Manganese in PDB 4fci: Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex

All present enzymatic activity of Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex:
3.5.3.1;

The structure of Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex, PDB code: 4fci was solved by E.L.D'antonio, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.82
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.848, 90.848, 69.767, 90.00, 90.00, 120.00
R / Rfree (%)	27.9 / 31

The binding sites of Manganese atom in the Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex (pdb code 4fci). 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 the MN2+2-Human Arginase I-Agpa Complex, PDB code: 4fci:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex


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 the MN2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:18.5 occ:1.00 OD1 A:ASP124 2.2 18.0 1.0 OD2 A:ASP234 2.3 17.4 1.0 OD1 A:ASP234 2.3 14.0 1.0 OD2 A:ASP232 2.4 15.4 1.0 ND1 A:HIS126 2.4 19.4 1.0 CG A:ASP234 2.6 15.0 1.0 O A:HOH519 3.1 33.0 1.0 CG A:ASP124 3.1 16.7 1.0 CG A:ASP232 3.2 17.0 1.0 MN A:MN402 3.3 16.2 1.0 CE1 A:HIS126 3.3 17.9 1.0 OD2 A:ASP124 3.4 17.8 1.0 CG A:HIS126 3.5 18.9 1.0 OD1 A:ASP232 3.7 18.0 1.0 CB A:HIS126 3.9 18.4 1.0 N A:HIS126 4.0 14.9 1.0 N A:ALA125 4.1 13.8 1.0 CB A:ASP234 4.2 15.1 1.0 CB A:ASP232 4.2 16.2 1.0 OG1 A:THR246 4.4 17.3 1.0 NE2 A:HIS126 4.5 17.2 1.0 CB A:ASP124 4.5 16.8 1.0 NH1 A:GPA403 4.5 25.7 1.0 CA A:HIS126 4.6 16.1 1.0 CD2 A:HIS126 4.6 18.0 1.0 CB A:ALA125 4.6 12.6 1.0 NH2 A:GPA403 4.7 23.8 1.0 OD2 A:ASP128 4.7 10.8 1.0 O A:HOH504 4.7 12.1 1.0 C A:ALA125 4.7 13.3 1.0 CA A:ALA125 4.8 14.0 1.0 OD1 A:ASP128 4.8 14.6 1.0 CA A:ASP124 4.9 14.8 1.0 CZ A:GPA403 4.9 23.1 1.0 C A:ASP124 4.9 13.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex


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 the MN2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:16.2 occ:1.00 OD2 A:ASP124 2.1 17.8 1.0 OD1 A:ASP128 2.2 14.6 1.0 OD2 A:ASP232 2.2 15.4 1.0 ND1 A:HIS101 2.4 16.8 1.0 CG A:ASP124 3.1 16.7 1.0 CG A:ASP128 3.2 12.5 1.0 CG A:ASP232 3.2 17.0 1.0 MN A:MN401 3.3 18.5 1.0 CG A:HIS101 3.3 16.2 1.0 CE1 A:HIS101 3.3 17.2 1.0 O A:HOH519 3.4 33.0 1.0 OD2 A:ASP128 3.5 10.8 1.0 OD1 A:ASP124 3.5 18.0 1.0 CB A:HIS101 3.5 16.2 1.0 CB A:ASP232 3.6 16.2 1.0 OD1 A:ASP232 4.3 18.0 1.0 NH2 A:GPA403 4.3 23.8 1.0 O A:HIS141 4.4 15.2 1.0 NE1 A:TRP122 4.4 14.9 1.0 CB A:ASP124 4.4 16.8 1.0 NE2 A:HIS101 4.5 15.2 1.0 CD2 A:HIS101 4.5 16.4 1.0 CB A:ASP128 4.5 14.1 1.0 CZ2 A:TRP122 4.6 14.9 1.0 CG A:GLU277 4.8 17.2 1.0 OE2 A:GLU277 4.8 17.9 1.0 CE2 A:TRP122 4.9 13.1 1.0 OD2 A:ASP234 5.0 17.4 1.0 CA A:ASP232 5.0 16.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex


