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Bromine in PDB 4nan: Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin

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

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

Protein crystallography data

The structure of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin, PDB code: 4nan 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) 15.00 / 1.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 75.120, 75.120, 224.130, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 24.7

Other elements in 4nan:

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

Cadmium (Cd) 4 atoms
Potassium (K) 6 atoms
Chlorine (Cl) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin (pdb code 4nan). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin, PDB code: 4nan:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 4nan

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Bromine binding site 1 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:56.6
occ:0.70
 BR1 A:2JM401 0.0 56.6 0.7
BR1 A:2JM401 1.6 49.6 0.3
C13 A:2JM401 2.0 53.3 0.7
C13 A:2JM401 2.1 42.2 0.3
N14 A:2JM401 2.5 39.9 0.3
N14 A:2JM401 3.0 48.1 0.7
O A:HOH537 3.0 79.2 1.0
C12 A:2JM401 3.0 51.9 0.7
C12 A:2JM401 3.3 40.9 0.3
CD A:CD403 3.3 62.2 1.0
OE1 A:GLN238 3.5 46.0 1.0
BR2 A:2JM401 3.7 49.3 0.7
C10 A:2JM401 3.7 39.0 0.3
CG2 A:VAL161 4.0 29.0 1.0
C11 A:2JM401 4.0 34.7 0.3
C10 A:2JM401 4.1 45.6 0.7
C11 A:2JM401 4.2 51.2 0.7
O A:HOH581 4.4 51.7 1.0
CL A:CL413 4.4 70.9 1.0
CG A:ARG157 4.4 61.4 1.0
BR2 A:2JM401 4.6 41.0 0.3
CD A:GLN238 4.7 37.8 1.0
CG2 A:ILE177 4.7 31.3 1.0
CD1 A:LEU84 4.8 35.4 1.0
C3 A:2JM401 4.9 37.5 0.3
CB A:ARG157 4.9 54.6 1.0

Bromine binding site 2 out of 8 in 4nan

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Bromine binding site 2 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:49.6
occ:0.30
 BR1 A:2JM401 0.0 49.6 0.3
BR1 A:2JM401 1.6 56.6 0.7
C13 A:2JM401 2.0 42.2 0.3
C13 A:2JM401 2.7 53.3 0.7
BR2 A:2JM401 2.9 49.3 0.7
N14 A:2JM401 2.9 39.9 0.3
C12 A:2JM401 3.0 40.9 0.3
C12 A:2JM401 3.1 51.9 0.7
BR2 A:2JM401 3.9 41.0 0.3
N14 A:2JM401 3.9 48.1 0.7
CA A:GLN158 4.0 42.1 1.0
N A:GLN158 4.0 45.9 1.0
C11 A:2JM401 4.1 34.7 0.3
CG2 A:VAL161 4.1 29.0 1.0
O A:HOH537 4.1 79.2 1.0
CD A:CD403 4.1 62.2 1.0
C10 A:2JM401 4.1 39.0 0.3
C A:ARG157 4.2 50.1 1.0
CB A:GLN158 4.2 43.1 1.0
O A:HOH581 4.3 51.7 1.0
O A:ARG157 4.3 41.8 1.0
CG A:ARG157 4.3 61.4 1.0
CB A:ARG157 4.3 54.6 1.0
C11 A:2JM401 4.4 51.2 0.7
OE1 A:GLN158 4.8 47.9 1.0
C10 A:2JM401 4.8 45.6 0.7
CB A:VAL161 4.8 29.1 1.0
CL A:CL413 4.9 70.9 1.0
CA A:ARG157 4.9 47.7 1.0

