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Nickel in PDB 6z81: Tsabd Bound to the Inhibitor

Enzymatic activity of Tsabd Bound to the Inhibitor

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

Protein crystallography data

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

Other elements in 6z81:

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

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

Nickel Binding Sites:

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 6z81

Go back to Nickel Binding Sites List in 6z81
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 6z81

Go back to Nickel Binding Sites List in 6z81
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 6z81

Go back to Nickel Binding Sites List in 6z81
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 6z81

Go back to Nickel Binding Sites List in 6z81
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

Reference:

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
Page generated: Wed Mar 3 15:41:01 2021

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