Manganese in PDB 9ixe: 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;

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

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
Copper	(Cu)	3 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Copper-Bound N(Omega)-Hydroxy-L-Arginine Hydrolase Without Oxidized CYS86, PDB code: 9ixe:
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 Without 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 Without Oxidized CYS86 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:8.9 occ:0.71 O A:HOH654 2.1 14.7 1.0 OD2 A:ASP109 2.2 12.1 1.0 OD2 A:ASP198 2.2 14.6 1.0 OD2 A:ASP113 2.3 12.7 1.0 O A:HOH530 2.5 13.6 1.0 SG A:CYS86 2.5 17.8 1.0 CG A:ASP109 3.2 12.1 1.0 CG A:ASP198 3.2 14.5 1.0 CG A:ASP113 3.2 16.1 1.0 CB A:CYS86 3.4 15.0 1.0 MN A:MN402 3.4 10.6 0.7 OD1 A:ASP113 3.5 14.3 1.0 OD1 A:ASP109 3.5 12.2 1.0 CB A:ASP198 3.5 10.8 1.0 OH A:TYR107 4.0 15.0 1.0 OE2 A:GLU241 4.3 14.8 1.0 OD1 A:ASP198 4.3 13.4 1.0 CE1 A:TYR107 4.4 12.4 1.0 CD A:GLU241 4.5 13.4 1.0 O A:GLY126 4.5 21.5 1.0 CB A:ASP109 4.5 10.7 1.0 CB A:ASP113 4.6 12.6 1.0 CZ A:TYR107 4.7 13.8 1.0 OE1 A:GLU241 4.8 14.2 1.0 CA A:CYS86 4.8 10.3 1.0 OD2 A:ASP200 4.9 12.3 1.0 NE2 A:HIS196 4.9 12.4 1.0 CA A:ASP198 4.9 11.5 1.0 CG A:GLU241 5.0 15.7 1.0

Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn 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 A:Mn402 b:10.6 occ:0.68 OD1 A:ASP109 2.1 12.2 1.0 OD2 A:ASP200 2.1 12.3 1.0 O A:HOH530 2.2 13.6 1.0 ND1 A:HIS111 2.2 12.9 1.0 OD2 A:ASP198 2.4 14.6 1.0 OD1 A:ASP200 2.5 14.9 1.0 CG A:ASP200 2.7 13.3 1.0 CG A:ASP109 3.1 12.1 1.0 CE1 A:HIS111 3.1 11.3 1.0 CG A:ASP198 3.1 14.5 1.0 CG A:HIS111 3.2 12.9 1.0 MN A:MN401 3.4 8.9 0.7 OD2 A:ASP109 3.4 12.1 1.0 CB A:HIS111 3.5 12.4 1.0 OD1 A:ASP198 3.6 13.4 1.0 N A:HIS111 3.8 11.6 1.0 CB A:ASP198 4.1 10.8 1.0 N A:GLY110 4.1 9.6 1.0 CB A:ASP200 4.2 11.6 1.0 NE2 A:HIS111 4.2 11.4 1.0 CA A:HIS111 4.3 11.8 1.0 CD2 A:HIS111 4.3 13.8 1.0 OD1 A:ASP113 4.4 14.3 1.0 O A:HOH654 4.4 14.7 1.0 O A:HOH560 4.4 24.8 1.0 CB A:ASP109 4.4 10.7 1.0 C A:GLY110 4.6 14.3 1.0 CA A:GLY110 4.7 13.4 1.0 CA A:ASP109 4.8 10.6 1.0 C A:ASP109 4.8 10.9 1.0 OD2 A:ASP113 4.8 12.7 1.0 CG A:ASP113 5.0 16.1 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