Bromine binding site 3 out of 8 in 4nan

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Bromine binding site 3 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:49.3
occ:0.70
 BR2 A:2JM401 0.0 49.3 0.7
BR2 A:2JM401 1.0 41.0 0.3
C12 A:2JM401 1.5 40.9 0.3
C12 A:2JM401 2.0 51.9 0.7
C13 A:2JM401 2.3 42.2 0.3
C11 A:2JM401 2.7 34.7 0.3
BR1 A:2JM401 2.9 49.6 0.3
C13 A:2JM401 3.0 53.3 0.7
C11 A:2JM401 3.1 51.2 0.7
N14 A:2JM401 3.5 39.9 0.3
BR1 A:2JM401 3.7 56.6 0.7
C10 A:2JM401 3.7 39.0 0.3
BR3 A:2JM401 3.8 27.3 0.3
BR3 A:2JM401 3.9 0.2 0.7
CD1 A:ILE265 3.9 55.8 1.0
CG1 A:VAL161 4.0 31.0 1.0
CB A:VAL161 4.1 29.1 1.0
CB A:GLN158 4.1 43.1 1.0
CZ A:PHE249 4.1 34.1 1.0
N14 A:2JM401 4.1 48.1 0.7
CG2 A:VAL161 4.2 29.0 1.0
C10 A:2JM401 4.2 45.6 0.7
CA A:GLN158 4.2 42.1 1.0
CG1 A:ILE265 4.5 53.8 1.0
CD1 A:LEU245 4.6 32.1 1.0
CE1 A:PHE249 4.7 37.2 1.0
CE2 A:PHE249 4.8 34.5 1.0
CB A:ILE265 4.8 53.2 1.0
O A:GLN158 4.9 35.8 1.0

Bromine binding site 4 out of 8 in 4nan

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Bromine binding site 4 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:41.0
occ:0.30
 BR2 A:2JM401 0.0 41.0 0.3
BR2 A:2JM401 1.0 49.3 0.7
C12 A:2JM401 2.0 40.9 0.3
C12 A:2JM401 2.5 51.9 0.7
C11 A:2JM401 2.9 34.7 0.3
C13 A:2JM401 3.1 42.2 0.3
C11 A:2JM401 3.2 51.2 0.7
CZ A:PHE249 3.4 34.1 1.0
BR3 A:2JM401 3.4 27.3 0.3
CD1 A:ILE265 3.5 55.8 1.0
BR3 A:2JM401 3.5 0.2 0.7
C13 A:2JM401 3.7 53.3 0.7
CD1 A:LEU245 3.8 32.1 1.0
CG1 A:VAL161 3.9 31.0 1.0
BR1 A:2JM401 3.9 49.6 0.3
CE2 A:PHE249 3.9 34.5 1.0
CE1 A:PHE249 4.1 37.2 1.0
C10 A:2JM401 4.1 39.0 0.3
N14 A:2JM401 4.2 39.9 0.3
CB A:VAL161 4.2 29.1 1.0
CG1 A:ILE265 4.2 53.8 1.0
CB A:GLN158 4.4 43.1 1.0
CB A:ILE265 4.4 53.2 1.0
C10 A:2JM401 4.5 45.6 0.7
BR1 A:2JM401 4.6 56.6 0.7
CG2 A:VAL161 4.6 29.0 1.0
CA A:GLN158 4.7 42.1 1.0
N14 A:2JM401 4.7 48.1 0.7
CG2 A:ILE265 4.9 56.4 1.0
CD2 A:PHE249 4.9 40.4 1.0
O A:GLN158 4.9 35.8 1.0
CG A:LEU245 5.0 29.4 1.0
CD1 A:PHE249 5.0 36.6 1.0

