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Cadmium in PDB 4nak: Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin

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

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

Protein crystallography data

The structure of Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin, PDB code: 4nak 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 (°) 75.240, 75.240, 224.140, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 21.8

Other elements in 4nak:

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

Bromine (Br) 5 atoms
Potassium (K) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin (pdb code 4nak). 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 Pentabromo-Pseudilin, PDB code: 4nak:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 4nak

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

b:40.0
occ:1.00
 N11 A:PBQ401 2.2 37.8 1.0
OE1 A:GLN238 2.4 35.7 1.0
O A:PBQ401 2.4 37.2 1.0
CR A:PBQ401 3.1 37.7 1.0
CD1 A:PBQ401 3.1 39.1 1.0
CD A:GLN238 3.2 36.7 1.0
C7 A:PBQ401 3.3 44.1 1.0
CG A:PBQ401 3.3 37.5 1.0
NE2 A:GLN238 3.4 35.1 1.0
O A:HOH526 3.7 57.5 1.0
BR19 A:PBQ401 3.9 48.1 1.0
CH A:PBQ401 4.1 41.2 1.0
OD1 A:ASP261 4.3 59.5 1.0
C9 A:PBQ401 4.3 43.4 1.0
CB A:SER264 4.4 45.2 1.0
O A:HOH560 4.4 50.4 1.0
C8 A:PBQ401 4.4 45.2 1.0
CD2 A:PBQ401 4.5 35.3 1.0
CD A:CD405 4.5 50.6 1.0
OG A:SER264 4.6 49.4 1.0
CG A:GLN238 4.7 33.3 1.0
O A:ASP261 4.7 60.0 1.0
BR14 A:PBQ401 4.9 63.6 1.0

Cadmium binding site 2 out of 5 in 4nak

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

b:40.5
occ:0.50
 OE1 A:GLU167 2.4 42.1 1.0
OE2 A:GLU167 2.5 43.8 1.0
CD A:GLU167 2.8 42.6 1.0
CG A:GLU167 4.3 39.3 1.0
O A:GLN166 4.4 36.6 1.0
O A:HOH511 4.7 37.8 1.0
CA A:GLU167 5.0 37.0 1.0
C A:GLN166 5.0 35.8 1.0

Cadmium binding site 3 out of 5 in 4nak

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

b:50.6
occ:1.00
 O A:HOH517 2.3 47.5 1.0
OD1 A:ASP261 2.4 59.5 1.0
O A:HOH560 2.5 50.4 1.0
OD2 A:ASP261 2.9 60.7 1.0
CG A:ASP261 3.0 64.4 1.0
O A:HOH526 3.0 57.5 1.0
NH1 A:ARG157 3.9 74.4 1.0
NE A:ARG157 4.1 64.7 1.0
O A:HOH561 4.5 54.1 1.0
CB A:ASP261 4.5 58.2 1.0
CZ A:ARG157 4.5 71.9 1.0
CD A:CD403 4.5 40.0 1.0
O A:HOH550 4.8 54.6 1.0
O A:HOH504 4.8 35.8 1.0

Cadmium binding site 4 out of 5 in 4nak

Go back to Cadmium Binding Sites List in 4nak
Cadmium binding site 4 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-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 Pentabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:54.2
occ:1.00
 OE2 A:GLU138 2.0 76.0 1.0
OE1 A:GLU141 2.3 49.6 1.0
OE2 A:GLU141 2.9 51.7 1.0
CD A:GLU141 2.9 51.2 1.0
CD A:GLU138 3.0 68.5 1.0
OE1 A:GLU138 3.4 65.5 1.0
O A:HOH563 4.3 49.4 1.0
CG A:GLU138 4.3 63.5 1.0
CG A:GLU141 4.4 46.4 1.0
CB A:GLU141 4.8 47.8 1.0

Cadmium binding site 5 out of 5 in 4nak

Go back to Cadmium Binding Sites List in 4nak
Cadmium binding site 5 out of 5 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-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 Pentabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd407

b:33.2
occ:1.00
 ND1 A:HIS271 2.3 29.0 1.0
O A:HOH507 2.5 35.8 1.0
CE1 A:HIS271 3.2 28.0 1.0
CG A:HIS271 3.4 26.8 1.0
CB A:HIS271 3.7 27.6 1.0
NE2 A:HIS271 4.3 28.0 1.0
CA A:HIS271 4.4 28.5 1.0
CD2 A:HIS271 4.5 26.4 1.0
CD1 A:LEU244 4.8 46.7 1.0
N A:HIS271 5.0 35.1 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 17:41:24 2024

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