Chlorine in PDB 8dse: Human Nampt in Complex with Substrate Nam and Activator Quercitrin

All present enzymatic activity of Human Nampt in Complex with Substrate Nam and Activator Quercitrin:
2.4.2.12;

The structure of Human Nampt in Complex with Substrate Nam and Activator Quercitrin, PDB code: 8dse 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 (°)	60.865, 106.786, 82.689, 90, 96.61, 90
R / Rfree (%)	16.5 / 18.4

The binding sites of Chlorine atom in the Human Nampt in Complex with Substrate Nam and Activator Quercitrin (pdb code 8dse). 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 Activator Quercitrin, PDB code: 8dse:
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 Activator Quercitrin


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 Activator Quercitrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1002 b:32.7 occ:0.79 O A:HOH1152 2.7 39.5 1.0 O A:HOH1570 2.8 40.1 1.0 N A:LYS77 3.1 19.7 1.0 O A:HOH1371 3.5 41.1 1.0 CA A:THR76 3.6 19.2 1.0 CB A:THR76 3.6 19.4 1.0 C A:THR76 3.8 18.1 1.0 NZ A:LYS73 4.0 30.3 1.0 CD1 A:LEU105 4.0 20.2 1.0 CB A:LYS77 4.1 19.5 1.0 OE1 A:GLU78 4.1 27.6 1.0 CA A:LYS77 4.2 18.5 1.0 CE A:LYS73 4.2 23.9 1.0 CG2 A:THR76 4.3 22.1 1.0 CD2 A:LEU105 4.3 20.3 1.0 CG A:LEU105 4.7 18.0 1.0 OG1 A:THR76 4.9 19.0 1.0 N A:THR76 4.9 17.9 1.0 O A:VAL75 4.9 19.3 1.0

Chlorine binding site 2 out of 3 in the Human Nampt in Complex with Substrate Nam and Activator Quercitrin


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 Activator Quercitrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1004 b:15.4 occ:0.81 O A:HOH1239 2.9 16.6 1.0 OH B:TYR18 2.9 11.4 1.0 NH2 A:ARG311 3.0 14.4 1.0 O A:HOH1280 3.1 29.3 1.0 CB A:GLU246 3.6 11.7 1.0 O B:HOH1441 3.8 12.7 1.0 CA A:GLU246 3.8 12.6 1.0 CZ B:TYR18 3.8 11.0 1.0 CE2 B:TYR18 3.8 13.0 1.0 NH1 A:ARG311 3.9 16.9 1.0 CZ A:ARG311 3.9 12.7 1.0 C2 A:NCA1001 4.0 12.2 1.0 N1 A:NCA1001 4.2 13.5 1.0 ND1 A:HIS247 4.3 12.8 1.0 N A:HIS247 4.3 12.7 1.0 O A:ALA245 4.5 11.7 1.0 NH1 A:ARG196 4.6 13.2 1.0 C A:GLU246 4.6 11.9 1.0 CE1 A:HIS247 4.7 12.4 1.0 O B:HOH1361 4.9 15.7 1.0 N A:GLU246 4.9 12.4 1.0 C3 A:NCA1001 5.0 11.3 1.0 NH2 A:ARG196 5.0 12.4 1.0 CG A:GLU246 5.0 13.1 1.0

Chlorine binding site 3 out of 3 in the Human Nampt in Complex with Substrate Nam and Activator Quercitrin


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 Activator Quercitrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1006 b:14.4 occ:0.78 OH A:TYR18 2.9 10.7 1.0 NH2 B:ARG311 2.9 13.5 1.0 O B:HOH1402 2.9 15.8 1.0 O B:HOH1309 3.3 27.2 1.0 CB B:GLU246 3.6 10.3 1.0 CA B:GLU246 3.7 9.7 1.0 O A:HOH1343 3.8 12.5 1.0 CZ A:TYR18 3.8 11.0 1.0 CE2 A:TYR18 3.9 11.3 1.0 CZ B:ARG311 3.9 12.6 1.0 NH1 B:ARG311 3.9 13.9 1.0 C2 B:NCA1101 4.1 11.6 1.0 N1 B:NCA1101 4.2 13.3 1.0 N B:HIS247 4.2 11.7 1.0 ND1 B:HIS247 4.3 12.6 1.0 O B:ALA245 4.5 11.8 1.0 C B:GLU246 4.5 11.5 1.0 CE1 B:HIS247 4.7 12.8 1.0 NH1 B:ARG196 4.7 12.9 1.0 N B:GLU246 4.9 11.1 1.0 O A:HOH1350 4.9 15.6 1.0 CG B:GLU246 5.0 10.6 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