Manganese in PDB 2pha: Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution

All present enzymatic activity of Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution:
3.5.3.1;

The structure of Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution, PDB code: 2pha was solved by L.Di Costanzo, M.E.Pique, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.03 / 1.90
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.770, 90.770, 69.740, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24.4

The binding sites of Manganese atom in the Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution (pdb code 2pha). 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 Native, Unliganded Human Arginase at 1.90 Resolution, PDB code: 2pha:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution


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 Native, Unliganded Human Arginase at 1.90 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn323 b:14.3 occ:1.00 OD1 A:ASP124 2.0 12.3 1.0 ND1 A:HIS126 2.2 10.8 1.0 O A:HOH388 2.3 30.2 1.0 OD1 A:ASP234 2.4 10.2 1.0 OD2 A:ASP234 2.5 10.7 1.0 OD2 A:ASP232 2.6 17.0 1.0 CG A:ASP234 2.8 10.6 1.0 CE1 A:HIS126 2.9 10.9 1.0 CG A:ASP124 2.9 13.2 1.0 OD2 A:ASP124 3.2 15.3 1.0 CG A:HIS126 3.3 12.0 1.0 MN A:MN324 3.3 15.8 1.0 CG A:ASP232 3.7 14.3 1.0 O A:HOH366 3.8 12.9 1.0 CB A:HIS126 3.9 13.2 1.0 N A:HIS126 3.9 11.8 1.0 N A:ALA125 4.0 11.7 1.0 NE2 A:HIS126 4.1 11.5 1.0 OG1 A:THR246 4.1 14.2 1.0 CD2 A:HIS126 4.3 10.7 1.0 CB A:ASP234 4.3 10.1 1.0 CB A:ASP124 4.3 12.3 1.0 OD1 A:ASP232 4.4 12.7 1.0 CB A:ASP232 4.5 13.8 1.0 CA A:HIS126 4.5 11.5 1.0 CB A:ALA125 4.5 9.6 1.0 CA A:ALA125 4.7 10.5 1.0 OD2 A:ASP128 4.7 9.8 1.0 C A:ALA125 4.7 11.1 1.0 O A:HOH442 4.7 33.5 1.0 CA A:ASP124 4.8 12.3 1.0 O A:HOH357 4.9 14.3 1.0 O A:THR246 4.9 13.5 1.0 C A:ASP124 4.9 11.2 1.0 OD1 A:ASP128 4.9 13.3 1.0 O A:HIS126 5.0 12.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution


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 Native, Unliganded Human Arginase at 1.90 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn324 b:15.8 occ:1.00 OD2 A:ASP124 2.2 15.3 1.0 O A:HOH388 2.4 30.2 1.0 OD1 A:ASP128 2.4 13.3 1.0 ND1 A:HIS101 2.5 12.2 1.0 OD2 A:ASP232 2.6 17.0 1.0 O A:HOH442 2.8 33.5 1.0 CG A:ASP124 3.3 13.2 1.0 CG A:ASP128 3.3 11.4 1.0 MN A:MN323 3.3 14.3 1.0 CG A:HIS101 3.4 12.9 1.0 CE1 A:HIS101 3.4 12.3 1.0 CG A:ASP232 3.5 14.3 1.0 CB A:HIS101 3.6 13.2 1.0 OD2 A:ASP128 3.6 9.8 1.0 OD1 A:ASP124 3.7 12.3 1.0 CB A:ASP232 3.7 13.8 1.0 O A:HIS141 4.3 14.9 1.0 NE2 A:HIS101 4.5 12.7 1.0 CB A:ASP124 4.6 12.3 1.0 CD2 A:HIS101 4.6 14.9 1.0 OD1 A:ASP232 4.6 12.7 1.0 NE1 A:TRP122 4.6 12.6 1.0 OE2 A:GLU277 4.6 18.3 1.0 O A:HOH366 4.7 12.9 1.0 CB A:ASP128 4.7 10.5 1.0 CG A:GLU277 4.7 16.5 1.0 CZ2 A:TRP122 4.9 7.1 1.0 OD2 A:ASP234 5.0 10.7 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution


