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Potassium in PDB 4nal: Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin

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

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

Protein crystallography data

The structure of Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin, PDB code: 4nal 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 (°) 74.460, 74.460, 224.500, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24.6

Other elements in 4nal:

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

Cadmium (Cd) 5 atoms
Bromine (Br) 3 atoms
Chlorine (Cl) 2 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 7 in 4nal

Go back to Potassium Binding Sites List in 4nal
Potassium binding site 1 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:62.1
occ:1.00
 OD2 A:ASP290 2.9 52.6 1.0
OD1 A:ASP290 3.1 64.4 1.0
CG A:ASP290 3.4 59.6 1.0
OG1 A:THR286 4.1 91.5 1.0
O A:LYS284 4.2 53.9 1.0
OG1 A:THR287 4.5 63.4 1.0
CG2 A:THR287 4.7 59.2 1.0
CB A:ASP290 4.9 61.9 1.0
O A:HOH534 5.0 40.0 1.0

Potassium binding site 2 out of 7 in 4nal

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Potassium binding site 2 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K409

b:60.7
occ:0.33
 S1 A:DTT402 2.8 58.9 1.0
O A:HOH549 3.0 61.1 1.0
CB A:ALA199 3.9 27.1 1.0
O3 A:DTT402 4.0 67.5 1.0
S4 A:DTT402 4.2 52.8 1.0
C1 A:DTT402 4.3 54.2 1.0
C2 A:DTT402 4.7 60.2 1.0
O A:HOH544 4.7 44.5 1.0
C3 A:DTT402 4.8 60.3 1.0

Potassium binding site 3 out of 7 in 4nal

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Potassium binding site 3 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K410

b:53.9
occ:1.00
 O A:ILE283 2.7 38.9 1.0
OD1 A:ASN282 2.9 30.8 1.0
N A:LEU184 3.0 34.3 1.0
N A:ILE283 3.3 39.3 1.0
C A:ASN282 3.4 36.9 1.0
CA A:ASN282 3.4 35.4 1.0
C A:ARG182 3.4 34.7 1.0
N A:PRO183 3.6 36.7 1.0
CA A:ARG182 3.6 35.0 1.0
CA A:LEU184 3.6 37.5 1.0
CB A:LEU184 3.7 41.6 1.0
C A:ILE283 3.7 40.6 1.0
O A:THR281 3.8 39.2 1.0
N A:VAL185 3.8 30.3 1.0
CD A:PRO183 3.9 38.2 1.0
O A:ARG182 3.9 32.9 1.0
CB A:ARG182 3.9 30.9 1.0
C A:LEU184 3.9 32.2 1.0
CG A:ASN282 3.9 31.6 1.0
O A:ASN282 4.0 37.3 1.0
C A:PRO183 4.1 37.5 1.0
CA A:ILE283 4.1 39.6 1.0
CG A:LEU184 4.1 47.0 1.0
CB A:ASN282 4.3 32.9 1.0
CA A:PRO183 4.3 37.2 1.0
CG A:PRO183 4.4 40.1 1.0
N A:ASN282 4.5 35.6 1.0
CG A:ARG182 4.5 32.4 1.0
CD1 A:LEU184 4.5 48.9 1.0
C A:THR281 4.6 39.0 1.0
CG1 A:ILE283 4.6 43.2 1.0
O A:LEU184 4.7 34.8 1.0
CA A:VAL185 4.9 29.5 1.0
N A:LYS284 4.9 41.4 1.0

Potassium binding site 4 out of 7 in 4nal

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Potassium binding site 4 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K411

b:58.2
occ:1.00
 OG A:SER112 2.7 32.8 1.0
O A:SER180 2.7 38.3 1.0
O A:ILE108 2.8 43.3 1.0
N A:SER112 3.3 36.6 1.0
O A:ALA109 3.4 39.8 1.0
CB A:SER112 3.4 37.9 1.0
CA A:PRO183 3.4 37.2 1.0
CA A:ALA109 3.6 44.0 1.0
C A:ALA109 3.6 45.2 1.0
C A:SER180 3.6 39.1 1.0
C A:ILE108 3.7 45.6 1.0
N A:PRO183 3.8 36.7 1.0
O A:ARG182 3.9 32.9 1.0
CA A:SER112 3.9 36.1 1.0
CA A:SER180 3.9 36.3 1.0
C A:ARG182 4.0 34.7 1.0
CB A:PRO183 4.1 38.8 1.0
N A:ALA109 4.1 44.0 1.0
N A:TYR111 4.2 36.9 1.0
C A:TYR111 4.3 38.7 1.0
CB A:TYR111 4.4 42.0 1.0
CG2 A:ILE108 4.4 47.2 1.0
CB A:SER180 4.4 40.4 1.0
CA A:TYR111 4.5 39.5 1.0
CD A:PRO183 4.5 38.2 1.0
N A:LEU110 4.6 44.9 1.0
C A:PRO183 4.6 37.5 1.0
N A:ARG182 4.6 38.3 1.0
O A:PRO183 4.7 38.4 1.0
N A:PHE113 4.7 33.3 1.0
N A:ALA181 4.8 40.2 1.0
C A:SER112 4.9 32.5 1.0
CB A:ALA109 4.9 44.8 1.0
NE2 A:HIS178 4.9 26.9 1.0
CA A:ARG182 4.9 35.0 1.0
C A:LEU110 5.0 37.9 1.0
CA A:ILE108 5.0 49.1 1.0
O A:ASP179 5.0 31.2 1.0
CG A:PRO183 5.0 40.1 1.0

