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Bromine 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:

Cadmium (Cd) 5 atoms
Potassium (K) 6 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 5 binding sites of Bromine where determined in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin, PDB code: 4nak:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in 4nak

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Bromine 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 Bromine with other atoms in the Br 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:Br401

b:35.0
occ:1.00
 BR13 A:PBQ401 0.0 35.0 1.0
CE2 A:PBQ401 1.8 33.7 1.0
C3 A:PBQ401 2.8 35.6 1.0
CD2 A:PBQ401 2.8 35.3 1.0
O A:VAL239 3.3 26.2 1.0
O A:ALA203 3.6 24.1 1.0
N A:VAL239 3.8 23.0 1.0
C A:VAL239 3.9 23.7 1.0
N A:ALA203 3.9 24.6 1.0
CB A:ALA202 4.0 24.8 1.0
CB A:GLN238 4.0 28.1 1.0
C A:GLN238 4.1 25.4 1.0
CH A:PBQ401 4.1 41.2 1.0
C A:ALA203 4.1 24.4 1.0
CG A:PBQ401 4.1 37.5 1.0
CB A:ILE240 4.2 24.6 1.0
CA A:GLN238 4.2 24.5 1.0
CA A:ALA202 4.4 24.1 1.0
C A:ALA202 4.4 25.1 1.0
CG1 A:VAL266 4.5 51.3 1.0
CA A:VAL239 4.5 22.6 1.0
CA A:ALA203 4.6 23.0 1.0
CG1 A:VAL273 4.6 27.1 1.0
N A:ILE240 4.6 22.0 1.0
CR A:PBQ401 4.6 37.7 1.0
O A:GLN238 4.7 27.8 1.0
CA A:ILE240 4.8 23.2 1.0
CB A:VAL204 4.8 25.5 1.0
N A:VAL204 4.8 23.6 1.0
CD1 A:ILE240 4.9 28.6 1.0
CG2 A:ILE240 4.9 29.8 1.0
CG1 A:ILE240 5.0 26.2 1.0

Bromine binding site 2 out of 5 in 4nak

Go back to Bromine Binding Sites List in 4nak
Bromine 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 Bromine with other atoms in the Br 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:Br401

b:63.6
occ:1.00
 BR14 A:PBQ401 0.0 63.6 1.0
CH A:PBQ401 1.8 41.2 1.0
C3 A:PBQ401 2.7 35.6 1.0
CR A:PBQ401 2.9 37.7 1.0
O A:PBQ401 3.1 37.2 1.0
CE2 A:PBQ401 4.1 33.7 1.0
CG A:PBQ401 4.1 37.5 1.0
CG2 A:VAL266 4.2 43.0 1.0
CG1 A:VAL204 4.3 28.6 1.0
NE2 A:GLN238 4.4 35.1 1.0
SD A:MET234 4.4 35.7 1.0
OG A:SER264 4.5 49.4 1.0
CG A:MET234 4.6 34.3 1.0
CD2 A:PBQ401 4.6 35.3 1.0
CB A:VAL204 4.6 25.5 1.0
CG2 A:VAL204 4.7 26.4 1.0
CG1 A:VAL273 4.8 27.1 1.0
CD A:GLN238 4.8 36.7 1.0
CD A:CD403 4.9 40.0 1.0
OE1 A:GLN238 5.0 35.7 1.0

Bromine binding site 3 out of 5 in 4nak

Go back to Bromine Binding Sites List in 4nak
Bromine 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 Bromine with other atoms in the Br 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:Br401

