Cobalt in PDB 4fck: Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex

All present enzymatic activity of Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex:
3.5.3.1;

The structure of Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex, PDB code: 4fck 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 / 1.90
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.451, 90.451, 69.362, 90.00, 90.00, 120.00
R / Rfree (%)	27.3 / 30.7

The binding sites of Cobalt atom in the Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex (pdb code 4fck). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex, PDB code: 4fck:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:16.6 occ:1.00 OD2 A:ASP124 1.9 14.9 1.0 O A:HOH628 2.0 46.4 1.0 OD2 A:ASP128 2.2 17.3 1.0 ND1 A:HIS101 2.2 15.8 1.0 OD2 A:ASP232 2.2 17.4 1.0 CG A:ASP124 2.9 14.8 1.0 CE1 A:HIS101 3.1 16.6 1.0 CO A:CO403 3.1 24.6 1.0 CG A:ASP232 3.2 18.8 1.0 CG A:HIS101 3.2 16.4 1.0 CG A:ASP128 3.2 14.0 1.0 OD1 A:ASP124 3.3 15.7 1.0 CB A:HIS101 3.5 15.9 1.0 CB A:ASP232 3.5 17.1 1.0 OD1 A:ASP128 3.5 11.5 1.0 NE1 A:TRP122 4.1 15.1 1.0 CB A:ASP124 4.2 14.6 1.0 O A:HOH543 4.2 17.5 1.0 NE2 A:HIS101 4.2 14.5 1.0 CD2 A:HIS101 4.3 15.0 1.0 OD1 A:ASP232 4.3 18.9 1.0 CB A:ASP128 4.5 15.2 1.0 O A:HIS141 4.5 15.7 1.0 NH1 A:GPA401 4.5 16.3 1.0 CZ2 A:TRP122 4.5 14.4 1.0 CE2 A:TRP122 4.7 13.8 1.0 CG A:GLU277 4.7 13.4 1.0 OD2 A:ASP234 4.8 16.1 1.0 ND1 A:HIS126 4.8 13.3 1.0 CA A:ASP232 4.9 15.9 1.0 OD1 A:ASP234 4.9 18.4 1.0 OE2 A:GLU277 4.9 11.7 1.0 O A:HIS126 4.9 14.9 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:24.6 occ:1.00 OD1 A:ASP124 2.0 15.7 1.0 OD2 A:ASP234 2.2 16.1 1.0 OD2 A:ASP232 2.3 17.4 1.0 ND1 A:HIS126 2.4 13.3 1.0 OD1 A:ASP234 2.4 18.4 1.0 CG A:ASP234 2.6 17.4 1.0 CG A:ASP124 2.9 14.8 1.0 CG A:ASP232 3.1 18.8 1.0 CE1 A:HIS126 3.1 13.4 1.0 CO A:CO402 3.1 16.6 1.0 OD2 A:ASP124 3.2 14.9 1.0 O A:HOH543 3.3 17.5 1.0 CG A:HIS126 3.5 15.2 1.0 O A:HOH628 3.5 46.4 1.0 OD1 A:ASP232 3.6 18.9 1.0 N A:HIS126 3.9 11.6 1.0 N A:ALA125 3.9 11.7 1.0 CB A:HIS126 4.0 15.5 1.0 CB A:ASP232 4.0 17.1 1.0 CB A:ASP234 4.1 16.3 1.0 CB A:ASP124 4.3 14.6 1.0 NE2 A:HIS126 4.3 13.1 1.0 NH1 A:GPA401 4.4 16.3 1.0 CD2 A:HIS126 4.5 13.0 1.0 CB A:ALA125 4.5 9.0 1.0 CA A:HIS126 4.6 13.7 1.0 OG1 A:THR246 