Magnesium in PDB 8h99: Crystal Structure of E. Coli Thrs Catalytic Domain Mutant

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

The structure of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant, PDB code: 8h99 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)	40.56 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.73, 109.99, 114.7, 90, 90, 90
R / Rfree (%)	17.7 / 20.2

The structure of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant (pdb code 8h99). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant, PDB code: 8h99:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:22.8 occ:1.00 O1B A:ATP701 2.2 19.6 1.0 O1G A:ATP701 2.2 21.8 1.0 OE1 A:GLN479 2.3 21.8 1.0 O A:HOH987 2.3 28.9 1.0 O A:HOH812 2.5 23.3 1.0 O A:HOH1055 2.5 27.1 1.0 PB A:ATP701 3.3 19.2 1.0 O3B A:ATP701 3.3 21.4 1.0 CD A:GLN479 3.3 22.0 1.0 PG A:ATP701 3.3 21.0 1.0 O A:HOH811 3.8 28.6 1.0 NE2 A:GLN479 3.8 18.7 1.0 O A:HOH1001 3.9 28.9 1.0 O A:HOH810 4.0 40.1 1.0 NZ A:LYS465 4.0 24.5 1.0 OE2 A:GLU467 4.0 22.9 1.0 O2B A:ATP701 4.1 16.9 1.0 OE1 A:GLU458 4.1 35.0 1.0 O2G A:ATP701 4.3 20.2 1.0 O A:HOH1066 4.3 24.1 1.0 O3G A:ATP701 4.4 18.9 1.0 O3A A:ATP701 4.5 18.9 1.0 CD A:GLU467 4.6 25.5 1.0 CG A:GLN479 4.6 19.9 1.0 OE1 A:GLU467 4.7 28.9 1.0 O A:GLU458 4.7 23.0 1.0 CB A:GLN479 4.8 18.7 1.0 MG A:MG704 4.9 21.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:21.9 occ:1.00 O2G A:ATP701 2.0 20.2 1.0 O2B A:ATP701 2.1 16.9 1.0 O A:HOH816 2.3 17.1 1.0 O A:HOH1066 2.3 24.1 1.0 O A:HOH907 2.3 23.0 1.0 O A:HOH959 2.3 24.3 1.0 PG A:ATP701 3.3 21.0 1.0 PB A:ATP701 3.3 19.2 1.0 O3B A:ATP701 3.3 21.4 1.0 O1G A:ATP701 3.9 21.8 1.0 O A:HOH873 3.9 27.5 1.0 NH1 A:ARG363 4.0 15.2 1.0 NH1 A:ARG375 4.1 21.3 1.0 O1B A:ATP701 4.2 19.6 1.0 OE2 A:GLU365 4.2 22.0 1.0 O A:HOH1047 4.2 30.3 1.0 N7 A:ATP701 4.4 15.7 1.0 O3A A:ATP701 4.5 18.9 1.0 O3G A:ATP701 4.5 18.9 1.0 O A:HOH1055 4.5 27.1 1.0 OE1 A:GLU365 4.5 25.0 1.0 O A:HOH1136 4.7 47.7 1.0 O A:HOH811 4.7 28.6 1.0 CD A:GLU365 4.8 23.9 1.0 OH A:TYR313 4.9 32.1 1.0 MG A:MG703 4.9 22.8 1.0 C8 A:ATP701 5.0 15.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:29.4 occ:1.00 OE1 B:GLN479 2.2 25.8 1.0 O1B B:ATP701 2.2 24.7 1.0 O B:HOH1047 2.2 34.1 1.0 O2G B:ATP701 2.3 26.4 1.0 O B:HOH861 2.4 28.1 1.0 O B:HOH847 2.6 33.8 1.0 O B:HOH834 2.8 43.4 1.0 CD B:GLN479 3.2 25.1 1.0 PB B:ATP701 3.3 23.5 1.0 O3B B:ATP701 3.4 24.8 1.0 O B:HOH846 3.4 44.3 1.0 PG B:ATP701 3.5 25.4 1.0 NE2 B:GLN479 3.7 20.9 1.0 O B:HOH1008 4.0 29.4 1.0 OE2 B:GLU467 4.1 28.0 1.0 O B:HOH885 4.2 33.2 1.0 NZ B:LYS465 4.2 25.3 1.0 O B:HOH808 4.2 38.9 1.0 O2B B:ATP701 4.2 24.2 1.0 CD B:GLU467 4.4 30.4 1.0 O1G B:ATP701 4.4 28.8 1.0 OE1 B:GLU467 4.4 30.7 1.0 CG B:GLN479 4.5 22.9 1.0 O3G B:ATP701 4.5 22.5 1.0 O3A B:ATP701 4.5 24.1 1.0 CB B:GLN479 4.7 19.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of E. Coli Thrs Catalytic Domain Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Thrs Catalytic Domain Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:26.3 occ:1.00 O2B B:ATP701 2.1 24.2 1.0 O1G B:ATP701 2.1 28.8 1.0 O B:HOH813 2.3 20.1 1.0 O B:HOH958 2.3 24.6 1.0 O B:HOH1008 2.3 29.4 1.0 O B:HOH1033 2.3 27.0 1.0 PG B:ATP701 3.2 25.4 1.0 O3B B:ATP701 3.2 24.8 1.0 PB B:ATP701 3.2 23.5 1.0 O B:HOH934 3.8 39.2 1.0 O B:HOH899 3.9 30.2 1.0 NH1 B:ARG363 3.9 18.6 1.0 O2G B:ATP701 4.0 26.4 1.0 NH1 B:ARG375 4.0 24.4 1.0 N7 B:ATP701 4.1 15.7 1.0 O1B B:ATP701 4.2 24.7 1.0 OE2 B:GLU365 4.2 22.6 1.0 O3A B:ATP701 4.3 24.1 1.0 O3G B:ATP701 4.4 22.5 1.0 O B:HOH1107 4.5 37.4 1.0 OE1 B:GLU365 4.5 25.6 1.0 O B:HOH1047 4.6 34.1 1.0 C8 B:ATP701 4.7 17.1 1.0 CD B:GLU365 4.8 22.8 1.0 O B:HOH885 4.9 33.2 1.0 OH B:TYR313 5.0 47.8 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