Chlorine in PDB 8dsc: Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R

All present enzymatic activity of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R:
2.4.2.12;

The structure of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R, PDB code: 8dsc was solved by K.Ratia, R.Xiong, Z.Shen, G.R.Thatcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.92 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.376, 106.338, 82.806, 90, 96.45, 90
R / Rfree (%)	16 / 17.5

The structure of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R (pdb code 8dsc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R, PDB code: 8dsc:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1005 b:13.9 occ:1.00 NH2 B:ARG311 3.0 12.8 1.0 O B:HOH1403 3.0 11.9 1.0 OH A:TYR18 3.0 8.3 1.0 O B:HOH1261 3.2 23.8 1.0 CB B:GLU246 3.6 8.5 1.0 CA B:GLU246 3.7 7.6 1.0 CE2 A:TYR18 3.8 8.6 1.0 CZ A:TYR18 3.9 7.6 1.0 O A:HOH1329 3.9 10.5 1.0 CZ B:ARG311 3.9 13.2 1.0 NH1 B:ARG311 3.9 14.2 1.0 C2 B:NCA1101 4.2 11.3 1.0 N B:HIS247 4.2 7.4 1.0 ND1 B:HIS247 4.2 9.1 1.0 N1 B:NCA1101 4.2 11.7 1.0 O B:ALA245 4.5 8.4 1.0 C B:GLU246 4.5 7.5 1.0 CE1 B:HIS247 4.6 9.4 1.0 NH1 B:ARG196 4.8 10.3 1.0 N B:GLU246 4.9 7.7 1.0 CG B:GLU246 5.0 9.1 1.0

Chlorine binding site 2 out of 3 in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1006 b:15.7 occ:1.00 NH2 A:ARG311 2.9 10.4 0.6 O A:HOH1295 3.0 15.0 1.0 OH B:TYR18 3.0 9.6 1.0 NH1 A:ARG311 3.2 11.9 0.4 O A:HOH1200 3.2 24.8 1.0 NH2 A:ARG311 3.4 9.9 0.4 CB A:GLU246 3.6 10.2 1.0 CZ A:ARG311 3.7 12.3 0.4 CA A:GLU246 3.7 9.5 1.0 CE2 B:TYR18 3.8 10.0 1.0 CZ A:ARG311 3.8 11.0 0.6 O B:HOH1432 3.8 11.4 1.0 CZ B:TYR18 3.8 8.8 1.0 NH1 A:ARG311 3.9 11.7 0.6 C2 A:NCA1001 4.2 11.6 1.0 N A:HIS247 4.2 9.5 1.0 ND1 A:HIS247 4.2 11.0 1.0 N1 A:NCA1001 4.3 13.3 1.0 O A:ALA245 4.5 9.4 1.0 C A:GLU246 4.5 9.3 1.0 CE1 A:HIS247 4.6 10.5 1.0 NH1 A:ARG196 4.7 12.1 1.0 N A:GLU246 4.9 9.6 1.0 CG A:GLU246 5.0 11.3 1.0 O B:HOH1399 5.0 14.5 1.0

Chlorine binding site 3 out of 3 in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1007 b:27.6 occ:1.00 O A:HOH1592 2.8 34.3 1.0 N A:LYS77 3.1 15.1 1.0 CA A:THR76 3.5 15.7 1.0 CB A:THR76 3.7 16.5 1.0 C A:THR76 3.8 14.3 1.0 NZ A:LYS73 3.9 26.3 1.0 CD1 A:LEU105 4.0 15.6 1.0 CB A:LYS77 4.1 18.0 1.0 OE1 A:GLU78 4.1 24.1 1.0 CE A:LYS73 4.2 17.3 1.0 CD2 A:LEU105 4.2 18.1 1.0 CA A:LYS77 4.2 15.7 1.0 CG A:LYS77 4.2 25.2 1.0 CG2 A:THR76 4.3 18.2 1.0 CG A:LEU105 4.7 13.9 1.0 O A:HOH1608 4.8 39.6 1.0 CD A:LYS77 4.9 32.7 1.0 OG1 A:THR76 4.9 15.2 1.0 N A:THR76 4.9 13.7 1.0 O A:VAL75 5.0 15.9 1.0

K.M.Ratia, Z.Shen, J.Gordon-Blake, H.Lee, M.S.Laham, I.S.Krider, N.Christie, M.Ackerman-Berrier, C.Penton, N.G.Knowles, S.R.Musku, J.Fu, G.R.Velma, R.Xiong, G.R.J.Thatcher. Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular Nad. Biochemistry V. 62 923 2023.
ISSN: ISSN 0006-2960
PubMed: 36746631
DOI: 10.1021/ACS.BIOCHEM.2C00655