4.6 14.7 1.0 CA A:ASP124 4.6 12.9 1.0 OD2 A:ASP128 4.6 17.3 1.0 CA A:ALA125 4.6 10.9 1.0 C A:ALA125 4.7 10.5 1.0 OD1 A:ASP128 4.7 11.5 1.0 C A:ASP124 4.7 12.4 1.0 NH2 A:GPA401 4.8 18.7 1.0 O A:HOH521 4.8 13.1 1.0 C A:ASP234 4.9 13.8 1.0 CA A:ASP234 5.0 14.4 1.0 CZ A:GPA401 5.0 16.1 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:21.7 occ:1.00 OD2 B:ASP124 1.9 17.6 1.0 O B:HOH604 1.9 30.2 1.0 OD2 B:ASP128 1.9 16.1 1.0 ND1 B:HIS101 2.2 21.2 1.0 OD2 B:ASP232 2.4 19.0 1.0 CG B:ASP124 3.0 15.8 1.0 CG B:ASP128 3.0 17.3 1.0 CE1 B:HIS101 3.1 18.4 1.0 CG B:HIS101 3.1 21.0 1.0 CO B:CO403 3.2 21.5 1.0 OD1 B:ASP128 3.4 15.8 1.0 OD1 B:ASP124 3.4 16.4 1.0 CG B:ASP232 3.4 17.7 1.0 CB B:HIS101 3.5 20.5 1.0 CB B:ASP232 3.7 16.5 1.0 NE1 B:TRP122 4.2 18.9 1.0 NE2 B:HIS101 4.2 20.3 1.0 CB B:ASP124 4.2 16.6 1.0 O B:HOH566 4.3 22.9 1.0 CD2 B:HIS101 4.3 21.7 1.0 CB B:ASP128 4.3 16.3 1.0 CZ2 B:TRP122 4.4 18.9 1.0 O B:HIS141 4.5 19.0 1.0 OD1 B:ASP232 4.6 16.4 1.0 CE2 B:TRP122 4.6 19.7 1.0 NH1 B:GPA401 4.7 23.2 1.0 O B:HIS126 4.8 17.8 1.0 ND1 B:HIS126 4.8 21.1 1.0 CG B:GLU277 4.9 18.2 1.0 CA B:HIS101 5.0 22.1 1.0 CA B:ASP232 5.0 16.5 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the CO2+2-Human Arginase I-Agpa Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co403 b:21.5 occ:1.00 OD1 B:ASP124 2.1 16.4 1.0 O B:HOH604 2.2 30.2 1.0 ND1 B:HIS126 2.2 21.1 1.0 OD2 B:ASP232 2.3 19.0 1.0 OD1 B:ASP234 2.3 17.6 1.0 OD2 B:ASP234 2.4 16.3 1.0 CG B:ASP234 2.7 20.5 1.0 CG B:ASP124 3.0 15.8 1.0 CE1 B:HIS126 3.0 21.0 1.0 CG B:ASP232 3.1 17.7 1.0 CO B:CO402 3.2 21.7 1.0 OD2 B:ASP124 3.2 17.6 1.0 CG B:HIS126 3.4 21.1 1.0 O B:HOH566 3.6 22.9 1.0 OD1 B:ASP232 3.7 16.4 1.0 CB B:HIS126 3.9 19.0 1.0 N B:HIS126 4.0 17.1 1.0 CB B:ASP232 4.0 16.5 1.0 N B:ALA125 4.1 16.9 1.0 NE2 B:HIS126 4.2 21.3 1.0 CB B:ASP234 4.2 17.9 1.0 CB B:ASP124 4.4 16.6 1.0 CD2 B:HIS126 4.4 22.3 1.0 OD1 B:ASP128 4.5 15.8 1.0 OG1 B:THR246 4.5 19.2 1.0 CA B:HIS126 4.5 18.0 1.0 OD2 B:ASP128 4.6 16.1 1.0 NH1 B:GPA401 4.6 23.2 1.0 NH2 B:GPA401 4.7 23.2 1.0 CB B:ALA125 4.7 13.5 1.0 O B:HOH520 4.7 13.7 1.0 CA B:ASP124 4.8 16.3 1.0 C B:ALA125 4.8 14.5 1.0 CA B:ALA125 4.8 15.1 1.0 C B:ASP124 4.9 16.8 1.0 CZ B:GPA401 5.0 22.5 1.0 CG B:ASP128 5.0 17.3 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