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Cadmium in PDB 2ycm: Inhibitors of Herbicidal Target Ispd

Enzymatic activity of Inhibitors of Herbicidal Target Ispd

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

Protein crystallography data

The structure of Inhibitors of Herbicidal Target Ispd, PDB code: 2ycm 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) 73.61 / 1.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 75.060, 75.060, 220.820, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 23.252

Other elements in 2ycm:

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

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

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 3 in 2ycm

Go back to Cadmium Binding Sites List in 2ycm
Cadmium binding site 1 out of 3 in the Inhibitors of 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 Herbicidal Target Ispd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1301

b:48.3
occ:1.00
OD2 A:ASP169 2.3 45.4 1.0
OD1 A:ASP169 2.5 40.0 1.0
CG A:ASP169 2.8 38.3 1.0
NZ A:LYS123 2.8 49.0 1.0
CE A:LYS123 4.0 48.3 1.0
CB A:ASP169 4.2 37.1 1.0
O A:HOH2040 4.4 38.7 1.0
N A:ASN171 4.7 37.4 1.0
CB A:ASN171 4.7 38.3 1.0
CD A:LYS123 4.8 44.9 1.0
N A:VAL170 4.9 38.1 1.0
ND2 A:ASN171 4.9 46.0 1.0

Cadmium binding site 2 out of 3 in 2ycm

Go back to Cadmium Binding Sites List in 2ycm
Cadmium binding site 2 out of 3 in the Inhibitors of 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 Herbicidal Target Ispd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1302

b:30.6
occ:1.00
O A:HOH2081 2.3 38.5 1.0
ND1 A:HIS271 2.3 26.2 1.0
CE1 A:HIS271 3.0 29.1 1.0
CG A:HIS271 3.5 23.1 1.0
CB A:HIS271 4.0 27.6 1.0
NE2 A:HIS271 4.2 26.2 1.0
CD2 A:HIS271 4.5 23.4 1.0
CA A:HIS271 4.5 27.5 1.0
CD1 A:LEU244 4.9 35.1 1.0

Cadmium binding site 3 out of 3 in 2ycm

Go back to Cadmium Binding Sites List in 2ycm
Cadmium binding site 3 out of 3 in the Inhibitors of 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 Herbicidal Target Ispd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1303

b:27.2
occ:0.50
OE2 A:GLU167 2.1 33.4 1.0
OE1 A:GLU167 2.2 31.9 1.0
CD A:GLU167 2.5 32.7 1.0
CG A:GLU167 4.0 31.8 1.0
O A:GLN166 4.5 31.6 1.0
O A:HOH2037 4.8 44.2 1.0
CB A:GLU167 4.9 30.6 1.0
CA A:GLU167 4.9 30.8 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: Sat Dec 12 08:18:44 2020

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