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Copper in PDB 2yc5: 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: 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

Other elements in 2yc5:

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

Cadmium (Cd) 3 atoms
Zinc (Zn) 1 atom
Magnesium (Mg) 1 atom
Sodium (Na) 1 atom
Chlorine (Cl) 1 atom

Copper Binding Sites:

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

Copper binding site 1 out of 3 in 2yc5

Go back to Copper Binding Sites List in 2yc5
Copper binding site 1 out of 3 in the Inhibitors of the Herbicidal Target Ispd


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Inhibitors of the Herbicidal Target Ispd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1301

b:58.1
occ:0.50
O A:HOH2044 2.1 39.9 1.0
OE2 A:GLU141 3.6 32.4 1.0
N A:LEU148 3.8 24.8 1.0
CA A:ASP147 3.9 24.9 1.0
CB A:ASP147 4.1 25.4 1.0
O A:LEU148 4.2 26.1 1.0
O A:HOH2043 4.3 43.9 1.0
OD1 A:ASP147 4.3 37.4 1.0
C A:ASP147 4.4 25.2 1.0
CG A:ASP147 4.5 32.2 1.0
CD A:GLU141 4.5 32.6 1.0
CA A:LEU148 4.9 24.2 1.0
CG A:GLU141 4.9 29.9 1.0
C A:LEU148 4.9 24.2 1.0

Copper binding site 2 out of 3 in 2yc5

Go back to Copper Binding Sites List in 2yc5
Copper binding site 2 out of 3 in the Inhibitors of the Herbicidal Target Ispd


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Inhibitors of the Herbicidal Target Ispd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1302

b:29.1
occ:0.50
NZ A:LYS123 2.3 41.9 1.0
O A:HOH2070 2.5 36.0 1.0
OD2 A:ASP147 2.6 39.8 1.0
O A:HOH2050 2.7 53.3 1.0
CE A:LYS123 2.8 39.7 1.0
CG A:ASP147 3.6 32.2 1.0
O A:HOH2026 3.8 52.6 1.0
OD1 A:ASP147 3.9 37.4 1.0
OD2 A:ASP169 4.1 32.7 1.0
CD A:LYS123 4.2 37.6 1.0
CG A:LYS123 4.8 31.5 1.0
CB A:ASP147 4.9 25.4 1.0
O A:HOH2051 4.9 58.0 0.5

Copper binding site 3 out of 3 in 2yc5

Go back to Copper Binding Sites List in 2yc5
Copper binding site 3 out of 3 in the Inhibitors of the Herbicidal Target Ispd


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Inhibitors of the Herbicidal Target Ispd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1305

b:0.8
occ:1.00
OD1 A:ASP290 2.4 45.8 1.0
O A:HOH2158 2.4 60.9 1.0
O A:HOH2156 3.0 0.1 1.0
CG A:ASP290 3.2 49.6 1.0
OD2 A:ASP290 3.4 46.9 1.0
O A:LYS284 4.4 32.7 1.0
OG1 A:THR286 4.4 49.1 1.0
CB A:ASP290 4.7 51.0 1.0
O A:HOH2154 4.8 48.2 1.0
OG1 A:THR287 4.8 52.2 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 Dec 13 11:08:05 2020

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