Nickel in PDB 5dot: Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form

All present enzymatic activity of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form:
6.3.4.16;

The structure of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form, PDB code: 5dot was solved by L.M.Polo, S.De Cima, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.95 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.337, 133.482, 142.907, 90.00, 102.51, 90.00
R / Rfree (%)	16.5 / 19.6

The binding sites of Nickel atom in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form (pdb code 5dot). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form, PDB code: 5dot:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form


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 Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1601 b:36.6 occ:1.00 OE1 A:GLN335 2.1 31.0 1.0 O A:HOH1847 2.1 35.9 1.0 OD1 A:ASN315 2.3 35.2 1.0 OE1 A:GLU362 2.3 28.1 1.0 NE2 A:HIS337 2.4 32.7 1.0 OE2 A:GLU362 2.4 33.8 1.0 CD A:GLU362 2.7 30.1 1.0 CD A:GLN335 3.1 32.1 1.0 CE1 A:HIS337 3.2 32.9 1.0 CG A:ASN315 3.2 31.7 1.0 CD2 A:HIS337 3.5 33.3 1.0 CB A:ASN315 3.5 28.1 1.0 NE2 A:GLN335 3.6 32.3 1.0 CG A:GLN375 3.9 30.0 1.0 ND2 A:ASN355 4.1 30.8 1.0 CG A:GLU362 4.1 30.6 1.0 OG1 A:THR360 4.2 33.8 1.0 ND1 A:HIS337 4.4 33.7 1.0 ND2 A:ASN315 4.5 31.0 1.0 CG A:GLN335 4.5 31.4 1.0 O A:ASN361 4.5 30.8 1.0 CG A:HIS337 4.5 33.7 1.0 CB A:GLN375 4.6 28.5 1.0 CB A:GLN335 4.8 27.8 1.0 CE A:MET311 4.9 32.3 1.0 CB A:GLU362 5.0 30.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form


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 Human Carbamoyl Phosphate Synthetase I (CPS1), Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1601 b:32.4 occ:1.00 OE1 B:GLN335 2.1 27.9 1.0 O B:HOH1819 2.3 27.8 1.0 OD1 B:ASN315 2.3 24.8 1.0 OE1 B:GLU362 2.3 24.6 1.0 NE2 B:HIS337 2.4 26.2 1.0 OE2 B:GLU362 2.4 28.8 1.0 CD B:GLU362 2.7 25.2 1.0 CD B:GLN335 3.1 27.2 1.0 CE1 B:HIS337 3.2 27.6 1.0 CG B:ASN315 3.2 23.3 1.0 CD2 B:HIS337 3.5 24.9 1.0 CB B:ASN315 3.5 22.3 1.0 NE2 B:GLN335 3.6 28.2 1.0 CG B:GLN375 3.9 26.8 1.0 ND2 B:ASN355 4.0 22.9 1.0 CG B:GLU362 4.1 24.3 1.0 OG1 B:THR360 4.2 26.1 1.0 ND1 B:HIS337 4.4 27.2 1.0 CG B:GLN335 4.5 25.9 1.0 ND2 B:ASN315 4.5 21.5 1.0 O B:ASN361 4.5 25.4 1.0 CG B:HIS337 4.5 26.9 1.0 CB B:GLN375 4.6 24.8 1.0 CB B:GLN335 4.8 23.9 1.0 CE B:MET311 4.9 25.8 1.0

S.De Cima, L.M.Polo, C.Diez-Fernandez, A.I.Martinez, J.Cervera, I.Fita, V.Rubio. Structure of Human Carbamoyl Phosphate Synthetase: Deciphering the on/Off Switch of Human Ureagenesis. Sci Rep V. 5 16950 2015.
ISSN: ESSN 2045-2322
PubMed: 26592762
DOI: 10.1038/SREP16950