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Potassium 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
Bromine (Br) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 6 binding sites of Potassium where determined in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin, PDB code: 4nak:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4nak

Go back to Potassium Binding Sites List in 4nak
Potassium binding site 1 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K408

b:70.7
occ:1.00
 OD2 A:ASP290 2.7 39.2 1.0
OD1 A:ASP290 3.3 62.9 1.0
CG A:ASP290 3.4 51.5 1.0
O A:LYS284 4.4 54.9 1.0
OG1 A:THR287 4.7 69.3 1.0
OG1 A:THR286 4.8 75.0 1.0
CB A:ASP290 4.9 54.2 1.0

Potassium binding site 2 out of 6 in 4nak

Go back to Potassium Binding Sites List in 4nak
Potassium binding site 2 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K409

b:45.8
occ:0.33
 S1 A:DTT402 2.8 52.4 1.0
O A:HOH538 3.2 59.7 1.0
CB A:ALA199 3.8 28.9 1.0
S4 A:DTT402 4.3 53.7 1.0
C1 A:DTT402 4.3 46.9 1.0
O A:HOH523 4.6 44.0 1.0
C2 A:DTT402 4.7 60.5 1.0
CA A:ALA199 5.0 28.8 1.0

Potassium binding site 3 out of 6 in 4nak

Go back to Potassium Binding Sites List in 4nak
Potassium binding site 3 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K410

b:47.1
occ:1.00
 O A:ILE283 2.8 38.5 1.0
OD1 A:ASN282 2.8 30.3 1.0
N A:LEU184 2.9 34.1 1.0
C A:ARG182 3.3 36.0 1.0
N A:PRO183 3.4 37.4 1.0
N A:ILE283 3.4 36.8 1.0
C A:ASN282 3.4 33.8 1.0
CA A:ARG182 3.5 34.8 1.0
CA A:ASN282 3.5 32.8 1.0
CA A:LEU184 3.6 35.9 1.0
CB A:ARG182 3.7 32.0 1.0
CD A:PRO183 3.7 39.1 1.0
CB A:LEU184 3.7 40.1 1.0
N A:VAL185 3.7 31.4 1.0
C A:ILE283 3.7 38.2 1.0
O A:ARG182 3.8 32.4 1.0
CG A:ASN282 3.9 30.0 1.0
C A:LEU184 3.9 34.8 1.0
C A:PRO183 3.9 34.6 1.0
O A:ASN282 4.0 35.0 1.0
O A:THR281 4.0 40.6 1.0
CA A:ILE283 4.1 37.5 1.0
CA A:PRO183 4.2 34.8 1.0
CG A:LEU184 4.2 44.1 1.0
CB A:ASN282 4.3 31.5 1.0
CG A:ARG182 4.3 34.1 1.0
CG A:PRO183 4.4 38.7 1.0
N A:ASN282 4.6 35.8 1.0
CD1 A:LEU184 4.6 44.8 1.0
CG1 A:ILE283 4.7 45.1 1.0
CA A:VAL185 4.7 28.8 1.0
O A:LEU184 4.8 37.1 1.0
C A:THR281 4.8 39.3 1.0
N A:ARG182 4.9 35.3 1.0
N A:LYS284 4.9 40.9 1.0

Potassium binding site 4 out of 6 in 4nak

Go back to Potassium Binding Sites List in 4nak
Potassium binding site 4 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K411

b:52.5
occ:1.00
 OG A:SER112 2.6 34.1 1.0
O A:SER180 2.7 38.5 1.0
O A:ILE108 2.8 39.8 1.0
N A:SER112 3.3 34.3 1.0
CB A:SER112 3.4 35.5 1.0
CA A:PRO183 3.4 34.8 1.0
O A:ALA109 3.5 36.1 1.0
C A:SER180 3.6 34.5 1.0
C A:ILE108 3.7 42.2 1.0
CA A:ALA109 3.7 42.8 1.0
C A:ALA109 3.7 41.4 1.0
N A:PRO183 3.7 37.4 1.0
O A:ARG182 3.8 32.4 1.0
CB A:PRO183 3.9 33.7 1.0
C A:ARG182 3.9 36.0 1.0
CA A:SER180 3.9 33.2 1.0
CA A:SER112 3.9 32.6 1.0
N A:ALA109 4.1 41.3 1.0
N A:TYR111 4.1 34.4 1.0
C A:TYR111 4.3 34.7 1.0
CB A:TYR111 4.3 38.3 1.0
CB A:SER180 4.3 33.5 1.0
CG2 A:ILE108 4.3 43.4 1.0
CA A:TYR111 4.4 36.6 1.0
CD A:PRO183 4.5 39.1 1.0
N A:ARG182 4.6 35.3 1.0
N A:LEU110 4.6 42.4 1.0
C A:PRO183 4.6 34.6 1.0
N A:PHE113 4.8 31.1 1.0
O A:PRO183 4.8 37.6 1.0
N A:ALA181 4.8 38.1 1.0
CG A:PRO183 4.8 38.7 1.0
CA A:ARG182 4.9 34.8 1.0
C A:SER112 4.9 30.5 1.0
NE2 A:HIS178 4.9 26.6 1.0
C A:LEU110 4.9 33.9 1.0
CA A:ILE108 4.9 41.3 1.0

