Fluorine in PDB 8dtj: Human Nampt in Complex with Small Molecule Activator Zn-43-S

Enzymatic activity of Human Nampt in Complex with Small Molecule Activator Zn-43-S

All present enzymatic activity of Human Nampt in Complex with Small Molecule Activator Zn-43-S:
2.4.2.12;

Protein crystallography data

The structure of Human Nampt in Complex with Small Molecule Activator Zn-43-S, PDB code: 8dtj 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) 19.67 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.499, 107.483, 83.399, 90, 96.64, 90
R / Rfree (%) 21.6 / 24.6

Other elements in 8dtj:

The structure of Human Nampt in Complex with Small Molecule Activator Zn-43-S also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Nampt in Complex with Small Molecule Activator Zn-43-S (pdb code 8dtj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Nampt in Complex with Small Molecule Activator Zn-43-S, PDB code: 8dtj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dtj

Go back to Fluorine Binding Sites List in 8dtj
Fluorine binding site 1 out of 6 in the Human Nampt in Complex with Small Molecule Activator Zn-43-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Nampt in Complex with Small Molecule Activator Zn-43-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:45.3
occ:0.68
 F29 A:TKF1003 0.0 45.3 0.7
C28 A:TKF1003 1.4 42.9 0.7
F30 A:TKF1003 2.1 40.9 0.7
F31 A:TKF1003 2.1 44.1 0.7
C27 A:TKF1003 2.5 40.5 0.7
C32 A:TKF1003 3.1 38.5 0.7
CG2 A:VAL242 3.5 36.4 1.0
C26 A:TKF1003 3.5 39.1 0.7
O A:HOH1249 3.7 44.4 1.0
CD1 A:ILE351 3.7 38.4 1.0
CB A:SER275 3.9 32.9 1.0
OG A:SER275 4.3 31.6 1.0
C33 A:TKF1003 4.4 42.1 0.7
CD1 A:ILE309 4.6 33.5 1.0
C25 A:TKF1003 4.7 37.7 0.7
CZ A:PHE193 4.9 39.3 1.0
CB A:VAL242 4.9 37.8 1.0
O A:HOH1270 4.9 44.1 1.0
ND1 A:HIS191 4.9 38.9 1.0
CG2 A:ILE351 5.0 29.8 1.0
CG1 A:ILE351 5.0 31.6 1.0

Fluorine binding site 2 out of 6 in 8dtj

Go back to Fluorine Binding Sites List in 8dtj
Fluorine binding site 2 out of 6 in the Human Nampt in Complex with Small Molecule Activator Zn-43-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Nampt in Complex with Small Molecule Activator Zn-43-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:40.9
occ:0.68
 F30 A:TKF1003 0.0 40.9 0.7
C28 A:TKF1003 1.4 42.9 0.7
F29 A:TKF1003 2.1 45.3 0.7
F31 A:TKF1003 2.1 44.1 0.7
C27 A:TKF1003 2.4 40.5 0.7
C26 A:TKF1003 2.8 39.1 0.7
CD1 A:ILE351 2.9 38.4 1.0
CG A:HIS191 3.3 30.4 1.0
ND1 A:HIS191 3.4 38.9 1.0
CZ A:PHE193 3.5 39.3 1.0
CB A:HIS191 3.5 27.9 1.0
C32 A:TKF1003 3.7 38.5 0.7
CE1 A:PHE193 3.7 40.5 1.0
CD2 A:HIS191 3.8 34.5 1.0
CE1 A:HIS191 4.0 37.8 1.0
NE2 A:HIS191 4.1 33.0 1.0
O A:HOH1249 4.2 44.4 1.0
C25 A:TKF1003 4.2 37.7 0.7
CG1 A:ILE351 4.4 31.6 1.0
CE2 A:PHE193 4.7 45.8 1.0
C33 A:TKF1003 4.9 42.1 0.7
O A:HOH1209 5.0 29.8 1.0
O A:HOH1270 5.0 44.1 1.0

