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Nickel in PDB 5dou: Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form

Enzymatic activity of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form

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

Protein crystallography data

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

Resolution Low / High (Å) 40.00 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.919, 98.558, 214.890, 90.66, 98.65, 90.08
R / Rfree (%) 19.5 / 22.9

Other elements in 5dou:

The structure of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms
Potassium (K) 18 atoms
Chlorine (Cl) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form (pdb code 5dou). 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form, PDB code: 5dou:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 5dou

Go back to Nickel Binding Sites List in 5dou
Nickel binding site 1 out of 4 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni2001

b:34.2
occ:1.00
OE1 A:GLN335 2.2 18.6 1.0
OD1 A:ASN315 2.2 17.9 1.0
OE2 A:GLU362 2.3 20.7 1.0
OE1 A:GLU362 2.3 21.6 1.0
NE2 A:HIS337 2.4 17.1 1.0
CD A:GLU362 2.5 21.6 1.0
CE1 A:HIS337 3.2 16.7 1.0
CG A:ASN315 3.2 17.7 1.0
CD A:GLN335 3.3 18.3 1.0
CD2 A:HIS337 3.4 16.6 1.0
CB A:ASN315 3.6 18.1 1.0
NE2 A:GLN335 3.7 17.9 1.0
CG A:GLU362 4.0 22.4 1.0
CG A:GLN375 4.0 20.0 1.0
ND2 A:ASN355 4.1 19.1 1.0
O A:ASN361 4.1 20.2 1.0
OG1 A:THR360 4.1 24.1 1.0
ND1 A:HIS337 4.4 16.9 1.0
ND2 A:ASN315 4.4 17.5 1.0
CG A:HIS337 4.5 16.7 1.0
CG A:GLN335 4.6 18.1 1.0
CB A:GLN375 4.6 19.5 1.0
CE A:MET311 4.8 22.0 1.0
CB A:ASN355 4.9 19.5 1.0
CB A:GLU362 4.9 22.8 1.0
CB A:GLN335 4.9 17.8 1.0
CG A:ASN355 5.0 19.3 1.0

Nickel binding site 2 out of 4 in 5dou

Go back to Nickel Binding Sites List in 5dou
Nickel binding site 2 out of 4 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2001

b:75.8
occ:1.00
OD1 B:ASN315 2.1 60.7 1.0
OE2 B:GLU362 2.4 62.1 1.0
NE2 B:HIS337 2.4 69.4 1.0
OE1 B:GLU362 2.5 64.3 1.0
CD B:GLU362 2.6 62.2 1.0
OE1 B:GLN335 2.7 51.6 1.0
CE1 B:HIS337 3.1 68.3 1.0
CG B:ASN315 3.2 60.2 1.0
CD2 B:HIS337 3.6 67.6 1.0
OG1 B:THR360 3.7 67.9 1.0
CD B:GLN335 3.7 51.8 1.0
CB B:ASN315 3.7 62.1 1.0
O B:ASN361 3.8 59.9 1.0
CG B:GLU362 4.0 61.4 1.0
CG B:GLN375 4.0 73.6 1.0
ND2 B:ASN355 4.1 72.5 1.0
NE2 B:GLN335 4.1 52.0 1.0
ND2 B:ASN315 4.3 59.5 1.0
ND1 B:HIS337 4.3 67.6 1.0
CE B:MET311 4.5 73.7 1.0
CG B:HIS337 4.6 67.5 1.0
CB B:GLN375 4.7 72.5 1.0
CB B:ASN355 4.8 67.8 1.0
CB B:THR360 4.8 66.3 1.0
C B:ASN361 4.9 60.5 1.0
CB B:GLU362 4.9 63.0 1.0
CG B:ASN355 4.9 70.3 1.0

Nickel binding site 3 out of 4 in 5dou

Go back to Nickel Binding Sites List in 5dou
Nickel binding site 3 out of 4 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form


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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni2001

b:56.9
occ:1.00
OD1 C:ASN315 2.2 88.9 1.0
OE2 C:GLU362 2.3 0.0 1.0
CD C:GLU362 2.5 0.3 1.0
OE1 C:GLU362 2.5 0.6 1.0
NE2 C:HIS337 2.7 0.0 1.0
OE1 C:GLN335 3.0 0.8 1.0
CE1 C:HIS337 3.2 0.9 1.0
CG C:ASN315 3.3 88.8 1.0
OG1 C:THR360 3.4 1.0 1.0
O C:ASN361 3.6 0.2 1.0
CG C:GLU362 3.8 0.9 1.0
CD2 C:HIS337 4.0 0.2 1.0
ND2 C:ASN355 4.0 0.4 1.0
CD C:GLN335 4.0 0.4 1.0
CB C:ASN315 4.0 89.8 1.0
CG C:GLN375 4.1 0.1 1.0
NE2 C:GLN335 4.3 99.2 1.0
ND2 C:ASN315 4.3 86.7 1.0
CB C:ASN355 4.5 0.5 1.0
CE C:MET311 4.5 0.5 1.0
CB C:THR360 4.5 1.0 1.0
ND1 C:HIS337 4.5 0.6 1.0
C C:ASN361 4.6 0.5 1.0
CG C:ASN355 4.7 0.7 1.0
CB C:GLN375 4.8 0.3 1.0
CB C:GLU362 4.8 0.3 1.0
CA C:GLU362 4.9 0.5 1.0
CG C:HIS337 4.9 0.1 1.0

Nickel binding site 4 out of 4 in 5dou

Go back to Nickel Binding Sites List in 5dou
Nickel binding site 4 out of 4 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form


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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni2001

b:34.5
occ:1.00
OE1 D:GLN335 2.2 14.8 1.0
OD1 D:ASN315 2.2 17.8 1.0
NE2 D:HIS337 2.3 19.7 1.0
OE2 D:GLU362 2.3 20.4 1.0
OE1 D:GLU362 2.3 23.3 1.0
CD D:GLU362 2.6 21.0 1.0
CE1 D:HIS337 3.2 18.9 1.0
CG D:ASN315 3.2 18.2 1.0
CD D:GLN335 3.3 14.8 1.0
CD2 D:HIS337 3.4 18.4 1.0
CB D:ASN315 3.6 18.6 1.0
NE2 D:GLN335 3.7 14.4 1.0
CG D:GLN375 3.9 17.6 1.0
CG D:GLU362 4.0 20.6 1.0
O D:ASN361 4.1 22.2 1.0
OG1 D:THR360 4.1 23.4 1.0
ND2 D:ASN355 4.1 18.6 1.0
ND1 D:HIS337 4.3 18.9 1.0
ND2 D:ASN315 4.4 17.5 1.0
CG D:HIS337 4.5 18.4 1.0
CB D:GLN375 4.5 17.0 1.0
CG D:GLN335 4.6 15.1 1.0
CE D:MET311 4.8 24.6 1.0
CB D:GLU362 4.9 20.2 1.0
CB D:GLN335 4.9 15.4 1.0
CB D:ASN355 4.9 20.0 1.0

Reference:

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
Page generated: Wed Dec 16 01:40:40 2020

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