Atomistry » Cadmium » PDB 4l8q-4qdp » 4nak
Atomistry »
  Cadmium »
    PDB 4l8q-4qdp »
      4nak »

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: Sat Dec 12 08:25:15 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy