Manganese 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
Copper	(Cu)	2 atoms

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

Manganese 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 Manganese with other atoms in the Mn 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:Mn401 b:9.5 occ:0.79 OD2 A:ASP113 2.2 11.9 1.0 OD2 A:ASP109 2.2 10.6 1.0 OD2 A:ASP198 2.3 13.2 1.0 O A:HOH528 2.3 12.7 1.0 O A:HOH656 2.3 16.9 1.0 SG A:CYS86 2.5 13.7 1.0 CG A:ASP113 3.1 13.1 1.0 CG A:ASP109 3.2 8.7 1.0 CG A:ASP198 3.2 11.0 1.0 MN A:MN402 3.4 13.0 0.8 OD1 A:ASP113 3.4 12.9 1.0 CB A:CYS86 3.4 13.1 1.0 OD1 A:ASP109 3.5 10.0 1.0 CB A:ASP198 3.6 10.2 1.0 OH A:TYR107 4.0 11.9 1.0 O A:GLY126 4.3 21.1 1.0 OD1 A:ASP198 4.4 11.4 1.0 OE2 A:GLU241 4.4 17.2 1.0 CE1 A:TYR107 4.5 10.0 1.0 CB A:ASP109 4.5 8.9 1.0 CB A:ASP113 4.5 12.6 1.0 CD A:GLU241 4.5 18.1 1.0 O A:HOH728 4.7 31.0 1.0 CZ A:TYR107 4.7 10.5 1.0 OE1 A:GLU241 4.7 18.7 1.0 OD2 A:ASP200 4.8 13.2 1.0 CA A:CYS86 4.8 11.7 1.0 NE2 A:HIS196 4.9 13.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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 A:Mn402 b:13.0 occ:0.76 OD2 A:ASP200 2.1 13.2 1.0 OD1 A:ASP109 2.1 10.0 1.0 O A:HOH528 2.1 12.7 1.0 ND1 A:HIS111 2.2 11.1 1.0 OD2 A:ASP198 2.3 13.2 1.0 OD1 A:ASP200 2.4 11.8 1.0 CG A:ASP200 2.6 13.8 1.0 CE1 A:HIS111 3.1 13.6 1.0 CG A:ASP109 3.1 8.7 1.0 CG A:ASP198 3.2 11.0 1.0 CG A:HIS111 3.3 10.6 1.0 MN A:MN401 3.4 9.5 0.8 OD2 A:ASP109 3.4 10.6 1.0 CB A:HIS111 3.6 10.9 1.0 OD1 A:ASP198 3.7 11.4 1.0 N A:HIS111 3.8 10.9 1.0 CB A:ASP200 4.1 11.3 1.0 N A:GLY110 4.1 9.3 1.0 CB A:ASP198 4.2 10.2 1.0 O A:HOH728 4.2 31.0 1.0 NE2 A:HIS111 4.2 11.3 1.0 OD1 A:ASP113 4.3 12.9 1.0 O A:HOH520 4.3 21.7 1.0 CD2 A:HIS111 4.3 11.3 1.0 CA A:HIS111 4.3 11.4 1.0 CB A:ASP109 4.4 8.9 1.0 O A:HOH617 4.4 21.9 1.0 O A:HOH656 4.4 16.9 1.0 C A:GLY110 4.6 11.3 1.0 CA A:GLY110 4.7 12.5 1.0 OD2 A:ASP113 4.7 11.9 1.0 CA A:ASP109 4.8 9.1 1.0 C A:ASP109 4.8 10.1 1.0 CG A:ASP113 4.9 13.1 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