Bromine binding site 5 out of 8 in 4nan

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Bromine binding site 5 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:0.2
occ:0.70
 BR3 A:2JM401 0.0 0.2 0.7
BR3 A:2JM401 0.2 27.3 0.3
C11 A:2JM401 2.0 51.2 0.7
C11 A:2JM401 2.1 34.7 0.3
C10 A:2JM401 3.0 45.6 0.7
O2 A:2JM401 3.0 40.5 0.3
C12 A:2JM401 3.0 40.9 0.3
C12 A:2JM401 3.1 51.9 0.7
C10 A:2JM401 3.1 39.0 0.3
CD1 A:LEU245 3.3 32.1 1.0
C4 A:2JM401 3.4 37.5 0.3
C3 A:2JM401 3.5 37.7 0.7
BR2 A:2JM401 3.5 41.0 0.3
C3 A:2JM401 3.5 37.5 0.3
CG1 A:VAL266 3.6 52.0 1.0
C2 A:2JM401 3.6 35.0 0.7
BR2 A:2JM401 3.9 49.3 0.7
CG2 A:ILE265 3.9 56.4 1.0
CB A:ILE265 4.0 53.2 1.0
N14 A:2JM401 4.1 48.1 0.7
C13 A:2JM401 4.2 53.3 0.7
CD1 A:ILE240 4.2 26.9 1.0
C13 A:2JM401 4.2 42.2 0.3
N14 A:2JM401 4.3 39.9 0.3
N A:VAL266 4.4 53.7 1.0
C5 A:2JM401 4.5 36.6 0.3
C4 A:2JM401 4.6 40.1 0.7
C2 A:2JM401 4.6 38.1 0.3
CB A:VAL266 4.7 51.7 1.0
C1 A:2JM401 4.8 28.2 0.7
CG A:LEU245 4.8 29.4 1.0
CG1 A:ILE265 4.9 53.8 1.0
C A:ILE265 4.9 54.0 1.0
CA A:ILE265 4.9 53.5 1.0
CD1 A:ILE265 4.9 55.8 1.0
CA A:VAL266 5.0 50.3 1.0

Bromine binding site 6 out of 8 in 4nan

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Bromine binding site 6 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:27.3
occ:0.30
 BR3 A:2JM401 0.0 27.3 0.3
BR3 A:2JM401 0.2 0.2 0.7
C11 A:2JM401 1.8 51.2 0.7
C11 A:2JM401 1.9 34.7 0.3
C10 A:2JM401 2.8 45.6 0.7
C12 A:2JM401 2.9 40.9 0.3
C12 A:2JM401 2.9 51.9 0.7
O2 A:2JM401 2.9 40.5 0.3
C10 A:2JM401 3.0 39.0 0.3
C4 A:2JM401 3.4 37.5 0.3
CD1 A:LEU245 3.4 32.1 1.0
C3 A:2JM401 3.4 37.5 0.3
C3 A:2JM401 3.4 37.7 0.7
BR2 A:2JM401 3.4 41.0 0.3
C2 A:2JM401 3.6 35.0 0.7
CG1 A:VAL266 3.7 52.0 1.0
BR2 A:2JM401 3.8 49.3 0.7
CB A:ILE265 4.0 53.2 1.0
CG2 A:ILE265 4.0 56.4 1.0
N14 A:2JM401 4.0 48.1 0.7
C13 A:2JM401 4.0 53.3 0.7
C13 A:2JM401 4.0 42.2 0.3
N14 A:2JM401 4.1 39.9 0.3
CD1 A:ILE240 4.3 26.9 1.0
N A:VAL266 4.4 53.7 1.0
C5 A:2JM401 4.4 36.6 0.3
C4 A:2JM401 4.5 40.1 0.7
C2 A:2JM401 4.5 38.1 0.3
CB A:VAL266 4.7 51.7 1.0
C1 A:2JM401 4.7 28.2 0.7
CG A:LEU245 4.9 29.4 1.0
CG1 A:ILE265 4.9 53.8 1.0
CD1 A:ILE265 4.9 55.8 1.0
CA A:ILE265 4.9 53.5 1.0
C A:ILE265 5.0 54.0 1.0
CG2 A:VAL266 5.0 48.4 1.0

