29.1 1.0 CG A:HIS511 3.3 33.8 1.0 CE1 A:HIS385 3.3 31.6 1.0 CB A:HIS511 3.6 34.2 1.0 C4 A:X5V701 4.2 34.8 1.0 CA A:CYS334 4.2 30.3 1.0 C1 A:X5V701 4.2 34.8 1.0 O A:HOH812 4.3 34.8 1.0 NE2 A:HIS511 4.3 36.8 1.0 CG A:HIS385 4.4 34.0 1.0 N A:CYS334 4.4 33.2 1.0 ND1 A:HIS385 4.4 33.5 1.0 CD2 A:HIS511 4.4 36.2 1.0 N1 A:X5V701 4.5 36.1 1.0 OD2 A:ASP383 4.6 42.1 1.0 CA A:HIS511 4.6 32.1 1.0 OD1 A:ASP383 4.6 39.3 1.0 O2 A:X5V701 4.9 42.1 1.0 C5 A:X5V701 4.9 34.5 1.0

H.Qiao, M.Xia, Y.Cheng, J.Zhou, L.Zheng, W.Li, J.Wang, P.Fang. Tyrosine-Targeted Covalent Inhibition of A Trna Synthetase Aided By Zinc Ion. Commun Biol V. 6 107 2023.
ISSN: ESSN 2399-3642
PubMed: 36707692
DOI: 10.1038/S42003-023-04517-7