Potassium binding site 5 out of 7 in 4nal

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Potassium binding site 5 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K412

b:46.0
occ:1.00
 O A:MET119 2.7 33.2 1.0
NZ A:LYS77 2.7 24.1 1.0
O A:SER117 2.8 35.9 1.0
O A:VAL122 3.2 33.0 1.0
O A:ASP145 3.2 47.8 1.0
CG1 A:VAL146 3.4 45.3 1.0
C A:MET119 3.5 30.4 1.0
C A:SER117 3.8 32.9 1.0
C A:ASP145 3.9 49.8 1.0
N A:MET119 4.1 31.7 1.0
CA A:PRO120 4.1 34.6 1.0
N A:PRO120 4.2 33.8 1.0
CB A:ASP145 4.2 59.1 1.0
CE A:LYS77 4.2 39.7 1.0
C A:VAL122 4.3 32.4 1.0
C A:ARG118 4.3 36.3 1.0
CA A:MET119 4.5 30.4 1.0
O A:PHE116 4.5 25.2 1.0
N A:VAL146 4.6 45.9 1.0
CB A:VAL122 4.6 27.9 1.0
C A:PRO120 4.6 34.4 1.0
CA A:ASP145 4.6 51.7 1.0
N A:ARG118 4.6 33.0 1.0
CA A:SER117 4.6 31.8 1.0
O A:PRO120 4.7 36.2 1.0
O A:ARG118 4.7 36.7 1.0
N A:VAL122 4.7 28.2 1.0
CB A:VAL146 4.7 46.2 1.0
CA A:ARG118 4.7 35.9 1.0
CA A:VAL122 4.7 29.0 1.0
CA A:VAL146 4.8 45.4 1.0
CD A:LYS77 4.9 53.0 1.0

Potassium binding site 6 out of 7 in 4nal

Go back to Potassium Binding Sites List in 4nal
Potassium binding site 6 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-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 Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K413

b:52.5
occ:1.00
 OD2 A:ASP189 2.6 33.1 1.0
O A:HOH501 2.6 29.3 1.0
O A:HOH509 2.7 34.4 1.0
N A:ASN186 3.3 30.5 1.0
CG A:ASP189 3.5 32.0 1.0
CB A:ASP189 3.6 28.1 1.0
ND2 A:ASN186 3.7 47.2 1.0
CB A:ASN282 3.7 32.9 1.0
CA A:VAL185 3.9 29.5 1.0
OG A:SER279 3.9 39.7 1.0
CB A:SER279 4.0 37.4 1.0
CB A:ASN186 4.0 39.4 1.0
CG2 A:VAL185 4.0 29.0 1.0
C A:VAL185 4.1 30.4 1.0
CG A:ASN186 4.1 45.4 1.0
N A:SER279 4.1 30.6 1.0
CG A:ASN282 4.2 31.6 1.0
CA A:ASN186 4.2 32.7 1.0
ND2 A:ASN282 4.4 29.0 1.0
O A:LEU184 4.5 34.8 1.0
CB A:VAL185 4.5 29.1 1.0
O A:SER279 4.6 32.3 1.0
CA A:SER279 4.6 33.3 1.0
OD1 A:ASP189 4.6 34.1 1.0
CA A:ASN282 4.7 35.4 1.0
O A:ASN186 4.7 28.0 1.0
OG1 A:THR281 4.7 38.4 1.0
N A:ASN282 4.7 35.6 1.0
OD1 A:ASN282 4.8 30.8 1.0
CD1 A:LEU205 4.8 26.9 1.0
N A:VAL185 4.9 30.3 1.0
OD1 A:ASN186 4.9 52.8 1.0
C A:ASN186 5.0 30.8 1.0
C A:SER279 5.0 33.9 1.0
CA A:ASP189 5.0 27.0 1.0

Potassium binding site 7 out of 7 in 4nal

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Potassium binding site 7 out of 7 in the Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Arabidopsis Thaliana Ispd in Complex with Tribromodichloro-Pseudilin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K414

b:43.0
occ:1.00
 O A:HOH507 2.7 46.1 1.0
OD2 A:ASP147 2.7 67.8 1.0
CG A:ASP147 3.9 63.8 1.0
CE A:LYS123 4.1 63.6 1.0
NZ A:LYS123 4.2 49.0 1.0
OD1 A:ASP147 4.3 67.4 1.0
OD2 A:ASP169 4.4 37.5 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 23:46:01 2020

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