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 the MN2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn400 b:20.6 occ:1.00 OD2 B:ASP234 2.1 20.6 1.0 OD1 B:ASP124 2.2 14.1 1.0 OD2 B:ASP232 2.3 20.9 1.0 OD1 B:ASP234 2.4 18.4 1.0 ND1 B:HIS126 2.5 18.0 1.0 CG B:ASP234 2.6 19.5 1.0 CG B:ASP232 3.1 20.1 1.0 O B:HOH515 3.1 51.7 1.0 CG B:ASP124 3.1 14.0 1.0 MN B:MN401 3.3 19.8 1.0 CE1 B:HIS126 3.3 18.0 1.0 OD2 B:ASP124 3.4 16.0 1.0 CG B:HIS126 3.6 19.7 1.0 OD1 B:ASP232 3.6 19.5 1.0 O B:HOH514 3.8 48.4 1.0 CB B:HIS126 3.9 17.2 1.0 CB B:ASP232 4.0 18.7 1.0 N B:HIS126 4.1 17.0 1.0 CB B:ASP234 4.1 18.0 1.0 N B:ALA125 4.2 16.4 1.0 OG1 B:THR246 4.3 24.9 1.0 NE2 B:HIS126 4.5 17.8 1.0 CB B:ASP124 4.5 17.4 1.0 OD2 B:ASP128 4.6 17.8 1.0 CA B:HIS126 4.6 16.9 1.0 CD2 B:HIS126 4.6 18.2 1.0 O B:HOH508 4.6 16.7 1.0 CB B:ALA125 4.8 14.0 1.0 OD1 B:ASP128 4.8 17.3 1.0 CA B:ASP124 4.9 16.6 1.0 C B:ALA125 4.9 15.0 1.0 CA B:ALA125 4.9 14.8 1.0 O B:THR246 4.9 24.2 1.0 CA B:ASP234 5.0 16.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the MN2+2-Human Arginase I-Agpa Complex


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 the MN2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:19.8 occ:1.00 OD1 B:ASP128 2.1 17.3 1.0 OD2 B:ASP124 2.2 16.0 1.0 ND1 B:HIS101 2.3 18.6 1.0 OD2 B:ASP232 2.3 20.9 1.0 CG B:ASP128 3.1 19.3 1.0 CG B:ASP124 3.2 14.0 1.0 CG B:HIS101 3.2 18.8 1.0 MN B:MN400 3.3 20.6 1.0 O B:HOH515 3.3 51.7 1.0 CE1 B:HIS101 3.3 16.1 1.0 CG B:ASP232 3.3 20.1 1.0 O B:HOH514 3.3 48.4 1.0 OD2 B:ASP128 3.4 17.8 1.0 CB B:HIS101 3.5 19.8 1.0 OD1 B:ASP124 3.5 14.1 1.0 CB B:ASP232 3.6 18.7 1.0 NE1 B:TRP122 4.3 17.2 1.0 NE2 B:HIS101 4.4 18.1 1.0 CD2 B:HIS101 4.4 20.2 1.0 O B:HIS141 4.4 19.2 1.0 CB B:ASP128 4.4 19.2 1.0 OD1 B:ASP232 4.5 19.5 1.0 CB B:ASP124 4.5 17.4 1.0 CZ2 B:TRP122 4.5 17.6 1.0 CE2 B:TRP122 4.8 17.8 1.0 CG B:GLU277 4.8 22.5 1.0 OD2 B:ASP234 4.9 20.6 1.0 OE2 B:GLU277 5.0 27.3 1.0 CA B:ASP232 5.0 18.9 1.0 CA B:HIS101 5.0 20.6 1.0

E.L.D'antonio, D.W.Christianson. Binding of the Unreactive Substrate Analog L-2-Amino-3-Guanidinopropionic Acid (Dinor-L-Arginine) to Human Arginase I. Acta Crystallogr.,Sect.F V. 68 889 2012.
ISSN: ESSN 1744-3091
PubMed: 22869115
DOI: 10.1107/S1744309112027820