Bromine binding site 7 out of 8 in 4nan

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Bromine binding site 7 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:47.1
occ:0.70
 BR8 A:2JM401 0.0 47.1 0.7
C1 A:2JM401 1.7 38.2 0.3
C6 A:2JM401 1.9 40.0 0.3
C5 A:2JM401 1.9 38.4 0.7
O2 A:2JM401 2.7 37.7 0.7
C4 A:2JM401 2.7 40.1 0.7
C6 A:2JM401 2.9 29.9 0.7
C2 A:2JM401 3.0 38.1 0.3
C5 A:2JM401 3.2 36.6 0.3
CB A:VAL204 3.6 25.9 1.0
CG1 A:VAL204 3.7 27.4 1.0
CG2 A:VAL204 3.9 27.4 1.0
C3 A:2JM401 4.0 37.5 0.3
CG1 A:VAL273 4.1 28.5 1.0
C3 A:2JM401 4.1 37.7 0.7
C4 A:2JM401 4.1 37.5 0.3
C1 A:2JM401 4.2 28.2 0.7
CG2 A:VAL266 4.3 48.4 1.0
BR8 A:2JM401 4.4 39.8 0.3
SD A:MET234 4.6 38.2 1.0
CG A:GLN238 4.6 32.8 1.0
C2 A:2JM401 4.6 35.0 0.7
NE2 A:GLN238 4.7 45.5 1.0
CD A:GLN238 4.8 37.8 1.0

Bromine binding site 8 out of 8 in 4nan

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Bromine binding site 8 out of 8 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Arabidopsis Thaliana Ispd in Complex with Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:39.8
occ:0.30
 BR8 A:2JM401 0.0 39.8 0.3
C1 A:2JM401 0.6 28.2 0.7
C6 A:2JM401 1.5 29.9 0.7
C5 A:2JM401 1.8 36.6 0.3
C2 A:2JM401 1.9 35.0 0.7
C5 A:2JM401 2.7 38.4 0.7
C6 A:2JM401 2.8 40.0 0.3
C4 A:2JM401 2.8 37.5 0.3
C3 A:2JM401 2.9 37.7 0.7
O2 A:2JM401 3.0 40.5 0.3
O A:VAL239 3.2 27.8 1.0
C4 A:2JM401 3.2 40.1 0.7
O A:ALA203 3.4 23.9 1.0
N A:VAL239 3.7 24.4 1.0
C A:VAL239 3.9 28.4 1.0
CB A:GLN238 3.9 27.9 1.0
N A:ALA203 3.9 22.8 1.0
C A:GLN238 4.0 28.3 1.0
C3 A:2JM401 4.0 37.5 0.3
C1 A:2JM401 4.1 38.2 0.3
CA A:GLN238 4.1 26.5 1.0
C A:ALA203 4.1 24.4 1.0
CB A:ILE240 4.2 28.2 1.0
CB A:ALA202 4.2 26.7 1.0
C10 A:2JM401 4.3 45.6 0.7
BR8 A:2JM401 4.4 47.1 0.7
CA A:ALA202 4.4 24.2 1.0
CA A:VAL239 4.4 25.2 1.0
C A:ALA202 4.5 26.9 1.0
O2 A:2JM401 4.5 37.7 0.7
C2 A:2JM401 4.6 38.1 0.3
CG1 A:VAL266 4.6 52.0 1.0
N A:ILE240 4.6 23.0 1.0
CG1 A:VAL273 4.6 28.5 1.0
CA A:ALA203 4.7 21.8 1.0
CG A:GLN238 4.7 32.8 1.0
O A:GLN238 4.8 29.3 1.0
CA A:ILE240 4.8 25.4 1.0
CG2 A:ILE240 4.8 31.2 1.0
CD1 A:ILE240 4.8 26.9 1.0
CG1 A:ILE240 5.0 26.0 1.0
CB A:VAL204 5.0 25.9 1.0
N A:VAL204 5.0 22.6 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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