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Cadmium in PDB 2yc3: Inhibitors of the Herbicidal Target Ispd

Enzymatic activity of Inhibitors of the Herbicidal Target Ispd

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

Protein crystallography data

The structure of Inhibitors of the Herbicidal Target Ispd, PDB code: 2yc3 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) 37.30 / 1.40
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 74.600, 74.600, 220.500, 90.00, 90.00, 120.00
R / Rfree (%) 16.248 / 20.408

Other elements in 2yc3:

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

Sodium (Na) 2 atoms
Copper (Cu) 2 atoms
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Inhibitors of the Herbicidal Target Ispd (pdb code 2yc3). 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: 2yc3:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 2yc3

Go back to Cadmium Binding Sites List in 2yc3
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:Cd1306

b:28.6
occ:0.75
OE1 A:GLU267 2.0 26.7 1.0
OD2 A:ASP261 2.3 31.2 1.0
CD A:GLU267 3.0 25.3 1.0
CG A:ASP261 3.1 25.2 1.0
OD1 A:ASP261 3.2 24.3 1.0
OE2 A:GLU267 3.5 34.3 1.0
O A:HOH2075 3.5 25.2 1.0
OG A:SER264 4.1 22.5 1.0
O A:HOH2152 4.4 39.3 1.0
CG A:GLU267 4.4 26.1 1.0
CA A:SER264 4.5 19.1 1.0
CB A:ASP261 4.6 20.8 1.0
CG2 A:VAL263 4.8 21.2 1.0
N A:SER264 4.8 18.3 1.0
CB A:SER264 4.8 21.1 1.0
OG1 A:THR260 4.8 28.9 1.0
CB A:GLU267 4.9 20.9 1.0

Cadmium binding site 2 out of 3 in 2yc3

Go back to Cadmium Binding Sites List in 2yc3
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:Cd1307

b:16.9
occ:1.00
OE2 A:GLU191 2.2 15.4 1.0
OE2 A:GLU121 2.2 21.5 1.0
OE1 A:GLU121 2.6 17.8 1.0
OE1 A:GLU191 2.6 16.8 1.0
CD A:GLU121 2.8 18.3 1.0
CD A:GLU191 2.8 14.9 1.0
O A:HOH2087 3.9 25.9 1.0
CG A:GLU121 4.2 19.2 1.0
CG A:GLU191 4.3 16.4 1.0
O A:HOH2021 4.4 33.1 1.0
CD A:PRO120 4.6 18.0 1.0
O A:HOH2088 4.7 20.4 1.0
CE A:MET119 4.9 16.6 1.0

Cadmium binding site 3 out of 3 in 2yc3

Go back to Cadmium Binding Sites List in 2yc3
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:Cd1308

b:18.3
occ:0.50
OE2 A:GLU167 2.2 23.5 1.0
OE1 A:GLU167 2.2 24.3 1.0
CD A:GLU167 2.6 24.8 1.0
O A:HOH2071 2.6 56.0 1.0
O A:HOH2070 2.8 31.7 1.0
CG A:GLU167 4.1 23.2 1.0
O A:GLN166 4.7 23.4 1.0
O A:HOH2068 4.8 24.4 1.0
CB A:GLU167 4.9 21.1 1.0

Reference:

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
Page generated: Sun Jan 24 09:43:52 2021

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