Nickel in PDB 4gsv: Crystal Structure of the NI2+2-Human Arginase I-Abh Complex

All present enzymatic activity of Crystal Structure of the NI2+2-Human Arginase I-Abh Complex:
3.5.3.1;

The structure of Crystal Structure of the NI2+2-Human Arginase I-Abh Complex, PDB code: 4gsv was solved by E.L.D'antonio, Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.48
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.711, 90.711, 69.658, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 19.3

The binding sites of Nickel atom in the Crystal Structure of the NI2+2-Human Arginase I-Abh Complex (pdb code 4gsv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the NI2+2-Human Arginase I-Abh Complex, PDB code: 4gsv:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the NI2+2-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the NI2+2-Human Arginase I-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:14.6 occ:1.00 OD2 A:ASP124 2.0 15.8 1.0 OD2 A:ASP128 2.1 13.7 1.0 ND1 A:HIS101 2.2 14.4 1.0 O1 A:ABH403 2.2 19.8 1.0 OD2 A:ASP232 2.2 15.7 1.0 O2 A:ABH403 2.4 21.4 1.0 B A:ABH403 2.8 19.5 1.0 CG A:ASP124 3.0 14.4 1.0 CG A:ASP128 3.1 13.8 1.0 CE1 A:HIS101 3.2 14.3 1.0 CG A:HIS101 3.2 15.2 1.0 CG A:ASP232 3.2 15.4 1.0 NI A:NI402 3.2 15.5 1.0 OD1 A:ASP124 3.3 15.5 1.0 OD1 A:ASP128 3.4 12.2 1.0 CB A:HIS101 3.4 16.0 1.0 CB A:ASP232 3.5 14.8 1.0 O3 A:ABH403 3.6 20.2 1.0 CE A:ABH403 4.1 18.0 1.0 NE2 A:HIS101 4.3 12.7 1.0 OD1 A:ASP232 4.3 14.9 1.0 CD2 A:HIS101 4.3 14.6 1.0 NE1 A:TRP122 4.3 15.2 1.0 CB A:ASP124 4.3 13.3 1.0 O A:HIS141 4.4 14.3 1.0 CB A:ASP128 4.5 14.3 1.0 CZ2 A:TRP122 4.6 13.3 1.0 CE2 A:TRP122 4.8 13.5 1.0 OD1 A:ASP234 4.8 14.2 1.0 OD2 A:ASP234 4.8 12.6 1.0 ND1 A:HIS126 4.9 13.5 1.0 CG A:GLU277 4.9 15.8 1.0 CA A:ASP232 4.9 14.3 1.0 CA A:HIS101 5.0 14.4 1.0 OE2 A:GLU277 5.0 18.7 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the NI2+2-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the NI2+2-Human Arginase I-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:15.5 occ:1.00 OD1 A:ASP124 2.0 15.5 1.0 ND1 A:HIS126 2.1 13.5 1.0 OD2 A:ASP232 2.2 15.7 1.0 O1 A:ABH403 2.3 19.8 1.0 OD1 A:ASP234 2.3 14.2 1.0 OD2 A:ASP234 2.3 12.6 1.0 CG A:ASP234 2.6 13.8 1.0 CE1 A:HIS126 2.9 12.5 1.0 CG A:ASP124 3.0 14.4 1.0 O3 A:ABH403 3.1 20.2 1.0 CG A:ASP232 3.2 15.4 1.0 B A:ABH403 3.2 19.5 1.0 NI A:NI401 3.2 14.6 1.0 CG A:HIS126 3.3 13.8 1.0 OD2 A:ASP124 3.3 15.8 1.0 CB A:HIS126 3.8 14.8 1.0 OD1 A:ASP232 3.8 14.9 1.0 N A:HIS126 3.9 12.5 1.0 N A:ALA125 4.0 11.8 1.0 O2 A:ABH403 4.1 21.4 1.0 CB A:ASP234 4.1 13.8 1.0 NE2 A:HIS126 4.1 14.2 1.0 CB A:ASP232 4.1 14.8 1.0 OG1 A:THR246 4.2 22.7 1.0 CD2 A:HIS126 4.3 13.5 1.0 CB A:ASP124 4.3 13.3 1.0 CE A:ABH403 4.4 18.0 1.0 CD A:ABH403 4.4 18.6 1.0 OD1 A:ASP128 