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Potassium in PDB 4nai: Arabidopsis Thaliana Ispd Apo

Enzymatic activity of Arabidopsis Thaliana Ispd Apo

All present enzymatic activity of Arabidopsis Thaliana Ispd Apo:
2.7.7.60;

Protein crystallography data

The structure of Arabidopsis Thaliana Ispd Apo, PDB code: 4nai 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 / 1.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 73.640, 73.640, 224.390, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 19.4

Other elements in 4nai:

The structure of Arabidopsis Thaliana Ispd Apo also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Potassium atom in the Arabidopsis Thaliana Ispd Apo (pdb code 4nai). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 14 binding sites of Potassium where determined in the Arabidopsis Thaliana Ispd Apo, PDB code: 4nai:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in 4nai

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Potassium binding site 1 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:25.4
occ:1.00
 O A:HOH595 2.4 43.8 1.0
OD1 A:ASP289 2.4 45.6 1.0
O A:HOH624 2.6 40.0 1.0
OD2 A:ASP289 2.6 43.0 1.0
CG A:ASP289 2.9 43.2 1.0
CB A:ASP289 4.4 35.7 1.0

Potassium binding site 2 out of 14 in 4nai

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Potassium binding site 2 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:27.5
occ:1.00
 O A:HOH540 2.5 33.5 1.0
O A:MET119 2.7 19.4 1.0
O A:HOH567 2.7 34.5 1.0
O A:ASP145 2.9 33.8 1.0
O A:VAL122 2.9 19.7 1.0
O A:SER117 2.9 20.2 1.0
CG1 A:VAL146 3.4 25.6 1.0
C A:MET119 3.6 19.6 1.0
C A:ASP145 3.8 31.9 1.0
C A:SER117 3.9 19.0 1.0
C A:VAL122 4.1 16.4 1.0
N A:MET119 4.1 20.7 1.0
CA A:PRO120 4.2 19.8 1.0
NZ A:LYS77 4.3 41.1 1.0
N A:PRO120 4.3 20.3 1.0
CB A:ASP145 4.3 38.9 1.0
C A:ARG118 4.4 23.6 1.0
CB A:VAL122 4.4 16.7 1.0
O A:PHE116 4.4 16.4 1.0
O A:PRO120 4.4 21.3 1.0
CA A:MET119 4.5 20.1 1.0
N A:VAL122 4.5 18.8 1.0
C A:PRO120 4.5 17.6 1.0
CA A:VAL122 4.5 17.4 1.0
O A:HOH619 4.6 42.4 1.0
N A:VAL146 4.6 23.7 1.0
CA A:ASP145 4.6 29.6 1.0
CA A:SER117 4.6 17.6 1.0
CB A:VAL146 4.7 23.3 1.0
N A:ARG118 4.7 19.4 1.0
O A:HOH569 4.7 36.7 1.0
O A:ARG118 4.8 27.9 1.0
CG A:ASP145 4.8 48.6 1.0
CA A:ARG118 4.8 22.1 1.0
CA A:VAL146 4.8 23.9 1.0
OD2 A:ASP145 4.9 54.3 1.0

Potassium binding site 3 out of 14 in 4nai

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Potassium binding site 3 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:30.2
occ:1.00
 OE1 A:GLN235 2.7 15.3 1.0
N A:SER279 2.7 15.5 1.0
K A:K406 2.9 29.7 1.0
CA A:GLY278 3.2 17.2 1.0
C A:GLY278 3.5 16.0 1.0
OD2 A:ASP189 3.5 20.9 1.0
CD1 A:LEU205 3.6 16.5 1.0
CB A:ASN282 3.6 14.3 1.0
O A:SER279 3.6 15.2 1.0
ND2 A:ASN282 3.7 13.4 1.0
CA A:SER279 3.8 16.5 1.0
CG A:ASP189 3.8 19.8 1.0
CD A:GLN235 3.8 15.0 1.0
CB A:ASP189 3.8 16.0 1.0
CB A:SER279 4.0 17.5 1.0
CG A:ASN282 4.1 15.0 1.0
C A:SER279 4.1 15.3 1.0
NE2 A:GLN235 4.2 16.2 1.0
CG A:LEU205 4.3 16.5 1.0
CD2 A:LEU205 4.3 15.3 1.0
CB A:LEU205 4.3 16.6 1.0
N A:GLY278 4.4 15.2 1.0
OG A:SER279 4.5 23.6 1.0
OD1 A:ASP189 4.7 23.5 1.0
O A:GLY278 4.7 18.3 1.0
O A:HOH501 4.7 19.6 1.0
CG2 A:VAL185 4.9 15.5 1.0
CA A:ASN282 5.0 14.5 1.0

