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Potassium 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
Bromine (Br) 8 atoms
Chlorine (Cl) 1 atom

Potassium Binding Sites:

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

Potassium binding site 1 out of 6 in 4nan

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Potassium binding site 1 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:86.8
occ:1.00
 OD2 A:ASP290 2.4 47.3 1.0
OD1 A:ASP290 2.9 59.3 1.0
CG A:ASP290 3.0 55.2 1.0
OG1 A:THR286 3.6 89.5 1.0
O A:LYS284 4.2 49.1 1.0
CG2 A:THR287 4.3 73.1 1.0
CB A:ASP290 4.6 55.5 1.0
OG1 A:THR287 4.6 71.2 1.0
CB A:THR286 4.9 89.6 1.0

Potassium binding site 2 out of 6 in 4nan

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Potassium binding site 2 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:45.1
occ:0.33
 S1 A:DTT402 2.8 52.9 1.0
O A:HOH549 2.9 53.4 1.0
CB A:ALA199 3.9 31.1 1.0
O3 A:DTT402 3.9 57.5 1.0
C1 A:DTT402 3.9 52.8 1.0
O A:HOH534 4.4 42.3 1.0
S4 A:DTT402 4.5 54.6 1.0
C2 A:DTT402 4.8 49.3 1.0
C3 A:DTT402 4.9 53.4 1.0
CA A:ALA199 5.0 31.3 1.0

Potassium binding site 3 out of 6 in 4nan

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Potassium binding site 3 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K409

b:56.6
occ:1.00
 N A:LEU184 2.8 31.8 1.0
O A:ILE283 2.8 36.1 1.0
OD1 A:ASN282 2.8 31.4 1.0
C A:ARG182 3.1 36.8 1.0
N A:PRO183 3.2 38.2 1.0
CA A:ARG182 3.4 33.0 1.0
CA A:LEU184 3.4 36.8 1.0
C A:ASN282 3.4 35.2 1.0
N A:ILE283 3.4 39.8 1.0
CB A:LEU184 3.5 39.3 1.0
CA A:ASN282 3.5 34.9 1.0
N A:VAL185 3.6 34.0 1.0
O A:ARG182 3.6 30.8 1.0
C A:LEU184 3.7 31.9 1.0
CB A:ARG182 3.7 31.7 1.0
C A:ILE283 3.8 37.4 1.0
C A:PRO183 3.8 35.2 1.0
CD A:PRO183 3.8 41.1 1.0
CG A:ASN282 3.9 33.2 1.0
CG A:LEU184 3.9 42.8 1.0
O A:ASN282 3.9 35.9 1.0
CA A:PRO183 4.0 36.6 1.0
O A:THR281 4.1 37.7 1.0
CA A:ILE283 4.1 38.9 1.0
CB A:ASN282 4.3 34.5 1.0
CG A:PRO183 4.4 44.2 1.0
CG A:ARG182 4.4 34.3 1.0
O A:LEU184 4.5 34.0 1.0
N A:ASN282 4.6 36.6 1.0
CA A:VAL185 4.6 26.6 1.0
CD1 A:LEU184 4.7 48.8 1.0
N A:ARG182 4.8 32.1 1.0
CG1 A:ILE283 4.8 48.0 1.0
C A:THR281 4.8 41.0 1.0
CB A:PRO183 4.9 39.2 1.0
O A:PRO183 4.9 38.8 1.0
N A:LYS284 5.0 34.8 1.0

Potassium binding site 4 out of 6 in 4nan

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Potassium binding site 4 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K410

b:63.8
occ:1.00
 O A:SER180 2.6 38.7 1.0
O A:ILE108 2.6 38.8 1.0
OG A:SER112 2.8 33.9 1.0
N A:SER112 3.3 33.0 1.0
CB A:SER112 3.3 35.0 1.0
CA A:PRO183 3.5 36.6 1.0
O A:ALA109 3.5 37.8 1.0
C A:ILE108 3.5 41.9 1.0
CA A:ALA109 3.5 42.7 1.0
C A:SER180 3.6 35.0 1.0
C A:ALA109 3.6 42.2 1.0
CA A:SER180 3.8 35.9 1.0
N A:ALA109 3.9 38.1 1.0
CA A:SER112 3.9 32.2 1.0
N A:PRO183 3.9 38.2 1.0
CB A:PRO183 4.0 39.2 1.0
O A:ARG182 4.0 30.8 1.0
C A:ARG182 4.1 36.8 1.0
CB A:SER180 4.2 37.2 1.0
N A:TYR111 4.2 33.1 1.0
CB A:TYR111 4.2 36.0 1.0
C A:TYR111 4.3 38.4 1.0
CG2 A:ILE108 4.4 40.0 1.0
N A:LEU110 4.4 41.6 1.0
CD A:PRO183 4.4 41.1 1.0
CA A:TYR111 4.5 33.9 1.0
C A:PRO183 4.6 35.2 1.0
N A:ARG182 4.7 32.1 1.0
CA A:ILE108 4.7 42.6 1.0
N A:ALA181 4.7 36.6 1.0
O A:PRO183 4.8 38.8 1.0
CB A:ALA109 4.8 41.4 1.0
N A:PHE113 4.8 30.1 1.0
CG A:PRO183 4.9 44.2 1.0
C A:SER112 4.9 31.8 1.0
C A:LEU110 4.9 32.5 1.0
O A:ASP179 5.0 32.4 1.0

