Manganese in PDB 2zav: Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution

All present enzymatic activity of Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution:
3.5.3.1;

The structure of Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution, PDB code: 2zav was solved by L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.480, 90.480, 69.449, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / 17.6

The binding sites of Manganese atom in the Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution (pdb code 2zav). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution, PDB code: 2zav:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2514 b:16.4 occ:1.00 OD1 A:ASP124 2.1 15.1 1.0 O A:HOH2555 2.2 23.1 1.0 ND1 A:HIS126 2.2 19.6 1.0 OD2 A:ASP232 2.2 14.5 1.0 OD2 A:ASP234 2.2 18.0 1.0 OD1 A:ASP234 2.3 14.8 1.0 CG A:ASP234 2.6 14.3 1.0 CG A:ASP124 3.1 19.2 1.0 CE1 A:HIS126 3.1 14.8 1.0 CG A:ASP232 3.1 13.9 1.0 CG A:HIS126 3.2 14.2 1.0 MN A:MN2515 3.3 15.3 1.0 OD2 A:ASP124 3.4 15.9 1.0 CB A:HIS126 3.6 17.6 1.0 OD1 A:ASP232 3.7 15.0 1.0 O A:HOH2549 3.8 22.8 1.0 N A:HIS126 3.9 12.5 1.0 OG1 A:THR246 4.1 14.5 1.0 N A:ALA125 4.1 18.2 1.0 O A:HOH2590 4.1 25.1 1.0 CB A:ASP232 4.1 14.8 1.0 CB A:ASP234 4.1 18.4 1.0 NE2 A:HIS126 4.2 22.0 1.0 CD2 A:HIS126 4.3 17.5 1.0 CB A:ASP124 4.4 21.0 1.0 CA A:HIS126 4.4 15.4 1.0 OD1 A:ASP128 4.6 12.0 1.0 CB A:ALA125 4.7 20.9 1.0 C A:ALA125 4.7 8.4 1.0 CA A:ALA125 4.7 12.3 1.0 CA A:ASP124 4.7 14.9 1.0 O A:HOH2540 4.8 17.4 1.0 OD2 A:ASP128 4.8 18.6 1.0 C A:ASP124 4.8 12.8 1.0 O A:THR246 5.0 16.4 1.0

Manganese binding site 2 out of 4 in the Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2515 b:15.3 occ:1.00 OD2 A:ASP124 2.1 15.9 1.0 OD2 A:ASP128 2.1 18.6 1.0 O A:HOH2555 2.2 23.1 1.0 OD2 A:ASP232 2.2 14.5 1.0 ND1 A:HIS101 2.3 14.6 1.0 O A:HOH2590 2.3 25.1 1.0 CG A:ASP128 3.1 8.7 1.0 CG A:ASP124 3.1 19.2 1.0 CG A:ASP232 3.2 13.9 1.0 CG A:HIS101 3.2 17.0 1.0 CE1 A:HIS101 3.2 19.3 1.0 MN A:MN2514 3.3 16.4 1.0 OD1 A:ASP124 3.4 15.1 1.0 OD1 A:ASP128 3.5 12.0 1.0 CB A:HIS101 3.5 17.9 1.0 CB A:ASP232 3.6 14.8 1.0 OD1 A:ASP232 4.3 15.0 1.0 NE2 A:HIS101 4.4 19.9 1.0 CD2 A:HIS101 4.4 24.3 1.0 O A:HOH2549 4.4 22.8 1.0 O A:HIS141 4.4 19.4 1.0 CB A:ASP128 4.4 17.7 1.0 CB A:ASP124 4.5 21.0 1.0 NE1 A:TRP122 4.5 14.4 1.0 CZ2 A:TRP122 4.7 15.8 1.0 CG A:GLU277 4.8 18.6 1.0 OE2 A:GLU277 4.8 20.9 1.0 OD1 A:ASP234 4.9 14.8 1.0 CA A:ASP232 4.9 16.7 1.0 CB A:HIS126 5.0 17.6 1.0 OD2 A:ASP234 5.0 18.0 1.0 CE2 A:TRP122 5.0 18.0 1.0 ND1 A:HIS126 5.0 19.6 1.0