Potassium binding site 4 out of 14 in 4nai

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Potassium binding site 4 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:29.7
occ:1.00
 O A:HOH501 2.6 19.6 1.0
OD2 A:ASP189 2.7 20.9 1.0
K A:K405 2.9 30.2 1.0
N A:ASN186 2.9 15.2 1.0
CB A:ASP189 3.5 16.0 1.0
ND2 A:ASN186 3.5 25.8 1.0
CA A:VAL185 3.5 15.2 1.0
CG A:ASP189 3.5 19.8 1.0
CB A:ASN282 3.6 14.3 1.0
CG2 A:VAL185 3.6 15.5 1.0
CG A:ASN186 3.7 27.4 1.0
CB A:ASN186 3.7 20.5 1.0
C A:VAL185 3.7 14.0 1.0
CA A:ASN186 3.9 17.2 1.0
CB A:SER279 3.9 17.5 1.0
CG A:ASN282 4.0 15.0 1.0
OG A:SER279 4.2 23.6 1.0
CB A:VAL185 4.2 14.7 1.0
O A:LEU184 4.3 16.8 1.0
ND2 A:ASN282 4.3 13.4 1.0
N A:SER279 4.4 15.5 1.0
OD1 A:ASN186 4.4 28.4 1.0
O A:ASN186 4.5 15.6 1.0
N A:VAL185 4.6 15.3 1.0
OD1 A:ASN282 4.6 15.2 1.0
CA A:ASN282 4.6 14.5 1.0
C A:ASN186 4.7 17.2 1.0
OD1 A:ASP189 4.7 23.5 1.0
N A:ASN282 4.8 15.5 1.0
CA A:SER279 4.8 16.5 1.0
O A:SER279 4.8 15.2 1.0
CD1 A:LEU205 4.8 16.5 1.0
OG1 A:THR281 4.9 19.1 1.0
C A:LEU184 4.9 14.6 1.0
CA A:ASP189 4.9 14.9 1.0
O A:VAL185 4.9 15.9 1.0

Potassium binding site 5 out of 14 in 4nai

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Potassium binding site 5 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:28.7
occ:1.00
 O A:ILE283 2.8 17.3 1.0
N A:LEU184 2.8 15.5 1.0
OD1 A:ASN282 2.8 15.2 1.0
C A:ARG182 3.1 15.9 1.0
N A:ILE283 3.3 16.2 1.0
CA A:ARG182 3.3 14.9 1.0
N A:PRO183 3.3 14.8 1.0
C A:ASN282 3.3 15.4 1.0
CB A:LEU184 3.4 18.3 1.0
CA A:LEU184 3.4 15.8 1.0
CA A:ASN282 3.5 14.5 1.0
CB A:ARG182 3.5 14.4 1.0
O A:ARG182 3.6 15.7 1.0
C A:ILE283 3.7 15.5 1.0
N A:VAL185 3.7 15.3 1.0
CD A:PRO183 3.7 16.5 1.0
CG A:ASN282 3.8 15.0 1.0
CG A:LEU184 3.8 20.1 1.0
C A:LEU184 3.8 14.6 1.0
O A:ASN282 3.9 16.4 1.0
C A:PRO183 3.9 15.7 1.0
CA A:ILE283 4.0 17.2 1.0
O A:THR281 4.1 16.8 1.0
CA A:PRO183 4.1 15.1 1.0
CB A:ASN282 4.2 14.3 1.0
CG A:ARG182 4.2 16.6 1.0
CG A:PRO183 4.4 16.7 1.0
CD1 A:LEU184 4.6 22.9 1.0
CG1 A:ILE283 4.6 20.4 1.0
N A:ASN282 4.7 15.5 1.0
O A:LEU184 4.7 16.8 1.0
N A:ARG182 4.7 15.3 1.0
CA A:VAL185 4.7 15.2 1.0
C A:THR281 4.8 15.6 1.0
N A:LYS284 4.9 18.2 1.0
ND2 A:ASN282 4.9 13.4 1.0
O A:ALA181 5.0 19.3 1.0
CB A:ILE283 5.0 18.1 1.0
CB A:PRO183 5.0 15.3 1.0

Potassium binding site 6 out of 14 in 4nai

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Potassium binding site 6 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:31.1
occ:1.00
 O A:SER180 2.7 17.8 1.0
O A:ILE108 2.7 19.0 1.0
OG A:SER112 2.7 15.6 1.0
N A:SER112 3.2 15.4 1.0
CB A:SER112 3.3 15.8 1.0
CA A:PRO183 3.3 15.1 1.0
O A:ALA109 3.5 18.4 1.0
CA A:ALA109 3.5 19.0 1.0
C A:ILE108 3.6 19.6 1.0
C A:ALA109 3.6 18.6 1.0
C A:SER180 3.7 16.7 1.0
CB A:PRO183 3.7 15.3 1.0
N A:PRO183 3.8 14.8 1.0
CA A:SER180 3.8 16.9 1.0
CA A:SER112 3.9 15.3 1.0
N A:ALA109 4.0 20.2 1.0
O A:ARG182 4.1 15.7 1.0
C A:ARG182 4.1 15.9 1.0
N A:TYR111 4.1 17.0 1.0
CG2 A:ILE108 4.2 27.4 1.0
CB A:SER180 4.2 19.1 1.0
C A:TYR111 4.2 15.4 1.0
CB A:TYR111 4.3 17.5 1.0
CA A:TYR111 4.4 16.5 1.0
CD A:PRO183 4.5 16.5 1.0
N A:LEU110 4.5 18.1 1.0
C A:PRO183 4.5 15.7 1.0
N A:ARG182 4.7 15.3 1.0
N A:PHE113 4.7 16.1 1.0
CG A:PRO183 4.7 16.7 1.0
O A:PRO183 4.7 16.8 1.0
CA A:ILE108 4.8 19.9 1.0
CB A:ALA109 4.8 20.4 1.0
C A:SER112 4.8 16.6 1.0
C A:LEU110 4.8 17.1 1.0
N A:ALA181 4.9 15.7 1.0

