Magnesium 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:

Manganese	(Mn)	2 atoms
Copper	(Cu)	2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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 A:Mg403 b:24.4 occ:0.52 O A:HOH561 2.0 28.4 1.0 O A:HOH669 2.0 30.2 1.0 O A:HOH636 2.1 27.6 1.0 O A:ASN77 2.1 21.3 1.0 O A:HOH533 2.2 26.0 1.0 O A:HOH716 2.2 33.1 1.0 C A:ASN77 3.2 24.4 1.0 O A:ILE235 3.7 16.5 1.0 O A:HOH542 3.8 33.8 1.0 N A:ASN77 4.0 25.3 1.0 N A:LEU78 4.0 21.0 1.0 O A:HOH503 4.0 45.6 1.0 CA A:LEU78 4.1 19.6 1.0 O A:HOH712 4.1 40.1 1.0 CA A:ASN77 4.1 28.5 1.0 C A:ASP76 4.2 26.9 1.0 O A:HOH697 4.2 41.3 1.0 O A:ASP76 4.4 30.1 1.0 O A:GLY75 4.4 28.5 1.0 N A:THR79 4.6 15.3 1.0 C A:ILE235 4.6 16.4 1.0 OG1 A:THR79 4.7 18.2 1.0 O A:SER72 4.7 22.6 1.0 C A:LEU78 4.7 19.4 1.0 CA A:ILE235 4.8 15.3 1.0 NH1 A:ARG272 4.8 32.4 1.0 O A:LEU234 4.8 18.6 1.0 CA A:ASP76 4.9 34.0 1.0 O A:HOH659 4.9 36.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403 b:15.5 occ:0.45 OD2 B:ASP198 2.0 20.9 1.0 O B:HOH576 2.0 22.9 1.0 O B:HOH672 2.1 28.8 1.0 OD2 B:ASP200 2.3 20.7 1.0 OD1 B:ASP198 2.4 18.1 1.0 CG B:ASP198 2.5 17.5 1.0 OE2 B:GLU241 2.7 34.2 1.0 CU B:CU1402 3.0 21.2 0.5 CG B:ASP200 3.1 20.8 1.0 CD B:GLU241 3.4 24.2 1.0 O B:HOH603 3.4 27.4 1.0 CG B:GLU241 3.8 18.6 1.0 OD1 B:ASP200 3.9 19.2 1.0 CB B:ASP200 3.9 17.8 1.0 O B:HOH647 3.9 28.9 1.0 CU B:CU401 3.9 16.9 0.5 CB B:GLU241 3.9 18.3 1.0 CB B:ASP198 4.0 14.5 1.0 OE1 B:GLU241 4.2 21.0 1.0 CD1 B:TYR211 4.3 34.9 0.5 SG B:CSD86 4.4 17.1 0.5 O B:ASP210 4.5 37.0 0.5 O B:HOH535 4.5 41.7 1.0 ND1 B:HIS111 4.6 19.6 0.7 OD1 B:ASP109 4.6 14.7 0.7 N B:ASP200 4.6 14.7 1.0 SG B:CSD86 4.7 18.3 0.2 O B:HOH503 4.7 28.8 0.6 SG B:CSD86 4.7 18.3 0.3 CE1 B:HIS111 4.7 23.1 0.7 OD2 B:ASP109 4.9 14.7 0.7 CA B:ASP200 4.9 16.4 1.0 OD B:CSD86 4.9 17.5 0.2 CA B:ASP198 5.0 13.5 1.0

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