Manganese binding site 3 out of 4 in the Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2516 b:19.6 occ:1.00 OD2 B:ASP232 1.9 17.8 1.0 OD1 B:ASP234 2.2 19.2 1.0 OD2 B:ASP234 2.2 18.1 1.0 OD1 B:ASP124 2.2 19.1 1.0 O B:HOH2587 2.2 21.1 1.0 ND1 B:HIS126 2.3 29.7 1.0 CG B:ASP234 2.5 29.1 1.0 CG B:ASP232 2.9 28.0 1.0 CG B:ASP124 3.1 22.0 1.0 CE1 B:HIS126 3.1 16.9 1.0 CG B:HIS126 3.3 32.8 1.0 MN B:MN2517 3.3 21.3 1.0 OD2 B:ASP124 3.4 16.9 1.0 OD1 B:ASP232 3.6 20.4 1.0 O B:HOH2579 3.7 35.4 1.0 CB B:HIS126 3.8 17.9 1.0 CB B:ASP232 4.0 17.9 1.0 O B:HOH2578 4.0 22.3 1.0 CB B:ASP234 4.0 22.1 1.0 N B:HIS126 4.1 17.5 1.0 OG1 B:THR246 4.2 27.5 1.0 N B:ALA125 4.3 19.4 1.0 NE2 B:HIS126 4.3 25.9 1.0 CD2 B:HIS126 4.4 35.1 1.0 CB B:ASP124 4.4 14.2 1.0 CA B:HIS126 4.6 25.4 1.0 OD1 B:ASP128 4.7 15.8 1.0 OD2 B:ASP128 4.8 18.2 1.0 CA B:ASP124 4.8 20.1 1.0 O B:HOH2532 4.8 24.9 1.0 CB B:ALA125 4.8 16.7 1.0 O B:THR246 4.9 26.8 1.0 C B:ALA125 4.9 9.5 1.0 CA B:ALA125 4.9 13.7 1.0 C B:ASP234 4.9 18.1 1.0 CA B:ASP234 4.9 18.3 1.0 C B:ASP124 4.9 23.5 1.0

Manganese binding site 4 out of 4 in the Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase I (Homo Sapiens): Native and Unliganded Structure at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2517 b:21.3 occ:1.00 O B:HOH2587 2.0 21.1 1.0 OD2 B:ASP128 2.2 18.2 1.0 O B:HOH2578 2.2 22.3 1.0 ND1 B:HIS101 2.2 21.9 1.0 OD2 B:ASP124 2.3 16.9 1.0 OD2 B:ASP232 2.4 17.8 1.0 CG B:ASP232 3.2 28.0 1.0 CG B:HIS101 3.2 22.9 1.0 CG B:ASP128 3.2 15.7 1.0 CE1 B:HIS101 3.2 15.2 1.0 CG B:ASP124 3.3 22.0 1.0 MN B:MN2516 3.3 19.6 1.0 CB B:HIS101 3.4 28.2 1.0 CB B:ASP232 3.5 17.9 1.0 OD1 B:ASP128 3.6 15.8 1.0 OD1 B:ASP124 3.6 19.1 1.0 OD1 B:ASP232 4.2 20.4 1.0 O B:HIS141 4.3 31.0 1.0 CD2 B:HIS101 4.3 31.4 1.0 O B:HOH2579 4.3 35.4 1.0 NE2 B:HIS101 4.3 25.1 1.0 NE1 B:TRP122 4.5 18.9 1.0 CB B:ASP128 4.5 18.0 1.0 CZ2 B:TRP122 4.6 21.1 1.0 CB B:ASP124 4.6 14.2 1.0 CG B:GLU277 4.6 21.9 1.0 OD1 B:ASP234 4.7 19.2 1.0 CE2 B:TRP122 4.9 26.1 1.0 CA B:ASP232 4.9 21.4 1.0 OE2 B:GLU277 4.9 29.5 1.0 CA B:HIS101 4.9 26.7 1.0 OD2 B:ASP234 5.0 18.1 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