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Copper in PDB 9ixe: Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86

Enzymatic activity of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86

All present enzymatic activity of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86:
3.5.3.25;

Protein crystallography data

The structure of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86, PDB code: 9ixe was solved by K.Oda, Y.Matoba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.65 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.502, 46.981, 59.559, 83.57, 84.69, 70.09
R / Rfree (%) 17.9 / 21.7

Other elements in 9ixe:

The structure of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86 (pdb code 9ixe). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86, PDB code: 9ixe:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 9ixe

Go back to Copper Binding Sites List in 9ixe
Copper binding site 1 out of 3 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:25.8
occ:0.70
 O B:HOH505 1.9 21.1 0.5
OD2 B:ASP113 2.0 18.6 1.0
OD2 B:ASP109 2.0 16.1 0.2
OD2 B:ASP109 2.1 15.2 0.8
O B:HOH633 2.2 28.2 1.0
SG B:CYS86 2.7 20.2 0.7
CG B:ASP113 2.9 17.0 1.0
OD2 B:ASP198 3.0 33.7 1.0
CG B:ASP109 3.0 22.0 0.8
OD1 B:ASP113 3.1 20.3 1.0
CG B:ASP109 3.2 19.1 0.2
SG B:CYS86 3.2 17.6 0.3
OD1 B:ASP109 3.3 20.3 0.8
CU B:CU1403 3.4 17.3 0.5
CU B:CU1402 3.4 22.9 0.6
CB B:CYS86 3.7 17.9 0.7
CB B:CYS86 3.7 17.9 0.3
OD1 B:ASP109 3.8 19.0 0.2
OH B:TYR107 3.9 17.7 1.0
CG B:ASP198 4.0 20.6 1.0
CB B:ASP198 4.1 17.0 1.0
O B:HOH693 4.2 27.8 1.0
O B:HOH645 4.3 25.9 1.0
CB B:ASP113 4.3 17.2 1.0
CE1 B:TYR107 4.3 15.4 1.0
CB B:ASP109 4.3 17.8 0.8
CB B:ASP109 4.4 17.4 0.2
O B:GLY126 4.4 22.6 1.0
CZ B:TYR107 4.6 18.9 1.0
ND1 B:HIS111 4.8 20.5 0.8
OD2 B:ASP200 4.8 23.8 1.0
CB B:HIS111 4.9 18.6 0.8

Copper binding site 2 out of 3 in 9ixe

Go back to Copper Binding Sites List in 9ixe
Copper binding site 2 out of 3 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:22.9
occ:0.58
 O B:HOH505 1.9 21.1 0.5
ND1 B:HIS111 2.0 20.5 0.8
OD2 B:ASP200 2.0 23.8 1.0
OD1 B:ASP109 2.1 20.3 0.8
OD1 B:ASP200 2.6 19.8 1.0
CG B:ASP200 2.6 23.5 1.0
CD2 B:HIS111 2.8 21.9 0.2
OD2 B:ASP198 2.8 33.7 1.0
CE1 B:HIS111 2.8 22.6 0.8
CG B:HIS111 3.1 18.0 0.8
OD1 B:ASP109 3.1 19.0 0.2
CG B:ASP109 3.1 22.0 0.8
OD2 B:ASP109 3.2 16.1 0.2
CG B:ASP109 3.4 19.1 0.2
CU B:CU1401 3.4 25.8 0.7
OD2 B:ASP109 3.5 15.2 0.8
CB B:HIS111 3.6 18.6 0.8
CG B:HIS111 3.6 19.2 0.2
CG B:ASP198 3.6 20.6 1.0
N B:HIS111 3.7 14.9 0.8
CB B:HIS111 3.8 19.6 0.2
NE2 B:HIS111 3.8 20.3 0.2
NE2 B:HIS111 4.0 22.3 0.8
N B:GLY110 4.0 17.2 0.8
N B:GLY110 4.1 17.3 0.2
N B:HIS111 4.1 15.7 0.2
CB B:ASP200 4.1 17.5 1.0
CD2 B:HIS111 4.1 20.7 0.8
OD1 B:ASP198 4.2 22.6 1.0
CA B:HIS111 4.2 19.1 0.8
C B:GLY110 4.4 15.6 0.8
CB B:ASP198 4.4 17.0 1.0
O B:HOH633 4.4 28.2 1.0
CA B:GLY110 4.5 14.8 0.8
O B:HOH693 4.5 27.8 1.0
CB B:ASP109 4.5 17.8 0.8
OD1 B:ASP113 4.6 20.3 1.0
CA B:HIS111 4.6 18.5 0.2
CB B:ASP109 4.7 17.4 0.2
CA B:GLY110 4.7 15.3 0.2
C B:GLY110 4.7 16.2 0.2
C B:ASP109 4.7 15.8 0.8
O B:HOH576 4.7 21.3 1.0
C B:ASP109 4.8 16.0 0.2
ND1 B:HIS111 4.8 20.9 0.2
CA B:ASP109 4.8 15.5 0.8
CA B:ASP109 4.9 15.7 0.2
OD2 B:ASP113 4.9 18.6 1.0
CE1 B:HIS111 4.9 22.7 0.2

Copper binding site 3 out of 3 in 9ixe

Go back to Copper Binding Sites List in 9ixe
Copper binding site 3 out of 3 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:17.3
occ:0.50
 NE2 B:HIS196 1.9 17.6 1.0
SG B:CYS86 2.1 20.2 0.7
SG B:CYS86 2.4 17.6 0.3
CE1 B:HIS196 2.8 20.3 1.0
CB B:CYS86 3.0 17.9 0.7
CB B:CYS86 3.0 17.9 0.3
CD2 B:HIS196 3.0 16.6 1.0
OH B:TYR107 3.3 17.7 1.0
CU B:CU1401 3.4 25.8 0.7
OD2 B:ASP109 3.4 15.2 0.8
CA B:CYS86 3.7 17.1 0.7
CA B:CYS86 3.7 17.1 0.3
CB B:ASP198 3.7 17.0 1.0
CZ B:TYR107 3.8 18.9 1.0
OD2 B:ASP109 3.8 16.1 0.2
ND1 B:HIS196 4.0 17.1 1.0
OD2 B:ASP113 4.0 18.6 1.0
CG B:HIS196 4.1 15.8 1.0
CE1 B:TYR107 4.1 15.4 1.0
OD2 B:ASP198 4.3 33.7 1.0
CE2 B:TYR107 4.5 19.3 1.0
CG B:ASP198 4.5 20.6 1.0
CB B:ALA240 4.5 15.5 1.0
CG B:ASP109 4.5 22.0 0.8
N B:ASP198 4.6 15.4 1.0
CA B:ASP198 4.6 15.3 1.0
C B:CYS86 4.6 16.4 1.0
O B:CYS86 4.6 18.0 1.0
O B:HOH633 4.7 28.2 1.0
N B:CYS86 4.7 15.5 1.0
O B:HOH622 4.7 19.6 1.0
O B:HOH505 4.9 21.1 0.5
CG B:ASP109 4.9 19.1 0.2
C B:ILE197 5.0 15.5 1.0

Reference:

K.Oda, Y.Matoba. Copper Inactivates Dcsb By Oxidizing the Metal Ligand CYS86 to Sulfinic Acid. Febs J. 2024.
ISSN: ISSN 1742-464X
DOI: 10.1111/FEBS.17325
Page generated: Mon Jul 14 09:59:14 2025

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