b:45.8
occ:1.00
 BR17 A:PBQ401 0.0 45.8 1.0
C9 A:PBQ401 1.9 43.4 1.0
CD1 A:PBQ401 2.9 39.1 1.0
C8 A:PBQ401 2.9 45.2 1.0
CD2 A:PBQ401 3.3 35.3 1.0
CG A:PBQ401 3.4 37.5 1.0
CD1 A:LEU245 3.6 31.1 1.0
BR18 A:PBQ401 3.6 45.4 1.0
CB A:ILE265 3.7 39.8 1.0
CG1 A:VAL266 3.7 51.3 1.0
CG2 A:ILE265 4.0 56.1 1.0
N11 A:PBQ401 4.0 37.8 1.0
C7 A:PBQ401 4.1 44.1 1.0
N A:VAL266 4.2 46.0 1.0
CD1 A:ILE240 4.3 28.6 1.0
CG1 A:ILE265 4.4 50.5 1.0
CE2 A:PBQ401 4.5 33.7 1.0
CB A:VAL266 4.6 44.4 1.0
CR A:PBQ401 4.6 37.7 1.0
CA A:ILE265 4.7 45.1 1.0
CG2 A:VAL266 4.7 43.0 1.0
N A:ILE265 4.8 42.4 1.0
CD1 A:ILE177 4.8 31.5 1.0
C A:ILE265 4.9 44.4 1.0
CG2 A:ILE240 4.9 29.8 1.0
CA A:VAL266 5.0 46.7 1.0
CG A:LEU245 5.0 31.4 1.0

Bromine binding site 4 out of 5 in 4nak

Go back to Bromine Binding Sites List in 4nak
Bromine 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 Bromine with other atoms in the Br 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:Br401

b:45.4
occ:1.00
 BR18 A:PBQ401 0.0 45.4 1.0
C8 A:PBQ401 1.9 45.2 1.0
C7 A:PBQ401 2.9 44.1 1.0
C9 A:PBQ401 2.9 43.4 1.0
BR19 A:PBQ401 3.6 48.1 1.0
BR17 A:PBQ401 3.6 45.8 1.0
CG1 A:ILE265 3.7 50.5 1.0
CG1 A:VAL161 3.7 35.8 1.0
CZ A:PHE249 3.8 35.2 1.0
CB A:VAL161 3.9 34.2 1.0
N11 A:PBQ401 4.0 37.8 1.0
CD1 A:PBQ401 4.1 39.1 1.0
CB A:GLN158 4.1 40.9 1.0
CG2 A:VAL161 4.2 33.4 1.0
CA A:GLN158 4.2 36.3 1.0
CD1 A:LEU245 4.3 31.1 1.0
CB A:ILE265 4.3 39.8 1.0
CE2 A:PHE249 4.4 32.8 1.0
CE1 A:PHE249 4.4 36.6 1.0
O A:GLN158 4.6 34.1 1.0
CD1 A:ILE265 4.9 50.4 1.0
C A:GLN158 5.0 35.9 1.0

Bromine binding site 5 out of 5 in 4nak

Go back to Bromine Binding Sites List in 4nak
Bromine 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 Bromine with other atoms in the Br 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:Br401

b:48.1
occ:1.00
 BR19 A:PBQ401 0.0 48.1 1.0
C7 A:PBQ401 1.8 44.1 1.0
N11 A:PBQ401 2.8 37.8 1.0
C8 A:PBQ401 2.9 45.2 1.0
BR18 A:PBQ401 3.6 45.4 1.0
CG A:ARG157 3.7 52.7 1.0
CD A:CD403 3.9 40.0 1.0
CD1 A:PBQ401 4.0 39.1 1.0
C9 A:PBQ401 4.0 43.4 1.0
O A:HOH526 4.1 57.5 1.0
CG2 A:VAL161 4.1 33.4 1.0
N A:GLN158 4.1 35.8 1.0
CA A:GLN158 4.2 36.3 1.0
CB A:ARG157 4.2 46.8 1.0
C A:ARG157 4.3 36.6 1.0
O A:HOH543 4.5 50.8 1.0
CB A:GLN158 4.5 40.9 1.0
O A:ARG157 4.5 35.0 1.0
CB A:VAL161 4.9 34.2 1.0
CA A:ARG157 4.9 42.0 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: Wed Jul 10 22:07:13 2024

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