Potassium binding site 5 out of 6 in 4nan

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Potassium binding site 5 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K411

b:51.4
occ:1.00
 O A:MET119 2.7 34.8 1.0
O A:SER117 2.9 35.3 1.0
O A:VAL122 3.1 35.1 1.0
CG1 A:VAL146 3.3 43.6 1.0
O A:ASP145 3.3 51.9 1.0
C A:MET119 3.6 36.3 1.0
C A:SER117 3.9 34.6 1.0
C A:ASP145 4.0 50.0 1.0
N A:MET119 4.1 35.4 1.0
CA A:PRO120 4.1 36.4 1.0
C A:VAL122 4.1 33.1 1.0
N A:PRO120 4.2 35.0 1.0
CB A:ASP145 4.3 54.5 1.0
O A:PRO120 4.4 38.6 1.0
CB A:VAL122 4.4 29.6 1.0
C A:ARG118 4.4 43.2 1.0
C A:PRO120 4.4 35.2 1.0
CA A:MET119 4.4 35.2 1.0
N A:VAL122 4.5 28.5 1.0
O A:PHE116 4.5 27.2 1.0
CA A:VAL122 4.5 26.5 1.0
CB A:VAL146 4.6 38.5 1.0
N A:VAL146 4.6 44.6 1.0
OD2 A:ASP145 4.6 57.5 1.0
CA A:SER117 4.6 30.5 1.0
N A:ARG118 4.7 36.6 1.0
CA A:ASP145 4.7 45.9 1.0
CA A:VAL146 4.8 39.4 1.0
CA A:ARG118 4.8 39.8 1.0
O A:ARG118 4.8 37.0 1.0

Potassium binding site 6 out of 6 in 4nan

Go back to Potassium Binding Sites List in 4nan
Potassium binding site 6 out of 6 in the Arabidopsis Thaliana Ispd in Complex with Tetrabromo-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 Tetrabromo-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K412

b:58.2
occ:1.00
 OD2 A:ASP189 2.5 35.9 1.0
O A:HOH519 2.6 29.8 1.0
O A:HOH516 2.8 37.1 1.0
N A:ASN186 3.2 29.8 1.0
CG A:ASP189 3.3 32.1 1.0
CB A:ASP189 3.4 30.9 1.0
ND2 A:ASN186 3.4 43.2 1.0
CB A:ASN282 3.8 34.5 1.0
CA A:VAL185 3.8 26.6 1.0
CB A:ASN186 3.8 42.7 1.0
CG2 A:VAL185 3.8 30.4 1.0
OG A:SER279 3.8 40.9 1.0
CG A:ASN186 3.9 45.3 1.0
CB A:SER279 3.9 38.7 1.0
C A:VAL185 4.0 30.3 1.0
CA A:ASN186 4.1 34.8 1.0
N A:SER279 4.2 34.9 1.0
CG A:ASN282 4.2 33.2 1.0
ND2 A:ASN282 4.4 28.0 1.0
CB A:VAL185 4.4 29.8 1.0
OD1 A:ASP189 4.5 39.2 1.0
O A:LEU184 4.5 34.0 1.0
O A:ASN186 4.5 27.0 1.0
CA A:SER279 4.6 35.6 1.0
CD1 A:LEU205 4.7 30.1 1.0
O A:SER279 4.7 31.7 1.0
OD1 A:ASN186 4.7 48.4 1.0
CA A:ASN282 4.7 34.9 1.0
CA A:ASP189 4.8 25.7 1.0
C A:ASN186 4.9 34.6 1.0
N A:ASN282 4.9 36.6 1.0
OD1 A:ASN282 4.9 31.4 1.0
OG1 A:THR281 4.9 39.4 1.0
N A:VAL185 4.9 34.0 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: Mon Aug 12 11:38:23 2024

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