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Potassium in PDB 1ynh: Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli

Protein crystallography data

The structure of Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli, PDB code: 1ynh was solved by A.Tocilj, J.D.Schrag, Y.Li, B.L.Schneider, L.Reitzer, A.Matte, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.30 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.862, 166.915, 185.894, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli (pdb code 1ynh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli, PDB code: 1ynh:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1ynh

Go back to Potassium Binding Sites List in 1ynh
Potassium binding site 1 out of 4 in the Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2001

b:41.3
occ:1.00
 O A:ILE345 2.3 32.5 1.0
OD1 A:ASN343 2.4 32.2 1.0
O A:ALA341 2.5 34.4 1.0
O A:LEU339 2.5 25.2 1.0
O A:LEU338 2.6 24.3 1.0
C A:LEU339 3.1 27.0 1.0
CG A:ASN343 3.2 31.5 1.0
C A:ILE345 3.5 31.1 1.0
ND2 A:ASN343 3.5 30.0 1.0
CA A:LEU339 3.6 24.9 1.0
C A:ALA341 3.6 34.6 1.0
C A:LEU338 3.7 25.1 1.0
O A:ASN343 3.9 31.9 1.0
N A:ALA341 3.9 31.8 1.0
N A:ASN343 4.0 34.1 1.0
N A:ALA340 4.1 28.6 1.0
CB A:ILE345 4.1 30.6 1.0
N A:LEU339 4.1 24.9 1.0
CA A:ILE345 4.1 30.9 1.0
C A:ALA340 4.1 31.3 1.0
N A:ILE345 4.2 31.1 1.0
CA A:ALA341 4.2 33.1 1.0
O A:HOH2090 4.3 27.8 1.0
C A:ASN343 4.3 31.8 1.0
CB A:ASN343 4.4 31.7 1.0
CA A:ASN343 4.5 32.8 1.0
O A:ALA340 4.5 30.9 1.0
N A:SER346 4.5 30.1 1.0
CA A:ALA340 4.5 30.4 1.0
CB A:ALA341 4.6 32.1 1.0
CG2 A:ILE345 4.7 30.0 1.0
N A:ASP342 4.7 35.0 1.0
CA A:SER346 4.8 32.0 1.0
C A:ASP342 4.9 36.2 1.0
CA A:ASP342 4.9 36.7 1.0
CB A:LEU339 5.0 25.9 1.0

Potassium binding site 2 out of 4 in 1ynh

Go back to Potassium Binding Sites List in 1ynh
Potassium binding site 2 out of 4 in the Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2002

b:44.0
occ:1.00
 O B:ILE345 2.4 27.6 1.0
O B:LEU339 2.5 25.1 1.0
O B:ALA341 2.5 30.9 1.0
O B:LEU338 2.5 25.9 1.0
O B:HOH2068 2.5 25.8 1.0
OD1 B:ASN343 2.6 27.4 1.0
C B:LEU339 3.1 26.7 1.0
CG B:ASN343 3.1 29.2 1.0
ND2 B:ASN343 3.3 27.6 1.0
C B:ILE345 3.5 27.8 1.0
CA B:LEU339 3.5 26.0 1.0
C B:LEU338 3.6 26.7 1.0
C B:ALA341 3.6 32.3 1.0
O B:ASN343 3.8 31.2 1.0
N B:ALA341 4.0 30.2 1.0
N B:LEU339 4.0 25.2 1.0
N B:ASN343 4.0 32.2 1.0
N B:ALA340 4.1 27.1 1.0
CA B:ILE345 4.1 28.8 1.0
CB B:ILE345 4.2 29.8 1.0
N B:ILE345 4.2 28.9 1.0
C B:ALA340 4.2 29.8 1.0
CA B:ALA341 4.3 31.1 1.0
C B:ASN343 4.3 30.4 1.0
CB B:ASN343 4.4 30.2 1.0
O B:HOH2069 4.4 25.6 1.0
CA B:ASN343 4.5 30.9 1.0
N B:SER346 4.5 27.7 1.0
O B:ALA340 4.6 30.7 1.0
CA B:ALA340 4.6 28.1 1.0
N B:ASP342 4.7 33.3 1.0
CB B:ALA341 4.7 29.9 1.0
C B:ASP342 4.8 34.0 1.0
CG2 B:ILE345 4.8 27.8 1.0
CA B:SER346 4.8 26.1 1.0
CA B:ASP342 4.9 35.0 1.0
CA B:LEU338 4.9 27.1 1.0
CB B:LEU339 4.9 24.9 1.0

