Copper in PDB 9ixd: Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86

All present enzymatic activity of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86:
3.5.3.25;

The structure of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86, PDB code: 9ixd 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)	44.22 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.4, 47.145, 59.393, 83.69, 84.7, 70.27
R / Rfree (%)	16.8 / 20.5

The structure of Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86 also contains other interesting chemical elements:

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

The binding sites of Copper atom in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86 (pdb code 9ixd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with Oxidized CYS86, PDB code: 9ixd:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with 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 with Oxidized CYS86 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:16.9 occ:0.53 OD B:CSD86 1.8 17.5 0.2 OD2 B:ASP109 2.0 14.7 0.7 OD2 B:ASP109 2.1 14.4 0.3 OD2 B:ASP113 2.2 18.2 1.0 O B:HOH603 2.2 27.4 1.0 O B:HOH647 2.2 28.9 1.0 OD2 B:CSD86 2.3 16.3 0.3 SG B:CSD86 2.4 17.1 0.5 OD2 B:ASP198 2.4 20.9 1.0 SG B:CSD86 2.7 18.3 0.2 SG B:CSD86 2.8 18.3 0.3 CG B:ASP109 2.9 16.7 0.7 CG B:ASP113 3.1 15.8 1.0 OD1 B:ASP109 3.2 14.7 0.7 CG B:ASP109 3.2 15.9 0.3 CU B:CU1402 3.3 21.2 0.5 OD1 B:ASP113 3.4 19.4 1.0 CG B:ASP198 3.4 17.5 1.0 CB B:CSD86 3.5 18.6 0.5 CB B:CSD86 3.5 18.6 0.3 CB B:CSD86 3.6 18.5 0.2 CB B:ASP198 3.6 14.5 1.0 OD1 B:ASP109 3.8 15.5 0.3 MG B:MG403 3.9 15.5 0.5 O B:HOH672 3.9 28.8 1.0 OH B:TYR107 4.0 17.3 1.0 OD1 B:CSD86 4.1 16.4 0.3 CB B:ASP109 4.3 15.7 0.7 CE1 B:TYR107 4.3 12.9 1.0 CB B:ASP109 4.4 15.4 0.3 O B:GLY126 4.5 24.1 1.0 CB B:ASP113 4.5 15.1 1.0 OD1 B:ASP198 4.6 18.1 1.0 CZ B:TYR107 4.6 17.0 1.0 OD2 B:ASP200 4.6 20.7 1.0 NE2 B:HIS196 4.7 21.1 1.0 CA B:CSD86 4.9 15.7 0.5 CA B:CSD86 5.0 15.7 0.3 ND1 B:HIS111 5.0 19.6 0.7

Copper binding site 2 out of 2 in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase with 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 with Oxidized CYS86 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:21.2 occ:0.51 O B:HOH603 1.9 27.4 1.0 OD2 B:ASP200 1.9 20.7 1.0 OD1 B:ASP109 2.1 14.7 0.7 ND1 B:HIS111 2.1 19.6 0.7 CG B:ASP200 2.6 20.8 1.0 OD1 B:ASP200 2.6 19.2 1.0 OD2 B:ASP198 2.7 20.9 1.0 CD2 B:HIS111 3.0 21.8 0.3 CE1 B:HIS111 3.0 23.1 0.7 MG B:MG403 3.0 15.5 0.5 CG B:ASP109 3.1 16.7 0.7 O B:HOH672 3.2 28.8 1.0 CG B:HIS111 3.2 19.4 0.7 OD1 B:ASP109 3.2 15.5 0.3 OD2 B:ASP109 3.3 14.4 0.3 CU B:CU401 3.3 16.9 0.5 CG B:ASP198 3.4 17.5 1.0 CG B:ASP109 3.5 15.9 0.3 OD2 B:ASP109 3.5 14.7 0.7 CB B:HIS111 3.6 18.2 0.7 N B:HIS111 3.7 14.8 0.7 CG B:HIS111 3.8 19.4 0.3 OD1 B:ASP198 4.0 18.1 1.0 CB B:HIS111 4.0 18.2 0.3 NE2 B:HIS111 4.0 20.7 0.3 CB B:ASP200 4.1 17.8 1.0 N B:GLY110 4.1 14.8 0.7 N B:GLY110 4.1 14.8 0.3 O B:HOH647 4.1 28.9 1.0 NE2 B:HIS111 4.2 25.1 0.7 N B:HIS111 4.2 16.4 0.3 CD2 B:HIS111 4.3 22.3 0.7 CA B:HIS111 4.3 17.1 0.7 CB B:ASP198 4.3 14.5 1.0 OD1 B:ASP113 4.3 19.4 1.0 CB B:ASP109 4.4 15.7 0.7 C B:GLY110 4.5 15.5 0.7 O B:HOH576 4.6 22.9 1.0 CA B:GLY110 4.6 14.6 0.7 OD2 B:ASP113 4.7 18.2 1.0 CB B:ASP109 4.7 15.4 0.3 CA B:HIS111 4.8 16.6 0.3 OD B:CSD86 4.8 17.5 0.2 CA B:GLY110 4.8 15.1 0.3 C B:GLY110 4.8 16.1 0.3 C B:ASP109 4.8 14.5 0.3 C B:ASP109 4.8 14.6 0.7 CA B:ASP109 4.9 14.3 0.7 CA B:ASP109 4.9 14.5 0.3 CG B:ASP113 4.9 15.8 1.0 ND1 B:HIS111 5.0 23.1 0.3

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