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Cadmium in PDB 4nal: Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin

Enzymatic activity of Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin

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

Protein crystallography data

The structure of Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin, PDB code: 4nal 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) 10.00 / 1.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 74.460, 74.460, 224.500, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24.6

Other elements in 4nal:

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

Bromine (Br) 3 atoms
Potassium (K) 7 atoms
Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin (pdb code 4nal). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin, PDB code: 4nal:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 4nal

Go back to Cadmium Binding Sites List in 4nal
Cadmium binding site 1 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:43.5
occ:1.00
 O A:H70401 2.2 35.6 1.0
O A:HOH552 2.2 40.8 1.0
N11 A:H70401 2.3 42.9 1.0
OE1 A:GLN238 2.4 35.9 1.0
CR A:H70401 3.0 41.4 1.0
CD1 A:H70401 3.2 44.0 1.0
CD A:GLN238 3.2 37.3 1.0
C7 A:H70401 3.3 48.1 1.0
NE2 A:GLN238 3.3 36.5 1.0
CG A:H70401 3.4 40.5 1.0
O A:HOH555 3.8 44.3 1.0
BR3 A:H70401 3.9 55.0 1.0
CH A:H70401 4.1 44.0 1.0
OD1 A:ASP261 4.3 51.7 1.0
CB A:SER264 4.3 50.8 1.0
C9 A:H70401 4.4 51.4 1.0
C8 A:H70401 4.4 51.3 1.0
OG A:SER264 4.4 49.1 1.0
CD A:CD405 4.5 52.4 1.0
O A:ASP261 4.6 55.9 1.0
CD2 A:H70401 4.6 40.2 1.0
CL2 A:H70401 4.6 55.1 1.0
CG A:GLN238 4.7 32.7 1.0
O A:HOH519 4.8 45.5 1.0

Cadmium binding site 2 out of 5 in 4nal

Go back to Cadmium Binding Sites List in 4nal
Cadmium binding site 2 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:38.1
occ:0.50
 O A:HOH510 1.4 22.8 1.0
O A:HOH548 2.3 47.9 1.0
OE2 A:GLU167 2.5 45.8 1.0
OE1 A:GLU167 2.8 44.1 1.0
CD A:GLU167 3.0 45.5 1.0
O A:HOH542 4.3 49.4 1.0
O A:GLN166 4.3 41.7 1.0
CG A:GLU167 4.5 41.3 1.0
C A:GLN166 4.9 40.4 1.0

Cadmium binding site 3 out of 5 in 4nal

Go back to Cadmium Binding Sites List in 4nal
Cadmium binding site 3 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:52.4
occ:1.00
 O A:HOH519 2.3 45.5 1.0
OD1 A:ASP261 2.4 51.7 1.0
O A:HOH511 2.5 47.7 1.0
O A:HOH552 2.5 40.8 1.0
O A:HOH517 2.5 52.0 1.0
OD2 A:ASP261 2.8 52.5 1.0
CG A:ASP261 2.9 57.1 1.0
NE A:ARG157 4.2 71.9 1.0
NH1 A:ARG157 4.4 74.8 1.0
CB A:ASP261 4.4 54.9 1.0
CD A:CD403 4.5 43.5 1.0
O A:HOH506 4.8 40.4 1.0
CZ A:ARG157 4.8 76.2 1.0

Cadmium binding site 4 out of 5 in 4nal

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Cadmium binding site 4 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:49.7
occ:1.00
 OE2 A:GLU138 1.8 67.8 1.0
OE1 A:GLU141 2.4 58.4 1.0
OE2 A:GLU141 2.8 48.6 1.0
CD A:GLU141 2.9 55.7 1.0
CD A:GLU138 3.0 69.9 1.0
OE1 A:GLU138 3.6 75.8 1.0
CG A:GLU138 4.2 67.2 1.0
CG A:GLU141 4.3 51.2 1.0
CB A:GLU141 4.8 50.8 1.0

Cadmium binding site 5 out of 5 in 4nal

Go back to Cadmium Binding Sites List in 4nal
Cadmium binding site 5 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd407

b:30.7
occ:1.00
 ND1 A:HIS271 2.3 29.5 1.0
O A:HOH502 2.4 38.8 1.0
CE1 A:HIS271 3.2 27.0 1.0
CG A:HIS271 3.4 27.7 1.0
CB A:HIS271 3.7 29.5 1.0
NE2 A:HIS271 4.3 27.9 1.0
CA A:HIS271 4.4 30.2 1.0
CD2 A:HIS271 4.5 26.7 1.0
O A:HOH515 5.0 39.3 1.0
N A:HIS271 5.0 34.2 1.0

Reference:

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
Page generated: Fri Jul 19 17:41:53 2024

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