Magnesium in PDB 7eun: Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh

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

The structure of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh, PDB code: 7eun 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)	44.26 / 1.28
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.577, 47.208, 59.641, 83.54, 84.44, 70.2
R / Rfree (%)	11.5 / 13.8

The structure of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

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

Magnesium binding site 1 out of 3 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:23.7 occ:1.00 O A:HOH547 2.0 22.0 1.0 O A:HOH740 2.0 24.9 1.0 O A:ASN77 2.1 16.3 1.0 O A:HOH690 2.1 30.4 1.0 O A:HOH675 2.1 19.9 1.0 O A:HOH521 2.1 20.0 1.0 C A:ASN77 3.2 15.1 1.0 HA A:LEU78 3.4 13.6 1.0 O A:HOH551 3.8 28.9 1.0 O A:ILE235 3.8 11.9 1.0 N A:ASN77 3.9 19.3 1.0 N A:LEU78 4.0 12.9 1.0 HA A:ILE235 4.0 13.1 1.0 H A:ASN77 4.0 23.2 1.0 O A:HOH738 4.1 49.2 1.0 CA A:LEU78 4.1 11.3 1.0 H A:THR79 4.1 11.5 1.0 CA A:ASN77 4.2 17.6 1.0 C A:ASP76 4.2 22.6 1.0 O A:HOH719 4.3 42.1 1.0 HG23 A:ILE235 4.4 15.0 1.0 O A:GLY75 4.4 22.1 1.0 HA A:ILE73 4.4 20.2 1.0 HA A:ASP76 4.4 29.4 1.0 O A:HOH723 4.4 29.7 1.0 O A:ASP76 4.5 24.1 1.0 HA A:ASN77 4.6 21.2 1.0 OG1 A:THR79 4.6 12.0 1.0 N A:THR79 4.6 9.6 1.0 O A:SER72 4.7 16.3 1.0 C A:ILE235 4.7 10.2 1.0 H A:LEU78 4.8 15.5 1.0 C A:LEU78 4.8 10.9 1.0 CA A:ASP76 4.8 24.5 1.0 CA A:ILE235 4.8 10.9 1.0 HG1 A:THR79 4.8 14.4 1.0 O A:LEU234 4.9 12.8 1.0 HD12 A:LEU78 4.9 13.7 1.0 O A:ILE73 4.9 18.5 1.0 O A:HOH656 5.0 34.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


