Nickel in PDB 6z81: Tsabd Bound to the Inhibitor

All present enzymatic activity of Tsabd Bound to the Inhibitor:
2.3.1.234;

The structure of Tsabd Bound to the Inhibitor, PDB code: 6z81 was solved by S.Missoury, H.Van Tilbeurgh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.47 / 2.31
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.23, 69.25, 86.54, 109.38, 92, 116.94
R / Rfree (%)	18.2 / 23.3

The structure of Tsabd Bound to the Inhibitor also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Nickel atom in the Tsabd Bound to the Inhibitor (pdb code 6z81). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Tsabd Bound to the Inhibitor, PDB code: 6z81:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Tsabd Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Tsabd Bound to the Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:75.6 occ:1.00 N A:HIS339 3.7 33.5 1.0 O A:ACT412 3.9 47.9 1.0 CA A:HIS338 4.3 32.0 1.0 CB A:HIS339 4.3 35.7 1.0 CA A:HIS339 4.5 34.1 1.0 C A:HIS338 4.5 34.6 1.0 O A:HIS339 4.6 35.4 1.0 CB A:HIS338 4.7 33.0 1.0 ND1 A:HIS338 4.7 39.3 1.0 C A:ACT412 4.8 50.1 1.0 CD2 A:PHE128 5.0 35.6 1.0 CG A:HIS338 5.0 37.1 1.0

Nickel binding site 2 out of 4 in the Tsabd Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Tsabd Bound to the Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:75.5 occ:1.00 O C:HOH415 3.7 59.5 1.0 N A:LEU321 3.7 30.4 1.0 CB A:LEU321 3.7 29.7 1.0 CG A:LEU321 3.9 32.7 1.0 CB A:ASP320 4.0 30.8 1.0 CD1 A:LEU321 4.1 32.6 1.0 CA A:LEU321 4.3 30.2 1.0 CG A:ASP320 4.5 44.4 1.0 CG C:PRO40 4.6 36.2 1.0 C A:ASP320 4.7 33.5 1.0 CA A:ASP320 4.8 28.7 1.0 OD1 A:ASP320 4.8 46.4 1.0 OD2 A:ASP320 4.9 56.5 1.0

Nickel binding site 3 out of 4 in the Tsabd Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Tsabd Bound to the Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:63.2 occ:1.00 O B:HOH521 3.5 31.4 1.0 NI B:NI402 3.6 105.5 1.0 N B:HIS339 3.8 29.8 1.0 O B:HIS339 4.1 34.0 1.0 CB B:HIS339 4.3 30.3 1.0 CA B:HIS338 4.4 30.6 1.0 CA B:HIS339 4.5 29.4 1.0 C B:HIS338 4.6 34.8 1.0 C B:HIS339 4.8 33.8 1.0 CB B:HIS338 4.8 31.0 1.0 CD2 B:PHE128 4.9 31.0 1.0 CE2 B:PHE128 4.9 33.6 1.0

Nickel binding site 4 out of 4 in the Tsabd Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Tsabd Bound to the Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:105.5 occ:1.00 CD2 B:HIS338 2.8 36.8 1.0 NE2 B:HIS338 3.1 36.9 1.0 CG B:HIS338 3.1 34.9 1.0 CE1 B:HIS338 3.5 36.4 1.0 ND1 B:HIS338 3.5 36.9 1.0 NI B:NI401 3.6 63.2 1.0 CB B:HIS338 3.9 31.0 1.0 CA B:HIS338 4.5 30.6 1.0

B.J.Kopina, S.Missoury, B.Collinet, M.G.Fulton, C.Cirio, H.Van Tilbeurgh, C.T.Lauhon. Structure of A Reaction Intermediate Mimic in T6A Biosynthesis Bound in the Active Site of the Tsabd Heterodimer From Escherichia Coli. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33524148
DOI: 10.1093/NAR/GKAB026