Potassium binding site 7 out of 14 in 4nai

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Potassium binding site 7 out of 14 in the Arabidopsis Thaliana Ispd Apo


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 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K409

b:35.0
occ:1.00
 OG1 A:THR115 2.7 18.2 1.0
O A:VAL185 2.7 15.9 1.0
O A:PRO183 2.8 16.8 1.0
CB A:THR115 3.4 16.6 1.0
CG1 A:VAL185 3.5 16.4 1.0
N A:VAL185 3.6 15.3 1.0
CA A:SER112 3.6 15.3 1.0
O A:HOH626 3.6 48.7 1.0
C A:PRO183 3.7 15.7 1.0
O A:TYR111 3.7 16.7 1.0
C A:VAL185 3.8 14.0 1.0
CG2 A:THR115 3.8 18.0 1.0
C A:LEU184 3.9 14.6 1.0
N A:SER112 3.9 15.4 1.0
C A:TYR111 4.0 15.4 1.0
CA A:VAL185 4.1 15.2 1.0
CB A:SER112 4.1 15.8 1.0
CA A:LEU184 4.2 15.8 1.0
N A:LEU184 4.2 15.5 1.0
O A:HOH611 4.4 40.0 1.0
CB A:VAL185 4.4 14.7 1.0
O A:LEU184 4.5 16.8 1.0
O A:HOH579 4.6 34.1 1.0
O A:HOH635 4.7 45.7 1.0
CA A:PRO183 4.7 15.1 1.0
C A:SER112 4.7 16.6 1.0
CA A:THR115 4.7 15.6 1.0
O A:SER112 4.8 16.8 1.0
CB A:TYR111 4.8 17.5 1.0
N A:THR115 5.0 16.2 1.0
O A:ARG182 5.0 15.7 1.0
N A:ASN186 5.0 15.2 1.0

Potassium binding site 8 out of 14 in 4nai

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Potassium binding site 8 out of 14 in the Arabidopsis Thaliana Ispd Apo


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Arabidopsis Thaliana Ispd Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K410

b:31.7
occ:0.33
 O A:HOH538 2.7 23.6 1.0
O A:HOH575 3.0 43.9 1.0
CB A:ALA199 3.7 17.9 1.0
O A:HOH514 4.3 25.1 1.0
O A:HOH528 4.4 28.3 1.0
O A:HOH543 4.6 33.6 1.0
O A:HOH566 4.7 34.3 1.0
CA A:ALA199 4.8 16.1 1.0

Potassium binding site 9 out of 14 in 4nai

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Potassium binding site 9 out of 14 in the Arabidopsis Thaliana Ispd Apo


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Arabidopsis Thaliana Ispd Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K411

b:35.0
occ:1.00
 CD A:CD401 2.3 19.2 0.5
O A:HOH520 2.7 25.9 1.0
O A:GLN166 2.8 19.8 1.0
O A:HOH518 2.8 33.2 1.0
O A:HOH587 3.1 43.3 1.0
OE2 A:GLU167 3.3 19.6 1.0
OE1 A:GLU167 3.4 18.7 1.0
CD A:GLU167 3.6 18.2 1.0
C A:GLN166 3.8 18.8 1.0
CB A:GLN166 4.4 22.9 1.0
CA A:GLU167 4.5 18.0 1.0
N A:GLU167 4.6 17.6 1.0
O A:HOH630 4.6 46.5 1.0
CA A:GLN166 4.7 18.0 1.0
CG A:GLU167 4.9 18.0 1.0

Potassium binding site 10 out of 14 in 4nai

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Potassium binding site 10 out of 14 in the Arabidopsis Thaliana Ispd Apo


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Arabidopsis Thaliana Ispd Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K412

b:39.0
occ:1.00
 OE1 A:GLU258 2.0 58.0 1.0
OE2 A:GLU156 2.1 52.3 1.0
OE1 A:GLU156 2.5 46.3 1.0
CD A:GLU156 2.6 41.8 1.0
OE2 A:GLU258 2.7 58.3 1.0
CD A:GLU258 2.7 54.2 1.0
CG A:GLU156 4.1 39.4 1.0
CG A:GLU258 4.2 49.1 1.0
O A:HOH612 4.7 52.0 1.0
OE1 A:GLN158 4.8 34.1 1.0
CB A:GLU258 4.8 44.1 1.0
CD A:GLN158 5.0 33.8 1.0
CB A:GLU156 5.0 31.7 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 11:37:51 2024

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