Manganese in PDB 7eul: Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase

All present enzymatic activity of Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase:
3.5.3.25;

The structure of Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase, PDB code: 7eul 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)	41.93 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.499, 50.343, 52.941, 90, 99.42, 90
R / Rfree (%)	16.9 / 19.3

The structure of Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase (pdb code 7eul). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase, PDB code: 7eul:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase


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 C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:11.2 occ:1.00 OD2 A:ASP109 2.1 12.2 1.0 O A:HOH611 2.2 13.3 1.0 OD2 A:ASP113 2.2 11.4 1.0 O A:HOH569 2.2 17.2 1.0 ND1 A:HIS86 2.3 8.7 1.0 OD2 A:ASP198 2.3 19.2 1.0 CG A:ASP109 3.1 15.0 1.0 CG A:ASP113 3.2 11.1 1.0 CE1 A:HIS86 3.2 10.0 1.0 CG A:ASP198 3.3 16.8 1.0 CG A:HIS86 3.3 11.6 1.0 MN A:MN403 3.3 12.2 0.5 OD1 A:ASP113 3.4 13.7 1.0 OD1 A:ASP109 3.4 18.9 1.0 CB A:ASP198 3.5 13.8 1.0 CB A:HIS86 3.6 12.1 1.0 O A:HOH703 4.0 25.5 1.0 OH A:TYR107 4.0 11.3 1.0 MN A:MN402 4.3 12.8 0.4 O A:GLY126 4.3 14.2 1.0 NE2 A:HIS86 4.3 11.7 1.0 OD1 A:ASP198 4.4 14.5 1.0 CD2 A:HIS86 4.4 11.9 1.0 CB A:ASP109 4.4 11.4 1.0 O A:HOH509 4.5 24.9 1.0 CE1 A:TYR107 4.5 10.1 1.0 CB A:ASP113 4.5 13.2 1.0 OD2 A:ASP200 4.6 17.1 1.0 CZ A:TYR107 4.7 9.2 1.0 OD1 A:ASP200 5.0 13.1 1.0 CA A:ASP198 5.0 11.3 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase


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 C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:12.8 occ:0.43 O A:HOH581 1.9 22.9 1.0 OE1 A:GLU241 2.2 20.1 1.0 OD2 A:ASP200 2.4 17.1 1.0 OD2 A:ASP198 2.4 19.2 1.0 O A:HOH703 2.4 25.5 1.0 OD1 A:ASP198 2.4 14.5 1.0 CG A:ASP198 2.7 16.8 1.0 CD A:GLU241 3.1 17.8 1.0 CG A:ASP200 3.2 14.2 1.0 MN A:MN403 3.5 12.2 0.5 CG A:GLU241 3.8 18.3 1.0 O A:HOH569 3.8 17.2 1.0 CB A:ASP200 3.9 14.1 1.0 OE2 A:GLU241 3.9 17.1 1.0 O A:HOH552 3.9 30.6 1.0 CB A:GLU241 3.9 15.6 1.0 O A:HOH509 3.9 24.9 1.0 OD1 A:ASP200 4.0 13.1 1.0 CB A:ASP198 4.3 13.8 1.0 MN A:MN401 4.3 11.2 1.0 O A:HOH611 4.4 13.3 1.0 CD1 A:TYR211 4.5 41.5 1.0 CB A:ASP210 4.6 24.4 1.0 N A:ASP200 4.6 12.4 1.0 N A:ASP210 4.7 20.6 1.0 N A:TYR211 4.8 36.2 1.0 CA A:ASP200 4.9 12.6 1.0 CB A:ALA209 5.0 21.9 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of C86H-H196S Mutant of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:12.2 occ:0.53 O A:HOH569 1.8 17.2 1.0 OD2 A:ASP200 2.0 17.1 1.0 OD1 A:ASP200 2.4 13.1 1.0 OD1 A:ASP109 2.5 18.9 1.0 ND1 A:HIS111 2.5 19.7 1.0 CG A:ASP200 2.5 14.2 1.0 OD2 A:ASP198 2.9 19.2 1.0 CG A:ASP109 3.2 15.0 1.0 MN A:MN401 3.3 11.2 1.0 CE1 A:HIS111 3.3 19.8 1.0 OD2 A:ASP109 3.4 12.2 1.0 CG A:ASP198 3.4 16.8 1.0 MN A:MN402 3.5 12.8 0.4 O A:HOH703 3.5 25.5 1.0 CG A:HIS111 3.5 17.6 1.0 CB A:HIS111 3.8 16.9 1.0 OD1 A:ASP198 3.8 14.5 1.0 N A:HIS111 3.9 14.6 1.0 N A:GLY110 4.0 11.8 1.0 CB A:ASP200 4.0 14.1 1.0 OD1 A:ASP113 4.2 13.7 1.0 CB A:ASP198 4.2 13.8 1.0 CA A:HIS111 4.5 15.9 1.0 O A:HOH611 4.5 13.3 1.0 NE2 A:HIS111 4.5 23.3 1.0 CB A:ASP109 4.5 11.4 1.0 CA A:GLY110 4.6 14.3 1.0 C A:GLY110 4.6 14.0 1.0 CD2 A:HIS111 4.6 20.0 1.0 OD2 A:ASP113 4.6 11.4 1.0 O A:HOH581 4.7 22.9 1.0 C A:ASP109 4.8 11.3 1.0 CA A:ASP109 4.8 10.3 1.0 CG A:ASP113 4.8 11.1 1.0

K.Oda, T.Sakaguchi, Y.Matoba. Catalytic Mechanism of Dcsb: Arginase Framework Used For Hydrolyzing Its Inhibitor. Protein Sci. V. 31 E4338 2022.
ISSN: ESSN 1469-896X
PubMed: 35634777
DOI: 10.1002/PRO.4338