Chlorine in PDB 8dsi: Human Nampt in Complex with Substrate Nam

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

The structure of Human Nampt in Complex with Substrate Nam, PDB code: 8dsi 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)	19.89 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.816, 106.625, 83.03, 90, 96.7, 90
R / Rfree (%)	16.1 / 18.1

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1004 b:33.2 occ:0.76 N A:LYS77 3.0 21.5 1.0 CA A:THR76 3.4 20.3 1.0 CB A:THR76 3.5 20.8 1.0 C A:THR76 3.7 19.7 1.0 O A:HOH1266 3.8 42.1 1.0 CB A:LYS77 3.9 22.7 1.0 NZ A:LYS73 4.0 35.2 1.0 CD1 A:LEU105 4.0 21.7 1.0 CA A:LYS77 4.0 21.2 1.0 OE1 A:GLU78 4.1 30.4 1.0 CG2 A:THR76 4.2 24.0 1.0 CE A:LYS73 4.2 26.2 1.0 CD2 A:LEU105 4.3 22.9 1.0 OG1 A:THR76 4.7 20.7 1.0 CG A:LEU105 4.7 19.6 1.0 N A:THR76 4.8 18.8 1.0 O A:VAL75 4.9 19.9 1.0 O A:THR76 4.9 18.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1005 b:20.6 occ:0.91 O A:HOH1294 2.9 20.8 1.0 NH2 A:ARG311 2.9 15.0 0.7 OH B:TYR18 3.0 13.1 1.0 O A:HOH1214 3.2 34.5 1.0 NH1 A:ARG311 3.3 15.0 0.3 NH2 A:ARG311 3.4 13.4 0.3 CB A:GLU246 3.6 13.3 1.0 CZ A:ARG311 3.8 14.0 0.3 CA A:GLU246 3.8 13.5 1.0 O B:HOH1396 3.8 16.0 1.0 CE2 B:TYR18 3.8 13.6 1.0 CZ A:ARG311 3.9 12.5 0.7 CZ B:TYR18 3.9 12.8 1.0 NH1 A:ARG311 3.9 15.3 0.7 C2 A:NCA1001 4.1 13.7 1.0 N1 A:NCA1001 4.2 16.9 1.0 N A:HIS247 4.2 12.4 1.0 ND1 A:HIS247 4.3 15.9 1.0 O A:ALA245 4.5 13.7 1.0 C A:GLU246 4.6 13.0 1.0 NH1 A:ARG196 4.6 15.9 1.0 CE1 A:HIS247 4.7 15.9 1.0 O B:HOH1380 4.9 20.2 1.0 N A:GLU246 5.0 13.8 1.0 NH2 A:ARG196 5.0 14.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1103 b:20.8 occ:0.96 NH2 B:ARG311 2.9 12.4 0.7 O B:HOH1373 2.9 18.9 1.0 OH A:TYR18 3.0 12.2 1.0 NH2 B:ARG311 3.2 13.1 0.3 O B:HOH1292 3.2 37.7 1.0 NH1 B:ARG311 3.4 13.3 0.3 CB B:GLU246 3.6 12.7 1.0 CZ B:ARG311 3.7 13.5 0.3 CA B:GLU246 3.8 10.3 1.0 CE2 A:TYR18 3.8 11.7 1.0 O A:HOH1307 3.8 15.6 1.0 CZ B:ARG311 3.8 13.3 0.7 CZ A:TYR18 3.9 11.8 1.0 NH1 B:ARG311 3.9 12.4 0.7 C2 B:NCA1101 4.1 13.8 1.0 N1 B:NCA1101 4.1 16.0 1.0 N B:HIS247 4.2 12.3 1.0 ND1 B:HIS247 4.3 15.4 1.0 O B:ALA245 4.5 12.0 1.0 C B:GLU246 4.6 11.4 1.0 CE1 B:HIS247 4.7 14.6 1.0 NH1 B:ARG196 4.7 16.3 1.0 O A:HOH1305 4.9 20.3 1.0 N B:GLU246 5.0 12.7 1.0 NH2 B:ARG196 5.0 13.0 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