Zinc in PDB 8wij: Crystal Structure of E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin

All present enzymatic activity of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin:
6.1.1.3;

The structure of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin, PDB code: 8wij was solved by H.Qiao, Z.Wang, J.Wang, P.Fang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.39 / 3.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.246, 84.244, 102.587, 90, 90, 90
R / Rfree (%)	23.8 / 27.8

The binding sites of Zinc atom in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin (pdb code 8wij). 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 E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin, PDB code: 8wij:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin


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 E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:68.0 occ:0.81 O1 B:X5V701 2.0 74.6 0.8 O7 B:X5V701 2.1 78.6 0.8 SG B:CYS334 2.3 68.8 0.9 ND1 B:HIS511 2.3 71.7 0.9 NE2 B:HIS385 2.3 68.2 0.9 C6 B:X5V701 2.5 73.2 0.8 C16 B:X5V701 2.6 76.1 0.8 CG B:HIS511 3.0 72.3 0.9 CB B:HIS511 3.1 71.7 0.9 CE1 B:HIS385 3.1 66.7 0.9 CD2 B:HIS385 3.3 67.5 0.9 CE1 B:HIS511 3.4 71.9 0.9 C1 B:X5V701 3.8 71.9 0.8 CB B:CYS334 3.9 67.4 0.9 C4 B:X5V701 3.9 75.5 0.8 CA B:HIS511 4.1 68.7 0.9 ND1 B:HIS385 4.2 65.6 0.9 CD2 B:HIS511 4.3 71.8 0.9 CG B:HIS385 4.3 66.1 0.9 N1 B:X5V701 4.3 76.8 0.8 OD1 B:ASP383 4.4 67.0 0.8 NE2 B:HIS511 4.4 71.8 0.9 OD2 B:ASP383 4.5 66.5 0.8 O2 B:X5V701 4.5 77.3 0.8 CA B:CYS334 4.6 66.7 0.9 C5 B:X5V701 4.7 75.8 0.8 N B:CYS334 4.7 66.2 0.9 C2 B:X5V701 4.8 72.3 0.8 C3 B:X5V701 4.8 73.7 0.8 O5 B:X5V701 4.9 77.8 0.8 CG B:ASP383 4.9 66.2 0.8 C B:HIS511 4.9 68.6 0.9

Zinc binding site 2 out of 2 in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin


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 E. Coli Thrs Catalytic Domain Mutant L489M in Complex with Obafluorin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:55.5 occ:0.88 O1 A:X5V701 2.0 67.0 0.8 O7 A:X5V701 2.1 68.0 0.8 ND1 A:HIS511 2.3 59.8 0.9 NE2 A:HIS385 2.3 58.7 1.0 SG A:CYS334 2.3 60.1 0.8 C6 A:X5V701 2.8 66.0 0.8 C16 A:X5V701 2.8 67.0 0.8 CD2 A:HIS385 3.2 58.5 1.0 CE1 A:HIS511 3.2 59.6 0.9 CB A:CYS334 3.3 58.2 0.8 CG A:HIS511 3.3 60.1 0.9 CE1 A:HIS385 3.3 56.9 1.0 CB A:HIS511 3.6 61.2 0.9 OD2 A:ASP383 4.1 58.1 0.8 C1 A:X5V701 4.1 66.1 0.8 CA A:CYS334 4.1 57.0 0.8 C4 A:X5V701 4.1 67.5 0.8 N A:CYS334 4.3 57.5 0.8 CG A:HIS385 4.4 56.3 1.0 NE2 A:HIS511 4.4 58.9 0.9 ND1 A:HIS385 4.4 55.9 1.0 OD1 A:ASP383 4.4 57.9 0.8 CD2 A:HIS511 4.4 59.4 0.9 CA A:HIS511 4.6 59.2 0.9 N1 A:X5V701 4.6 70.7 0.8 CG A:ASP383 4.7 57.1 0.8 O2 A:X5V701 4.8 69.8 0.8 C5 A:X5V701 4.9 69.3 0.8

H.Qiao, Z.Wang, H.Yang, M.Xia, G.Yang, F.Bai, J.Wang, P.Fang. Specific Glycine-Dependent Enzyme Motion Determines the Potency of Conformation Selective Inhibitors of Threonyl-Trna Synthetase. Commun Biol V. 7 867 2024.
ISSN: ESSN 2399-3642
PubMed: 39014102
DOI: 10.1038/S42003-024-06559-X