Cadmium in PDB 5mrq: Arabidopsis Thaliana Ispd ASP262ALA Mutant

All present enzymatic activity of Arabidopsis Thaliana Ispd ASP262ALA Mutant:
2.7.7.60;

The structure of Arabidopsis Thaliana Ispd ASP262ALA Mutant, PDB code: 5mrq was solved by A.Schwab, B.Illarionov, A.Frank, A.Kunfermann, M.Seet, A.Bacher, M.Witschel, M.Fischer, 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 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	74.530, 74.530, 224.160, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.7

The binding sites of Cadmium atom in the Arabidopsis Thaliana Ispd ASP262ALA Mutant (pdb code 5mrq). 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 ASP262ALA Mutant, PDB code: 5mrq:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Arabidopsis Thaliana Ispd ASP262ALA Mutant


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 ASP262ALA Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:60.9 occ:1.00 OE1 A:GLU138 2.0 72.1 1.0 OE1 A:GLU141 2.2 72.0 1.0 O A:HOH524 2.2 52.8 1.0 O A:HOH535 2.5 54.5 1.0 CD A:GLU141 2.9 64.8 1.0 OE2 A:GLU141 2.9 60.5 1.0 CD A:GLU138 3.0 70.3 1.0 OE2 A:GLU138 3.3 70.3 1.0 CG A:GLU141 4.3 62.9 1.0 CG A:GLU138 4.4 66.3 1.0 CB A:GLU141 4.7 59.8 1.0

Cadmium binding site 2 out of 4 in the Arabidopsis Thaliana Ispd ASP262ALA Mutant


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 ASP262ALA Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:49.8 occ:0.50 O A:HOH541 2.3 43.8 1.0 OE1 A:GLU167 2.5 45.0 1.0 OE2 A:GLU167 2.7 49.0 1.0 CD A:GLU167 3.0 46.4 1.0 O A:GLN166 4.4 43.2 1.0 CG A:GLU167 4.5 44.5 1.0 CA A:GLU167 5.0 43.0 1.0 C A:GLN166 5.0 43.7 1.0

Cadmium binding site 3 out of 4 in the Arabidopsis Thaliana Ispd ASP262ALA Mutant


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 ASP262ALA Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:43.1 occ:1.00 OE2 A:GLU121 2.2 51.8 1.0 OE2 A:GLU191 2.3 36.9 1.0 O A:HOH542 2.5 61.0 1.0 OE1 A:GLU121 2.8 41.7 1.0 O A:HOH562 2.8 50.0 1.0 OE1 A:GLU191 2.8 41.6 1.0 CD A:GLU121 2.8 48.5 1.0 CD A:GLU191 2.9 37.9 1.0 O A:HOH526 4.0 52.2 1.0 CG A:GLU121 4.3 47.9 1.0 CG A:GLU191 4.4 34.9 1.0 O A:HOH557 4.6 64.9 1.0 CD A:PRO120 4.8 46.5 1.0 O A:HOH506 4.9 42.0 1.0 CE A:MET119 5.0 37.6 1.0

Cadmium binding site 4 out of 4 in the Arabidopsis Thaliana Ispd ASP262ALA Mutant


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 ASP262ALA Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:0.6 occ:1.00 O A:HOH567 2.5 61.5 1.0 OD2 A:ASP290 2.6 65.6 1.0 OD1 A:ASP290 2.6 73.6 1.0 CG A:ASP290 2.9 69.8 1.0 O A:HOH529 3.1 67.8 1.0 OG1 A:THR286 3.9 91.5 1.0 O A:LYS284 4.3 57.4 1.0 CB A:ASP290 4.4 74.2 1.0 OG1 A:THR287 4.5 80.1 1.0

A.Schwab, B.Illarionov, A.Frank, A.Kunfermann, M.Seet, A.Bacher, M.C.Witschel, M.Fischer, M.Groll, F.Diederich. Mechanism of Allosteric Inhibition of the Enzyme Ispd By Three Different Classes of Ligands. Acs Chem. Biol. V. 12 2132 2017.
ISSN: ESSN 1554-8937
PubMed: 28686408
DOI: 10.1021/ACSCHEMBIO.7B00004