Nickel in PDB 4gsm: Crystal Structure of NI2+2-Human Arginase I

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

The structure of Crystal Structure of NI2+2-Human Arginase I, PDB code: 4gsm 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 / 1.70
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.353, 90.353, 69.814, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 18.9

The binding sites of Nickel atom in the Crystal Structure of NI2+2-Human Arginase I (pdb code 4gsm). 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 NI2+2-Human Arginase I, PDB code: 4gsm:
Jump to Nickel binding site number: 1; 2; 3; 4;

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


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 NI2+2-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:19.2 occ:1.00 OD1 A:ASP124 2.0 21.6 1.0 OD1 A:ASP234 2.1 15.5 1.0 ND1 A:HIS126 2.2 15.5 1.0 OD2 A:ASP232 2.3 19.1 1.0 O A:HOH589 2.3 30.7 1.0 OD2 A:ASP234 2.3 18.5 1.0 CG A:ASP234 2.5 16.6 1.0 CG A:ASP124 3.0 20.6 1.0 CE1 A:HIS126 3.0 15.5 1.0 CG A:ASP232 3.1 21.0 1.0 NI A:NI402 3.2 18.2 1.0 OD2 A:ASP124 3.3 18.6 1.0 CG A:HIS126 3.4 17.2 1.0 OD1 A:ASP232 3.7 20.4 1.0 CB A:HIS126 3.8 17.9 1.0 N A:HIS126 3.9 13.8 1.0 O A:HOH573 3.9 28.2 1.0 N A:ALA125 3.9 15.1 1.0 CB A:ASP234 4.0 15.7 1.0 CB A:ASP232 4.1 18.4 1.0 NE2 A:HIS126 4.2 17.1 1.0 OG1 A:THR246 4.3 15.9 1.0 CB A:ASP124 4.3 19.2 1.0 CD2 A:HIS126 4.4 16.2 1.0 O A:HOH559 4.4 32.4 1.0 CA A:HIS126 4.4 15.0 1.0 CB A:ALA125 4.6 14.1 1.0 OD2 A:ASP128 4.6 13.8 1.0 CA A:ALA125 4.6 14.2 1.0 CA A:ASP124 4.6 17.0 1.0 C A:ALA125 4.6 12.2 1.0 OD1 A:ASP128 4.7 18.1 1.0 C A:ASP124 4.7 15.8 1.0 CA A:ASP234 4.9 15.6 1.0 O A:HOH536 4.9 16.7 1.0 C A:ASP234 4.9 15.2 1.0

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


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 NI2+2-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:18.2 occ:1.00 OD2 A:ASP124 2.1 18.6 1.0 OD1 A:ASP128 2.1 18.1 1.0 OD2 A:ASP232 2.1 19.1 1.0 ND1 A:HIS101 2.2 17.8 1.0 O A:HOH589 2.3 30.7 1.0 O A:HOH559 2.7 32.4 1.0 CG A:ASP124 3.1 20.6 1.0 CG A:ASP128 3.1 13.5 1.0 CG A:ASP232 3.1 21.0 1.0 CE1 A:HIS101 3.2 18.2 1.0 NI A:NI401 3.2 19.2 1.0 CG A:HIS101 3.3 17.9 1.0 OD1 A:ASP124 3.4 21.6 1.0 OD2 A:ASP128 3.4 13.8 1.0 CB A:ASP232 3.6 18.4 1.0 CB A:HIS101 3.6 18.5 1.0 O A:HIS141 4.2 17.8 1.0 OD1 A:ASP232 4.2 20.4 1.0 NE2 A:HIS101 4.3 16.3 1.0 CD2 A:HIS101 4.4 18.6 1.0 CB A:ASP128 4.4 15.4 1.0 CB A:ASP124 4.4 19.2 1.0 NE1 A:TRP122 4.4 17.1 1.0 CZ2 A:TRP122 4.6 16.3 1.0 O A:HOH573 4.6 28.2 1.0 OD2 A:ASP234 4.7 18.5 1.0 OD1 A:ASP234 4.8 15.5 1.0 ND1 A:HIS126 4.9 15.5 1.0 CE2 A:TRP122 4.9 16.1 1.0 CG A:GLU277 4.9 18.2 1.0 CA A:ASP232 4.9 18.4 1.0 OE2 A:GLU277 5.0 19.1 1.0