Potassium binding site 3 out of 4 in 1ynh

Go back to Potassium Binding Sites List in 1ynh
Potassium binding site 3 out of 4 in the Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K2003

b:72.2
occ:1.00
 O C:ILE345 2.5 36.4 1.0
O C:ALA341 2.6 42.1 1.0
O C:LEU339 2.7 35.4 1.0
OD1 C:ASN343 2.9 39.5 1.0
O C:ASN343 3.3 38.4 1.0
O C:LEU338 3.4 33.1 1.0
CG C:ASN343 3.5 39.2 1.0
C C:ILE345 3.5 37.0 1.0
C C:LEU339 3.6 34.2 1.0
C C:ALA341 3.8 42.2 1.0
N C:ASN343 3.8 40.9 1.0
ND2 C:ASN343 3.8 39.2 1.0
C C:ASN343 4.0 37.6 1.0
CA C:LEU339 4.2 34.5 1.0
N C:SER346 4.3 37.0 1.0
N C:ILE345 4.3 35.9 1.0
CA C:ASN343 4.3 39.2 1.0
CA C:ILE345 4.3 35.9 1.0
CA C:SER346 4.4 36.7 1.0
C C:ALA340 4.4 38.7 1.0
O C:ALA340 4.4 40.3 1.0
N C:ALA341 4.5 40.2 1.0
C C:LEU338 4.5 34.7 1.0
CB C:ASN343 4.5 39.8 1.0
N C:ALA340 4.6 36.1 1.0
C C:ASP342 4.6 42.8 1.0
CB C:ILE345 4.6 35.4 1.0
CA C:ASP342 4.7 43.7 1.0
N C:ASP342 4.7 43.5 1.0
CA C:ALA341 4.7 41.2 1.0
C C:PRO344 4.8 35.9 1.0
N C:LEU339 4.8 33.8 1.0
CA C:ALA340 4.9 37.5 1.0
N C:PRO344 4.9 36.6 1.0
CB C:SER346 5.0 37.7 1.0

Potassium binding site 4 out of 4 in 1ynh

Go back to Potassium Binding Sites List in 1ynh
Potassium binding site 4 out of 4 in the Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of N-Succinylarginine Dihydrolase, Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2004

b:63.7
occ:1.00
 O D:LEU339 2.4 32.9 1.0
O D:ALA341 2.5 36.4 1.0
O D:ILE345 2.5 30.8 1.0
OD1 D:ASN343 2.6 31.0 1.0
O D:HOH2124 2.6 28.8 1.0
O D:LEU338 2.7 30.7 1.0
C D:LEU339 3.1 33.0 1.0
CG D:ASN343 3.2 31.9 1.0
ND2 D:ASN343 3.5 31.8 1.0
C D:ILE345 3.5 30.9 1.0
CA D:LEU339 3.6 32.0 1.0
C D:ALA341 3.6 38.2 1.0
C D:LEU338 3.7 31.2 1.0
O D:ASN343 3.9 34.6 1.0
C D:ALA340 4.0 37.0 1.0
N D:ALA340 4.0 34.9 1.0
N D:ALA341 4.1 37.5 1.0
N D:ASN343 4.1 37.1 1.0
N D:LEU339 4.1 31.1 1.0
O D:ALA340 4.2 38.5 1.0
CA D:ILE345 4.2 32.0 1.0
N D:ILE345 4.3 31.8 1.0
CA D:ALA341 4.4 37.6 1.0
CB D:ILE345 4.4 33.0 1.0
C D:ASN343 4.4 34.0 1.0
N D:SER346 4.5 30.7 1.0
CB D:ASN343 4.5 33.4 1.0
CA D:ALA340 4.5 36.1 1.0
CA D:ASN343 4.6 35.2 1.0
CA D:SER346 4.6 30.2 1.0
N D:ASP342 4.7 39.4 1.0
C D:ASP342 4.8 39.0 1.0
CA D:ASP342 4.9 39.7 1.0
CB D:ALA341 4.9 37.6 1.0
OG D:SER346 4.9 31.4 1.0
CG2 D:ILE345 4.9 31.5 1.0
CB D:LEU339 4.9 30.8 1.0

Reference:

A.Tocilj, J.D.Schrag, Y.Li, B.L.Schneider, L.Reitzer, A.Matte, M.Cygler. Crystal Structure of N-Succinylarginine Dihydrolase Astb, Bound to Substrate and Product, An Enzyme From the Arginine Catabolic Pathway of Escherichia Coli. J.Biol.Chem. V. 280 15800 2005.
ISSN: ISSN 0021-9258
PubMed: 15703173
DOI: 10.1074/JBC.M413833200
Page generated: Sat Aug 9 02:58:49 2025

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