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

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

The structure of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-S, PDB code: 8dsd 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)	19.86 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.512, 106.691, 82.803, 90, 96.55, 90
R / Rfree (%)	16.4 / 18.6

The binding sites of Chlorine atom in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-S (pdb code 8dsd). 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-S, PDB code: 8dsd:
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-S


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-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1004 b:15.8 occ:0.77 O B:HOH1391 2.9 16.7 1.0 NH2 B:ARG311 2.9 15.9 1.0 OH A:TYR18 3.2 12.9 1.0 O B:HOH1254 3.2 34.3 1.0 CB B:GLU246 3.6 12.6 1.0 CA B:GLU246 3.7 11.5 1.0 CE2 A:TYR18 3.8 12.1 1.0 O A:HOH1325 3.9 13.6 1.0 CZ B:ARG311 3.9 16.2 1.0 NH1 B:ARG311 3.9 17.2 1.0 CZ A:TYR18 4.0 11.6 1.0 C2 B:NCA1101 4.1 14.4 1.0 N B:HIS247 4.2 11.4 1.0 N1 B:NCA1101 4.2 16.3 1.0 ND1 B:HIS247 4.2 13.0 1.0 O B:ALA245 4.5 12.4 1.0 C B:GLU246 4.5 11.1 1.0 CE1 B:HIS247 4.6 13.5 1.0 NH1 B:ARG196 4.8 15.2 1.0 N B:GLU246 4.9 12.4 1.0 CG B:GLU246 5.0 12.2 1.0 O A:HOH1262 5.0 16.6 1.0

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


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-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1005 b:17.2 occ:0.77 O A:HOH1273 2.9 18.8 1.0 NH2 A:ARG311 3.0 15.3 0.7 OH B:TYR18 3.1 15.4 1.0 O A:HOH1197 3.1 30.4 1.0 NH1 A:ARG311 3.3 14.3 0.3 NH2 A:ARG311 3.4 14.0 0.3 CB A:GLU246 3.5 13.7 1.0 CA A:GLU246 3.7 14.0 1.0 O B:HOH1430 3.8 16.0 1.0 CE2 B:TYR18 3.8 13.1 1.0 CZ A:ARG311 3.8 16.0 0.3 CZ A:ARG311 3.9 14.2 0.7 NH1 A:ARG311 3.9 15.7 0.7 CZ B:TYR18 3.9 13.3 1.0 C2 A:NCA1001 4.1 13.9 1.0 N A:HIS247 4.2 13.2 1.0 N1 A:NCA1001 4.2 17.5 1.0 ND1 A:HIS247 4.3 14.3 1.0 O A:ALA245 4.5 13.5 1.0 C A:GLU246 4.5 13.4 1.0 CE1 A:HIS247 4.6 15.4 1.0 NH1 A:ARG196 4.6 15.6 1.0 O B:HOH1350 4.9 18.0 1.0 N A:GLU246 4.9 13.9 1.0 CG A:GLU246 5.0 15.5 1.0

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


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-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1006 b:31.6 occ:0.74 O A:HOH1583 2.9 39.1 1.0 N A:LYS77 3.1 20.9 1.0 O A:HOH1256 3.5 40.9 1.0 CA A:THR76 3.5 19.6 1.0 CB A:THR76 3.6 20.0 1.0 C A:THR76 3.8 18.8 1.0 NZ A:LYS73 3.9 30.5 1.0 CD1 A:LEU105 4.0 19.9 1.0 CB A:LYS77 4.0 20.3 1.0 OE1 A:GLU78 4.1 28.8 1.0 CA A:LYS77 4.1 21.0 1.0 CD2 A:LEU105 4.2 22.7 1.0 CE A:LYS73 4.2 26.0 1.0 CG2 A:THR76 4.2 21.8 1.0 CG A:LEU105 4.7 19.3 1.0 OG1 A:THR76 4.8 20.2 1.0 N A:THR76 4.9 18.1 1.0 O A:VAL75 4.9 21.3 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