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 N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:10.1 occ:1.00 OE1 B:GLU241 1.9 12.7 1.0 OD1 B:ASP210 2.0 16.2 1.0 O3 B:ABH405 2.2 9.9 1.0 OD2 B:ASP200 2.2 8.2 1.0 OD2 B:ASP198 2.3 7.4 1.0 OD1 B:ASP198 2.4 7.8 1.0 HO3 B:ABH405 2.5 11.9 1.0 CG B:ASP198 2.7 6.5 1.0 CG B:ASP210 2.9 18.4 1.0 OD2 B:ASP210 3.1 19.8 1.0 CD B:GLU241 3.1 11.6 1.0 CG B:ASP200 3.2 7.7 1.0 MN B:MN402 3.2 8.8 1.0 B B:ABH405 3.4 10.3 1.0 HD2 B:TYR211 3.5 26.4 1.0 HB3 B:ASP200 3.5 9.0 1.0 HB3 B:GLU241 3.5 11.9 1.0 HO2 B:ABH405 3.6 14.0 1.0 O2 B:ABH405 3.6 11.7 1.0 O1 B:ABH405 3.7 8.2 1.0 HB2 B:GLU241 3.8 11.9 1.0 OD1 B:ASP200 3.9 8.0 1.0 O B:HOH509 3.9 27.4 1.0 CG B:GLU241 3.9 11.6 1.0 CB B:ASP200 3.9 7.5 1.0 CB B:GLU241 3.9 9.9 1.0 H B:ASP200 4.0 8.0 1.0 H B:ASP210 4.0 20.7 1.0 OE2 B:GLU241 4.0 11.1 1.0 MN B:MN401 4.1 7.8 1.0 HG3 B:GLU241 4.1 14.0 1.0 CB B:ASP198 4.2 6.1 1.0 CD2 B:TYR211 4.3 22.0 1.0 CB B:ASP210 4.3 18.2 1.0 HB1 B:ALA209 4.4 19.4 1.0 HE1 B:HIS111 4.4 10.9 1.0 H B:TYR211 4.4 20.7 1.0 HB2 B:ASP198 4.5 7.4 1.0 HE1 B:MET18 4.5 18.2 0.8 HE2 B:TYR211 4.5 27.7 1.0 HB3 B:ASP210 4.6 21.8 1.0 HB2 B:ASP200 4.6 9.0 1.0 HO1 B:ABH405 4.6 9.8 1.0 HB3 B:ASP198 4.7 7.4 1.0 CE B:ABH405 4.7 10.9 1.0 ND1 B:HIS111 4.7 8.4 1.0 HB2 B:TYR211 4.7 23.0 1.0 N B:ASP210 4.7 17.3 1.0 N B:ASP200 4.8 6.7 1.0 HCE1 B:ABH405 4.8 13.1 1.0 HG2 B:GLU241 4.8 14.0 1.0 CE2 B:TYR211 4.9 23.1 1.0 CE1 B:HIS111 4.9 9.1 1.0 SG B:CYS86 4.9 8.2 1.0 OD1 B:ASP109 4.9 6.6 1.0 HB2 B:ASP210 4.9 21.8 1.0 N B:TYR211 4.9 17.2 1.0 CA B:ASP200 5.0 7.4 1.0 HCD1 B:ABH405 5.0 14.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:30.3 occ:1.00 H B:THR61 2.2 20.0 1.0 HB2 B:GLU60 2.7 26.7 1.0 O B:HOH513 2.8 18.1 1.0 H B:GLU60 2.8 22.2 1.0 O B:GLN57 2.9 20.4 1.0 HA B:ALA58 2.9 18.8 1.0 O B:HOH748 2.9 38.9 1.0 N B:THR61 3.0 16.7 1.0 OE1 B:GLU60 3.0 31.0 1.0 N B:GLU60 3.3 18.5 1.0 C B:ALA58 3.4 16.1 1.0 OG1 B:THR61 3.4 16.4 1.0 HB B:THR61 3.5 19.1 1.0 HG1 B:THR61 3.5 19.7 1.0 O B:ALA58 3.5 16.8 1.0 CB B:GLU60 3.5 22.2 1.0 CA B:ALA58 3.5 15.7 1.0 CA B:GLU60 3.7 19.4 1.0 CD B:GLU60 3.7 30.3 1.0 CB B:THR61 3.8 15.9 1.0 N B:ARG59 3.8 17.2 1.0 C B:GLU60 3.8 17.3 1.0 C B:GLN57 3.9 18.9 1.0 O B:HOH532 3.9 24.9 1.0 H B:ARG59 4.0 20.7 1.0 CA B:THR61 4.0 15.8 1.0 N B:ALA58 4.1 16.5 1.0 C B:ARG59 4.1 17.5 1.0 HB3 B:GLU60 4.2 26.7 1.0 CG B:GLU60 4.2 26.5 1.0 HA B:THR61 4.5 18.9 1.0 OE2 B:GLU60 4.5 32.4 1.0 CA B:ARG59 4.6 17.8 1.0 H B:LEU62 4.6 17.8 1.0 HA B:GLU60 4.7 23.2 1.0 O B:HOH517 4.7 25.0 1.0 CB B:ALA58 4.8 15.4 1.0 HB1 B:ALA58 4.8 18.6 1.0 HG3 B:GLU60 4.8 31.8 1.0 HG2 B:GLU60 4.9 31.8 1.0 O B:ARG10 5.0 11.2 1.0 H B:ALA58 5.0 19.9 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