4.4 12.2 1.0 CA A:HIS126 4.4 12.5 1.0 CB A:ALA125 4.6 13.6 1.0 CA A:ASP124 4.7 12.8 1.0 OD2 A:ASP128 4.7 13.7 1.0 CA A:ALA125 4.7 12.6 1.0 C A:ALA125 4.7 11.6 1.0 C A:ASP124 4.8 11.4 1.0 O A:HOH501 4.8 12.1 1.0 CA A:ASP234 5.0 12.9 1.0 O A:HIS126 5.0 13.8 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the NI2+2-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the NI2+2-Human Arginase I-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:18.4 occ:1.00 OD2 B:ASP128 2.1 17.2 1.0 OD2 B:ASP124 2.1 13.5 1.0 ND1 B:HIS101 2.2 19.8 1.0 OD2 B:ASP232 2.3 16.4 1.0 O1 B:ABH403 2.3 24.0 1.0 O2 B:ABH403 2.4 24.7 1.0 B B:ABH403 2.8 24.6 1.0 CG B:ASP128 3.1 16.6 1.0 CG B:ASP124 3.1 13.9 1.0 NI B:NI402 3.2 18.4 1.0 CG B:HIS101 3.2 19.8 1.0 CE1 B:HIS101 3.2 18.2 1.0 CG B:ASP232 3.3 17.4 1.0 OD1 B:ASP128 3.4 15.6 1.0 OD1 B:ASP124 3.4 15.1 1.0 CB B:HIS101 3.5 20.9 1.0 CB B:ASP232 3.6 16.3 1.0 O3 B:ABH403 3.6 23.6 1.0 CE B:ABH403 4.1 23.8 1.0 NE2 B:HIS101 4.3 18.9 1.0 CD2 B:HIS101 4.3 21.6 1.0 OD1 B:ASP232 4.4 14.7 1.0 NE1 B:TRP122 4.4 18.9 1.0 CB B:ASP128 4.4 16.7 1.0 O B:HIS141 4.4 20.4 1.0 CB B:ASP124 4.4 14.6 1.0 CZ2 B:TRP122 4.6 19.0 1.0 OD1 B:ASP234 4.8 16.9 1.0 CE2 B:TRP122 4.8 20.0 1.0 CG B:GLU277 4.9 21.5 1.0 OD2 B:ASP234 4.9 14.3 1.0 ND1 B:HIS126 4.9 15.5 1.0 CA B:ASP232 5.0 16.3 1.0 CA B:HIS101 5.0 20.2 1.0 CB B:HIS126 5.0 15.6 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the NI2+2-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the NI2+2-Human Arginase I-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:18.4 occ:1.00 OD1 B:ASP124 2.1 15.1 1.0 O1 B:ABH403 2.2 24.0 1.0 OD1 B:ASP234 2.2 16.9 1.0 OD2 B:ASP232 2.3 16.4 1.0 ND1 B:HIS126 2.3 15.5 1.0 OD2 B:ASP234 2.3 14.3 1.0 CG B:ASP234 2.6 16.9 1.0 CG B:ASP124 3.0 13.9 1.0 O3 B:ABH403 3.0 23.6 1.0 CG B:ASP232 3.1 17.4 1.0 B B:ABH403 3.1 24.6 1.0 NI B:NI401 3.2 18.4 1.0 CE1 B:HIS126 3.2 15.0 1.0 OD2 B:ASP124 3.3 13.5 1.0 CG B:HIS126 3.4 16.9 1.0 CB B:HIS126 3.7 15.6 1.0 OD1 B:ASP232 3.7 14.7 1.0 O2 B:ABH403 3.9 24.7 1.0 N B:HIS126 4.0 14.3 1.0 CB B:ASP232 4.1 16.3 1.0 CB B:ASP234 4.1 17.0 1.0 N B:ALA125 4.1 13.9 1.0 CE B:ABH403 4.3 23.8 1.0 NE2 B:HIS126 4.3 15.8 1.0 CB B:ASP124 4.4 14.6 1.0 OD1 B:ASP128 4.4 15.6 1.0 CD B:ABH403 4.4 23.3 1.0 CA B:HIS126 4.4 15.3 1.0 CD2 B:HIS126 4.4 14.8 1.0 OD2 B:ASP128 4.6 17.2 1.0 CB B:ALA125 4.8 13.0 1.0 CA B:ASP124 4.8 13.9 1.0 C B:ALA125 4.8 13.0 1.0 CA B:ALA125 4.9 12.9 1.0 C B:ASP124 4.9 13.7 1.0 CG B:ASP128 4.9 16.6 1.0 O B:HOH535 4.9 18.1 1.0 C B:ASP234 5.0 14.2 1.0 CA B:ASP234 5.0 14.3 1.0

E.L.D'antonio, Y.Hai, D.W.Christianson. Structure and Function of Non-Native Metal Clusters in Human Arginase I. Biochemistry V. 51 8399 2012.
ISSN: ISSN 0006-2960
PubMed: 23061982
DOI: 10.1021/BI301145N