Manganese in PDB 6lug: Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase

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

The structure of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase, PDB code: 6lug 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)	44.10 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.440, 47.020, 59.350, 83.44, 84.59, 70.31
R / Rfree (%)	20.4 / 25

The binding sites of Manganese atom in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase (pdb code 6lug). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase, PDB code: 6lug:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure 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 N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:23.0 occ:1.00 O A:HOH523 2.2 7.8 1.0 OD2 A:ASP198 2.2 9.9 1.0 OD2 A:ASP109 2.2 13.9 1.0 O A:HOH640 2.2 13.5 1.0 OD2 A:ASP113 2.4 12.1 1.0 SG A:CYS86 2.5 10.3 1.0 CG A:ASP198 3.2 12.7 1.0 CG A:ASP109 3.2 9.1 1.0 CG A:ASP113 3.3 13.8 1.0 MN A:MN402 3.3 23.7 1.0 CB A:ASP198 3.5 12.7 1.0 OD1 A:ASP113 3.5 14.3 1.0 CB A:CYS86 3.5 8.2 1.0 OD1 A:ASP109 3.5 9.2 1.0 OH A:TYR107 4.1 12.8 1.0 OE2 A:GLU241 4.2 15.8 1.0 OD1 A:ASP198 4.3 13.7 1.0 CD A:GLU241 4.5 21.6 1.0 CB A:ASP109 4.5 11.1 1.0 O A:GLY126 4.6 14.2 1.0 CE1 A:TYR107 4.6 15.4 1.0 CB A:ASP113 4.7 10.8 1.0 OD2 A:ASP200 4.8 11.8 1.0 OE1 A:GLU241 4.8 15.4 1.0 CZ A:TYR107 4.8 16.5 1.0 O B:HOH562 4.9 19.3 1.0 CA A:CYS86 4.9 11.3 1.0 CA A:ASP198 4.9 11.8 1.0 NE2 A:HIS196 4.9 16.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure 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 N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:23.7 occ:1.00 OD2 A:ASP200 2.2 11.8 1.0 OD1 A:ASP109 2.2 9.2 1.0 OD2 A:ASP198 2.3 9.9 1.0 OD1 A:ASP200 2.3 11.7 1.0 O A:HOH523 2.4 7.8 1.0 ND1 A:HIS111 2.4 14.3 1.0 CG A:ASP200 2.6 12.6 1.0 CG A:ASP109 3.1 9.1 1.0 CG A:ASP198 3.1 12.7 1.0 MN A:MN401 3.3 23.0 1.0 CE1 A:HIS111 3.3 16.4 1.0 CG A:HIS111 3.4 14.3 1.0 OD2 A:ASP109 3.4 13.9 1.0 CB A:HIS111 3.6 11.3 1.0 OD1 A:ASP198 3.7 13.7 1.0 N A:HIS111 3.7 11.8 1.0 N A:GLY110 4.0 9.9 1.0 CB A:ASP200 4.1 10.2 1.0 CB A:ASP198 4.1 12.7 1.0 O A:HOH503 4.2 20.9 1.0 CA A:HIS111 4.3 12.4 1.0 O A:HOH640 4.4 13.5 1.0 O A:HOH594 4.4 17.6 1.0 O B:HOH562 4.4 19.3 1.0 OD1 A:ASP113 4.4 14.3 1.0 NE2 A:HIS111 4.4 15.4 1.0 CB A:ASP109 4.5 11.1 1.0 CD2 A:HIS111 4.5 16.1 1.0 C A:GLY110 4.5 16.7 1.0 CA A:GLY110 4.6 11.7 1.0 C A:ASP109 4.7 12.1 1.0 CA A:ASP109 4.8 13.0 1.0 OD2 A:ASP113 4.9 12.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure 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 N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:18.2 occ:1.00 OD2 B:ASP109 2.2 9.5 1.0 O B:HOH616 2.2 13.6 1.0 OD2 B:ASP198 2.3 12.8 1.0 O B:HOH540 2.3 6.8 1.0 OD2 B:ASP113 2.3 13.3 1.0 SG B:CYS86 2.4 14.4 1.0 CG B:ASP109 3.2 13.5 1.0 CG B:ASP113 3.2 13.8 1.0 CG B:ASP198 3.2 13.6 1.0 OD1 B:ASP113 3.3 13.6 1.0 CB B:CYS86 3.3 16.1 1.0 O B:HOH689 3.4 22.9 1.0 MN B:MN402 3.4 24.3 1.0 OD1 B:ASP109 3.5 12.0 1.0 CB B:ASP198 3.6 14.0 1.0 OH B:TYR107 4.0 10.8 1.0 OD1 B:ASP198 4.3 12.6 1.0 OE2 B:GLU241 4.5 14.7 1.0 CB B:ASP109 4.5 9.1 1.0 O B:GLY126 4.5 17.8 1.0 CD B:GLU241 4.5 15.2 1.0 CE1 B:TYR107 4.6 10.2 1.0 CB B:ASP113 4.6 13.8 1.0 CZ B:TYR107 4.7 12.4 1.0 CA B:CYS86 4.8 11.7 1.0 NE2 B:HIS196 4.8 12.7 1.0 OE1 B:GLU241 4.8 14.8 1.0 OD2 B:ASP200 4.9 14.8 1.0 CG B:GLU241 4.9 11.4 1.0 CA B:ASP198 5.0 13.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure 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 4 of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:24.3 occ:1.00 OD1 B:ASP109 2.1 12.0 1.0 OD2 B:ASP200 2.2 14.8 1.0 ND1 B:HIS111 2.2 14.2 1.0 O B:HOH540 2.3 6.8 1.0 OD2 B:ASP198 2.3 12.8 1.0 OD1 B:ASP200 2.4 13.7 1.0 CG B:ASP200 2.6 14.9 1.0 CE1 B:HIS111 3.1 15.7 1.0 CG B:ASP109 3.1 13.5 1.0 CG B:ASP198 3.1 13.6 1.0 CG B:HIS111 3.3 13.1 1.0 O B:HOH689 3.3 22.9 1.0 MN B:MN401 3.4 18.2 1.0 OD2 B:ASP109 3.4 9.5 1.0 OD1 B:ASP198 3.6 12.6 1.0 CB B:HIS111 3.8 11.5 1.0 N B:HIS111 3.8 15.1 1.0 N B:GLY110 4.0 12.3 1.0 CB B:ASP198 4.1 14.0 1.0 CB B:ASP200 4.1 12.4 1.0 O B:HOH616 4.2 13.6 1.0 NE2 B:HIS111 4.3 17.7 1.0 CD2 B:HIS111 4.4 16.2 1.0 CB B:ASP109 4.4 9.1 1.0 CA B:HIS111 4.4 15.2 1.0 OD1 B:ASP113 4.4 13.6 1.0 CA B:GLY110 4.5 12.7 1.0 C B:GLY110 4.5 14.9 1.0 O B:HOH570 4.5 18.8 1.0 C B:ASP109 4.7 12.3 1.0 CA B:ASP109 4.7 12.8 1.0 OD2 B:ASP113 5.0 13.3 1.0

K.Oda, N.Shimotani, T.Kuroda, Y.Matoba. Crystal Structure of An Nomega-Hydroxy-L-Arginine Hydrolase Found in the D-Cycloserine Biosynthetic Pathway. Acta Crystallogr D Struct V. 76 506 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32496212
DOI: 10.1107/S2059798320004908