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Cadmium in PDB 5mrq: Arabidopsis Thaliana Ispd ASP262ALA Mutant

Enzymatic activity of Arabidopsis Thaliana Ispd ASP262ALA Mutant

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

Protein crystallography data

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

Cadmium Binding Sites:

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 5mrq

Go back to Cadmium Binding Sites List in 5mrq
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 5mrq

Go back to Cadmium Binding Sites List in 5mrq
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 5mrq

Go back to Cadmium Binding Sites List in 5mrq
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 5mrq

Go back to Cadmium Binding Sites List in 5mrq
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

Reference:

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
Page generated: Sat Dec 12 08:27:09 2020

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