Potassium binding site 5 out of 6 in 4nak

Go back to Potassium Binding Sites List in 4nak
Potassium binding site 5 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K412

b:55.9
occ:1.00
 O A:MET119 2.8 33.3 1.0
O A:SER117 3.1 38.2 1.0
CG1 A:VAL146 3.3 39.3 1.0
O A:VAL122 3.3 33.2 1.0
O A:ASP145 3.4 51.3 1.0
C A:MET119 3.5 33.5 1.0
C A:ASP145 4.0 49.9 1.0
CA A:PRO120 4.0 34.8 1.0
C A:SER117 4.1 35.9 1.0
N A:PRO120 4.1 34.3 1.0
N A:MET119 4.2 31.5 1.0
CB A:ASP145 4.3 57.7 1.0
C A:ARG118 4.4 36.0 1.0
C A:PRO120 4.4 32.9 1.0
O A:PRO120 4.4 35.9 1.0
C A:VAL122 4.4 31.4 1.0
CA A:MET119 4.5 30.6 1.0
N A:VAL146 4.6 41.6 1.0
CB A:VAL146 4.6 39.8 1.0
O A:PHE116 4.7 28.6 1.0
CB A:VAL122 4.7 28.6 1.0
O A:ARG118 4.7 37.6 1.0
N A:VAL122 4.7 28.3 1.0
CA A:ASP145 4.7 50.5 1.0
CA A:VAL146 4.8 40.7 1.0
N A:ARG118 4.8 34.2 1.0
CA A:ARG118 4.8 35.2 1.0
CA A:VAL122 4.8 29.1 1.0
OD2 A:ASP145 4.8 72.6 1.0
CA A:SER117 4.9 34.0 1.0
CG A:ASP145 4.9 69.4 1.0

Potassium binding site 6 out of 6 in 4nak

Go back to Potassium Binding Sites List in 4nak
Potassium binding site 6 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Arabidopsis Thaliana Ispd in Complex with Pentabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K413

b:48.9
occ:1.00
 OD2 A:ASP189 2.6 36.7 1.0
O A:HOH508 2.7 31.7 1.0
O A:HOH505 2.7 34.3 1.0
N A:ASN186 3.2 29.4 1.0
CG A:ASP189 3.5 35.1 1.0
CB A:ASP189 3.5 31.1 1.0
ND2 A:ASN186 3.6 44.7 1.0
CB A:ASN282 3.7 31.5 1.0
CA A:VAL185 3.8 28.8 1.0
OG A:SER279 3.9 39.0 1.0
CG2 A:VAL185 3.9 30.9 1.0
CB A:SER279 4.0 35.3 1.0
CB A:ASN186 4.0 38.1 1.0
CG A:ASN186 4.0 43.5 1.0
C A:VAL185 4.0 28.9 1.0
CG A:ASN282 4.1 30.0 1.0
CA A:ASN186 4.2 32.0 1.0
N A:SER279 4.2 31.4 1.0
ND2 A:ASN282 4.4 29.5 1.0
CB A:VAL185 4.5 29.9 1.0
O A:LEU184 4.5 37.1 1.0
CA A:SER279 4.6 32.2 1.0
O A:ASN186 4.6 27.1 1.0
CA A:ASN282 4.7 32.8 1.0
OD1 A:ASP189 4.7 36.7 1.0
O A:SER279 4.7 31.7 1.0
OD1 A:ASN282 4.7 30.3 1.0
N A:ASN282 4.7 35.8 1.0
OG1 A:THR281 4.8 41.1 1.0
CD1 A:LEU205 4.8 26.2 1.0
N A:VAL185 4.8 31.4 1.0
OD1 A:ASN186 4.9 50.2 1.0
C A:ASN186 4.9 29.0 1.0
CA A:ASP189 5.0 28.5 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: Sun Dec 13 23:46:00 2020

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