Cadmium in PDB 2yc5: Inhibitors of the Herbicidal Target Ispd

All present enzymatic activity of Inhibitors of the Herbicidal Target Ispd:
2.7.7.60;

The structure of Inhibitors of the Herbicidal Target Ispd, PDB code: 2yc5 was solved by H.W.Hoeffken, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.11 / 1.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	74.900, 74.900, 220.060, 90.00, 90.00, 120.00
R / Rfree (%)	15.037 / 18.897

The structure of Inhibitors of the Herbicidal Target Ispd also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Magnesium	(Mg)	1 atom
Sodium	(Na)	1 atom
Copper	(Cu)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Cadmium atom in the Inhibitors of the Herbicidal Target Ispd (pdb code 2yc5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Inhibitors of the Herbicidal Target Ispd, PDB code: 2yc5:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Inhibitors of the Herbicidal Target Ispd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Inhibitors of the Herbicidal Target Ispd within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1304 b:28.6 occ:0.50 O A:HOH2065 2.1 31.1 1.0 OE1 A:GLU167 2.3 29.5 1.0 OE2 A:GLU167 2.6 27.1 1.0 O A:HOH2066 2.7 45.8 0.5 CD A:GLU167 2.8 26.3 1.0 O A:GLN166 4.3 27.1 1.0 CG A:GLU167 4.4 23.4 1.0

Cadmium binding site 2 out of 3 in the Inhibitors of the Herbicidal Target Ispd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Inhibitors of the Herbicidal Target Ispd within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1308 b:19.2 occ:0.75 OE1 A:GLU267 2.0 20.9 1.0 OD2 A:ASP261 2.2 25.6 1.0 OD1 A:ASP261 2.9 21.1 1.0 CG A:ASP261 2.9 21.1 1.0 CD A:GLU267 2.9 20.0 1.0 O A:HOH2138 3.0 40.1 1.0 OE2 A:GLU267 3.2 25.0 1.0 OG A:SER264 4.1 20.8 1.0 O A:HOH2134 4.3 34.2 1.0 CG A:GLU267 4.3 21.3 1.0 CB A:ASP261 4.4 21.9 1.0 CA A:SER264 4.5 18.9 1.0 CG2 A:VAL263 4.6 19.4 1.0 N A:SER264 4.7 19.5 1.0 CB A:SER264 4.9 18.9 1.0 CB A:GLU267 4.9 21.3 1.0

Cadmium binding site 3 out of 3 in the Inhibitors of the Herbicidal Target Ispd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Inhibitors of the Herbicidal Target Ispd within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1311 b:39.2 occ:1.00 OD1 A:ASP169 2.4 33.4 1.0 OD2 A:ASP169 2.6 32.7 1.0 CG A:ASP169 2.8 30.1 1.0 OD1 A:ASN171 3.4 32.6 0.5 O A:HOH2070 3.9 36.0 1.0 CB A:ASN171 4.1 32.0 0.5 O A:HOH2072 4.3 43.9 1.0 CG A:ASN171 4.3 33.6 0.5 CB A:ASP169 4.3 27.2 1.0 NZ A:LYS123 4.5 41.9 1.0 CG2 A:VAL170 4.6 34.0 1.0 CE A:LYS123 4.6 39.7 1.0 N A:ASN171 4.7 32.8 0.5 N A:ASN171 4.7 33.0 0.5 O A:HOH2001 4.9 41.1 1.0 CA A:ASN171 4.9 31.7 0.5 ND2 A:ASN171 4.9 35.7 0.5

M.C.Witschel, H.W.Hoeffken, M.Seet, L.Parra, T.Mietzner, F.Thater, R.Niggeweg, F.Rohl, B.Illarionov, F.Rohdich, J.Kaiser, M.Fischer, A.Bacher, F.Diederich. Inhibitors of the Herbicidal Target Ispd: Allosteric Site Binding. Angew.Chem.Int.Ed.Engl. V. 50 7931 2011.
ISSN: ISSN 1433-7851
PubMed: 21766403
DOI: 10.1002/ANIE.201102281