Zinc 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:

Nickel (Ni) 4 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 6z81

Go back to Zinc Binding Sites List in 6z81
Zinc binding site 1 out of 2 in the Tsabd Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tsabd Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:43.4
occ:1.00
OD1 A:ASP300 1.9 31.2 1.0
NE2 A:HIS115 2.1 27.7 1.0
NE2 A:HIS111 2.2 31.9 1.0
OX A:QCB404 2.3 42.7 1.0
OP1 A:QCB404 2.4 32.2 1.0
NX A:QCB404 2.9 36.7 1.0
CG A:ASP300 3.0 33.1 1.0
CD2 A:HIS115 3.1 28.2 1.0
CD2 A:HIS111 3.1 32.3 1.0
CE1 A:HIS115 3.2 27.2 1.0
CX A:QCB404 3.2 43.1 1.0
CE1 A:HIS111 3.3 31.4 1.0
CCA A:QCB404 3.4 33.8 1.0
P1 A:QCB404 3.5 30.8 1.0
CAX A:QCB404 3.6 39.1 1.0
OD2 A:ASP300 3.6 37.0 1.0
CP2 A:QCB404 3.7 31.3 1.0
OCA A:QCB404 4.2 36.9 1.0
OP3 A:QCB404 4.2 32.8 1.0
CG A:HIS115 4.2 26.5 1.0
ND1 A:HIS115 4.3 28.0 1.0
CB A:ASP300 4.3 30.0 1.0
CG A:HIS111 4.3 30.8 1.0
OXT A:QCB404 4.3 46.5 1.0
CBX A:QCB404 4.4 36.2 1.0
CB A:SER136 4.4 30.9 1.0
ND1 A:HIS111 4.4 32.2 1.0
OGX A:QCB404 4.4 39.3 1.0
CA A:ASP300 4.5 28.4 1.0
N A:ASP300 4.5 28.0 1.0
OG A:SER136 4.7 40.9 1.0
CGX A:QCB404 4.8 28.4 1.0
O5' A:QCB404 4.8 31.0 1.0
CE A:MET304 4.8 32.6 1.0

Zinc binding site 2 out of 2 in 6z81

Go back to Zinc Binding Sites List in 6z81
Zinc binding site 2 out of 2 in the Tsabd Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tsabd Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:43.4
occ:1.00
OD1 B:ASP300 2.0 34.2 1.0
NE2 B:HIS115 2.1 25.9 1.0
OX B:QCB404 2.2 28.2 1.0
NE2 B:HIS111 2.3 30.1 1.0
OP3 B:QCB404 2.5 24.7 1.0
NX B:QCB404 2.9 29.4 1.0
CD2 B:HIS115 2.9 26.7 1.0
CG B:ASP300 3.1 32.0 1.0
CX B:QCB404 3.2 30.0 1.0
CE1 B:HIS115 3.2 25.7 1.0
CD2 B:HIS111 3.3 30.3 1.0
CE1 B:HIS111 3.3 30.0 1.0
CCA B:QCB404 3.4 27.7 1.0
OD2 B:ASP300 3.5 33.9 1.0
CAX B:QCB404 3.5 30.6 1.0
P1 B:QCB404 3.5 26.3 1.0
CP2 B:QCB404 3.8 24.1 1.0
OCA B:QCB404 4.1 27.8 1.0
CG B:HIS115 4.1 25.9 1.0
OP1 B:QCB404 4.2 29.1 1.0
ND1 B:HIS115 4.3 27.0 1.0
CB B:SER136 4.3 29.9 1.0
OXT B:QCB404 4.3 30.8 1.0
CBX B:QCB404 4.4 28.4 1.0
CB B:ASP300 4.4 23.7 1.0
OGX B:QCB404 4.4 33.1 1.0
CG B:HIS111 4.4 29.2 1.0
ND1 B:HIS111 4.5 30.8 1.0
N B:ASP300 4.6 23.1 1.0
CA B:ASP300 4.6 22.7 1.0
OG B:SER136 4.6 32.2 1.0
CE B:MET304 4.8 32.8 1.0
CGX B:QCB404 4.8 20.7 1.0
O5' B:QCB404 4.8 26.9 1.0
SD B:MET112 4.9 37.5 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 16:14:46 2021

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