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 Native, Unliganded Human Arginase at 1.90 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn323 b:15.4 occ:1.00 ND1 B:HIS126 2.1 10.7 1.0 OD2 B:ASP234 2.2 19.0 1.0 OD2 B:ASP232 2.3 16.7 1.0 OD1 B:ASP124 2.3 13.4 1.0 O B:HOH436 2.4 40.4 1.0 OD1 B:ASP234 2.6 17.8 1.0 CG B:ASP234 2.7 19.4 1.0 CE1 B:HIS126 2.9 12.8 1.0 CG B:ASP124 3.1 13.7 1.0 OD2 B:ASP124 3.2 14.7 1.0 CG B:ASP232 3.2 16.9 1.0 CG B:HIS126 3.3 12.7 1.0 MN B:MN324 3.4 21.9 1.0 CB B:HIS126 3.8 11.6 1.0 OD1 B:ASP232 3.9 17.1 1.0 CB B:ASP232 4.1 15.9 1.0 NE2 B:HIS126 4.1 9.2 1.0 N B:HIS126 4.1 12.2 1.0 CB B:ASP234 4.2 18.0 1.0 OG1 B:THR246 4.2 19.7 1.0 CD2 B:HIS126 4.3 11.5 1.0 N B:ALA125 4.3 11.7 1.0 O B:HOH430 4.4 40.4 1.0 CB B:ASP124 4.5 13.5 1.0 OD2 B:ASP128 4.6 14.9 1.0 CA B:HIS126 4.6 12.5 1.0 OD1 B:ASP128 4.7 15.3 1.0 C B:ALA125 4.9 11.3 1.0 CB B:ALA125 4.9 10.9 1.0 O B:THR246 5.0 21.8 1.0 CA B:ASP124 5.0 13.0 1.0 CA B:ALA125 5.0 12.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Native, Unliganded Human Arginase at 1.90 Resolution


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 Native, Unliganded Human Arginase at 1.90 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn324 b:21.9 occ:1.00 O B:HOH436 2.1 40.4 1.0 OD1 B:ASP128 2.2 15.3 1.0 ND1 B:HIS101 2.3 19.7 1.0 OD2 B:ASP124 2.4 14.7 1.0 OD2 B:ASP232 2.5 16.7 1.0 O B:HOH430 2.7 40.4 1.0 CG B:ASP128 3.2 15.9 1.0 CG B:HIS101 3.2 21.1 1.0 CE1 B:HIS101 3.3 19.1 1.0 CG B:ASP232 3.4 16.9 1.0 CB B:HIS101 3.4 20.9 1.0 MN B:MN323 3.4 15.4 1.0 CG B:ASP124 3.5 13.7 1.0 OD2 B:ASP128 3.5 14.9 1.0 CB B:ASP232 3.6 15.9 1.0 OD1 B:ASP124 3.9 13.4 1.0 O B:HIS141 4.3 19.7 1.0 CD2 B:HIS101 4.4 21.6 1.0 NE2 B:HIS101 4.4 21.0 1.0 OD1 B:ASP232 4.5 17.1 1.0 CB B:ASP128 4.5 16.8 1.0 NE1 B:TRP122 4.6 15.9 1.0 CB B:ASP124 4.7 13.5 1.0 CG B:GLU277 4.8 20.5 1.0 CZ2 B:TRP122 4.8 18.5 1.0 CA B:ASP232 4.9 17.7 1.0 CA B:HIS101 4.9 20.8 1.0 ND1 B:HIS126 5.0 10.7 1.0

L.Di Costanzo, M.E.Pique, D.W.Christianson. Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide Reveals An Unusual Thiocarbonyl Mu-Sulfide Ligand in the Binuclear Manganese Cluster. J.Am.Chem.Soc. V. 129 6388 2007.
ISSN: ISSN 0002-7863
PubMed: 17469833
DOI: 10.1021/JA071567J