Cadmium in PDB 4nan: Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin

All present enzymatic activity of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin:
2.7.7.60;

The structure of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin, PDB code: 4nan was solved by A.Kunfermann, M.Witschel, B.Illarionov, R.Martin, M.Rottmann, H.W.Hoffken, M.Seet, W.Eisenreich, H.-J.Knolker, M.Fischer, A.Bacher, M.Groll, F.Diederich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	75.120, 75.120, 224.130, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.7

The structure of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin also contains other interesting chemical elements:

Bromine	(Br)	8 atoms
Potassium	(K)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Cadmium atom in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin (pdb code 4nan). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin, PDB code: 4nan:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:62.2 occ:1.00 N14 A:2JM401 2.5 39.9 0.3 O A:HOH581 2.5 51.7 1.0 OE1 A:GLN238 2.8 46.0 1.0 N14 A:2JM401 2.9 48.1 0.7 NE2 A:GLN238 3.0 45.5 1.0 O2 A:2JM401 3.1 37.7 0.7 CD A:GLN238 3.2 37.8 1.0 CL A:CL413 3.2 70.9 1.0 C13 A:2JM401 3.2 53.3 0.7 BR1 A:2JM401 3.3 56.6 0.7 C10 A:2JM401 3.4 39.0 0.3 C2 A:2JM401 3.4 38.1 0.3 C13 A:2JM401 3.5 42.2 0.3 C3 A:2JM401 3.7 37.5 0.3 C10 A:2JM401 4.0 45.6 0.7 BR1 A:2JM401 4.1 49.6 0.3 C4 A:2JM401 4.2 40.1 0.7 C12 A:2JM401 4.4 51.9 0.7 C1 A:2JM401 4.4 38.2 0.3 O A:HOH537 4.4 79.2 1.0 C11 A:2JM401 4.6 34.7 0.3 C3 A:2JM401 4.6 37.7 0.7 CG A:GLN238 4.6 32.8 1.0 O A:HOH572 4.6 54.6 1.0 C12 A:2JM401 4.7 40.9 0.3 C11 A:2JM401 4.7 51.2 0.7 C4 A:2JM401 4.8 37.5 0.3 O A:HOH571 4.8 55.4 1.0

Cadmium binding site 2 out of 4 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:29.0 occ:0.50 OE2 A:GLU167 1.9 42.5 1.0 OE1 A:GLU167 2.1 38.9 1.0 CD A:GLU167 2.3 37.3 1.0 CG A:GLU167 3.8 35.0 1.0 O A:HOH522 4.4 38.3 1.0 O A:GLN166 4.6 34.9 1.0 CB A:GLU167 4.7 33.5 1.0 CA A:GLU167 4.9 33.9 1.0

Cadmium binding site 3 out of 4 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:54.7 occ:1.00 OE2 A:GLU138 1.1 27.4 1.0 OE1 A:GLU141 2.3 46.1 1.0 CD A:GLU138 2.3 59.1 1.0 OE2 A:GLU141 2.7 46.0 1.0 CD A:GLU141 2.8 47.5 1.0 OE1 A:GLU138 3.0 67.3 1.0 CG A:GLU138 3.6 52.3 1.0 O A:HOH574 4.0 44.8 1.0 CG A:GLU141 4.3 46.3 1.0 CB A:GLU141 4.8 43.8 1.0 CB A:GLU138 4.9 51.5 1.0

Cadmium binding site 4 out of 4 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:32.3 occ:1.00 ND1 A:HIS271 2.3 31.1 1.0 O A:HOH518 2.6 34.4 1.0 CE1 A:HIS271 3.2 31.1 1.0 CG A:HIS271 3.4 27.3 1.0 CB A:HIS271 3.8 28.5 1.0 NE2 A:HIS271 4.3 31.6 1.0 CA A:HIS271 4.4 26.9 1.0 CD2 A:HIS271 4.5 26.5 1.0

A.Kunfermann, M.Witschel, B.Illarionov, R.Martin, M.Rottmann, H.W.Hoffken, M.Seet, W.Eisenreich, H.J.Knolker, M.Fischer, A.Bacher, M.Groll, F.Diederich. Pseudilins: Halogenated, Allosteric Inhibitors of the Non-Mevalonate Pathway Enzyme Ispd. Angew.Chem.Int.Ed.Engl. V. 53 2235 2014.
ISSN: ISSN 1433-7851
PubMed: 24446431
DOI: 10.1002/ANIE.201309557