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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 8dsc:

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

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A1-R, PDB code: 8dsc:

Sodium binding site 1 out of 1 in 8dsc

Go back to Sodium Binding Sites List in 8dsc
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
B:Na1106

b:27.8
occ:1.00
 O B:HOH1404 3.2 34.2 1.0
N B:LYS77 3.3 19.9 1.0
CA B:THR76 3.6 17.1 1.0
CB B:THR76 3.7 19.2 1.0
NZ B:LYS73 3.9 28.5 1.0
C B:THR76 3.9 18.7 1.0
CD1 B:LEU105 4.0 18.4 1.0
CE B:LYS73 4.0 20.4 1.0
CB B:LYS77 4.2 21.4 1.0
CG2 B:THR76 4.3 22.1 1.0
CD2 B:LEU105 4.3 19.0 1.0
OE1 B:GLU78 4.3 28.3 1.0
CA B:LYS77 4.4 20.6 1.0
CG B:LEU105 4.7 17.5 1.0
O B:VAL75 4.9 17.5 1.0
N B:THR76 4.9 16.8 1.0
OG1 B:THR76 5.0 18.4 1.0

Reference:

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
Page generated: Mon Aug 18 13:56:53 2025

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