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


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 NI2+2-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:21.5 occ:1.00 OD1 B:ASP124 2.1 16.1 1.0 OD1 B:ASP234 2.2 18.8 1.0 OD2 B:ASP234 2.3 18.7 1.0 ND1 B:HIS126 2.3 18.0 1.0 O B:HOH565 2.3 34.6 1.0 OD2 B:ASP232 2.4 23.5 1.0 CG B:ASP234 2.5 20.9 1.0 CG B:ASP124 3.0 15.5 1.0 CG B:ASP232 3.1 21.6 1.0 NI B:NI402 3.1 22.4 1.0 CE1 B:HIS126 3.2 18.2 1.0 OD2 B:ASP124 3.2 14.8 1.0 CG B:HIS126 3.4 20.2 1.0 OD1 B:ASP232 3.6 20.8 1.0 CB B:HIS126 3.7 17.5 1.0 N B:HIS126 3.9 17.0 1.0 CB B:ASP232 4.0 19.9 1.0 CB B:ASP234 4.1 19.5 1.0 N B:ALA125 4.1 18.3 1.0 O B:HOH530 4.2 30.1 1.0 OG1 B:THR246 4.2 25.0 1.0 NE2 B:HIS126 4.3 18.0 1.0 CB B:ASP124 4.4 16.6 1.0 CA B:HIS126 4.4 18.1 1.0 CD2 B:HIS126 4.5 18.2 1.0 OD2 B:ASP128 4.5 16.8 1.0 CB B:ALA125 4.6 17.1 1.0 OD1 B:ASP128 4.7 17.7 1.0 C B:ALA125 4.7 15.9 1.0 CA B:ALA125 4.7 16.7 1.0 CA B:ASP124 4.8 16.5 1.0 C B:ASP124 4.8 17.4 1.0 O B:HOH502 4.9 18.2 1.0 CA B:ASP234 4.9 18.4 1.0 C B:ASP234 4.9 16.3 1.0 O B:THR246 5.0 23.3 1.0 CG B:ASP128 5.0 18.6 1.0

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


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 NI2+2-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:22.4 occ:1.00 OD1 B:ASP128 2.1 17.7 1.0 OD2 B:ASP124 2.1 14.8 1.0 OD2 B:ASP232 2.2 23.5 1.0 ND1 B:HIS101 2.2 22.6 1.0 O B:HOH565 2.3 34.6 1.0 O B:HOH530 2.5 30.1 1.0 CG B:ASP128 3.1 18.6 1.0 NI B:NI401 3.1 21.5 1.0 CG B:ASP124 3.1 15.5 1.0 CE1 B:HIS101 3.2 22.6 1.0 CG B:ASP232 3.2 21.6 1.0 CG B:HIS101 3.2 21.9 1.0 OD2 B:ASP128 3.4 16.8 1.0 OD1 B:ASP124 3.5 16.1 1.0 CB B:HIS101 3.5 22.8 1.0 CB B:ASP232 3.6 19.9 1.0 O B:HIS141 4.2 24.4 1.0 NE2 B:HIS101 4.3 21.4 1.0 OD1 B:ASP232 4.4 20.8 1.0 CD2 B:HIS101 4.4 24.4 1.0 CB B:ASP128 4.4 18.8 1.0 NE1 B:TRP122 4.4 20.7 1.0 CB B:ASP124 4.5 16.6 1.0 CZ2 B:TRP122 4.6 20.1 1.0 OD2 B:ASP234 4.7 18.7 1.0 CG B:GLU277 4.8 25.6 1.0 OD1 B:ASP234 4.8 18.8 1.0 ND1 B:HIS126 4.8 18.0 1.0 CE2 B:TRP122 4.9 21.2 1.0 CB B:HIS126 4.9 17.5 1.0 CA B:ASP232 4.9 19.9 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