Fluorine binding site 3 out of 6 in 8dtj

Go back to Fluorine Binding Sites List in 8dtj
Fluorine binding site 3 out of 6 in the Human Nampt in Complex with Small Molecule Activator Zn-43-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Nampt in Complex with Small Molecule Activator Zn-43-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:44.1
occ:0.68
 F31 A:TKF1003 0.0 44.1 0.7
C28 A:TKF1003 1.4 42.9 0.7
F30 A:TKF1003 2.1 40.9 0.7
F29 A:TKF1003 2.1 45.3 0.7
C27 A:TKF1003 2.4 40.5 0.7
C32 A:TKF1003 3.0 38.5 0.7
CE1 A:HIS191 3.1 37.8 1.0
ND1 A:HIS191 3.2 38.9 1.0
O A:HOH1249 3.2 44.4 1.0
C26 A:TKF1003 3.5 39.1 0.7
NE2 A:HIS191 3.6 33.0 1.0
CG2 A:VAL242 3.6 36.4 1.0
CG A:HIS191 3.8 30.4 1.0
CD2 A:HIS191 4.0 34.5 1.0
N A:VAL242 4.2 35.6 1.0
OG A:SER241 4.3 44.1 1.0
C33 A:TKF1003 4.4 42.1 0.7
CB A:VAL242 4.6 37.8 1.0
CB A:HIS191 4.6 27.9 1.0
C25 A:TKF1003 4.7 37.7 0.7
CG1 A:VAL242 4.7 36.8 1.0
OD1 A:ASP219 4.7 32.3 1.0
CA A:SER241 4.8 44.1 1.0
CE1 A:PHE193 4.8 40.5 1.0
CD1 A:ILE351 4.8 38.4 1.0
O A:HOH1209 4.9 29.8 1.0
C A:SER241 5.0 36.9 1.0
CA A:VAL242 5.0 32.0 1.0

Fluorine binding site 4 out of 6 in 8dtj

Go back to Fluorine Binding Sites List in 8dtj
Fluorine binding site 4 out of 6 in the Human Nampt in Complex with Small Molecule Activator Zn-43-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Nampt in Complex with Small Molecule Activator Zn-43-S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1204

b:42.4
occ:0.72
 F29 B:TKF1204 0.0 42.4 0.7
C28 B:TKF1204 1.4 35.7 0.7
F31 B:TKF1204 2.1 44.5 0.7
F30 B:TKF1204 2.1 41.4 0.7
C27 B:TKF1204 2.5 36.2 0.7
C32 B:TKF1204 3.1 39.6 0.7
CG2 B:VAL242 3.3 34.2 1.0
C26 B:TKF1204 3.5 35.4 0.7
O B:HOH1394 3.6 38.6 1.0
O B:HOH1473 3.6 38.8 1.0
CB B:SER275 3.9 33.0 1.0
CD1 B:ILE351 4.0 37.7 1.0
OG B:SER275 4.4 31.6 1.0
C33 B:TKF1204 4.4 41.1 0.7
CB B:VAL242 4.7 33.7 1.0
C25 B:TKF1204 4.7 35.2 0.7
CD1 B:ILE309 4.7 21.8 1.0
ND1 B:HIS191 4.9 34.0 1.0
CZ B:PHE193 4.9 40.5 1.0
CE1 B:HIS191 5.0 39.1 1.0

Fluorine binding site 5 out of 6 in 8dtj

Go back to Fluorine Binding Sites List in 8dtj
Fluorine binding site 5 out of 6 in the Human Nampt in Complex with Small Molecule Activator Zn-43-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Nampt in Complex with Small Molecule Activator Zn-43-S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1204

b:41.4
occ:0.72
 F30 B:TKF1204 0.0 41.4 0.7
C28 B:TKF1204 1.4 35.7 0.7
F31 B:TKF1204 2.1 44.5 0.7
F29 B:TKF1204 2.1 42.4 0.7
C27 B:TKF1204 2.4 36.2 0.7
CE1 B:HIS191 2.9 39.1 1.0
C32 B:TKF1204 3.1 39.6 0.7
ND1 B:HIS191 3.1 34.0 1.0
O B:HOH1473 3.3 38.8 1.0
NE2 B:HIS191 3.4 38.4 1.0
C26 B:TKF1204 3.5 35.4 0.7
CG2 B:VAL242 3.7 34.2 1.0
CG B:HIS191 3.7 37.7 1.0
CD2 B:HIS191 3.9 32.4 1.0
N B:VAL242 4.1 40.1 1.0
OD1 B:ASP219 4.3 40.2 1.0
C33 B:TKF1204 4.4 41.1 0.7
OG B:SER241 4.5 40.7 1.0
CB B:VAL242 4.6 33.7 1.0
CA B:SER241 4.6 41.5 1.0
CG1 B:VAL242 4.7 29.6 1.0
CB B:HIS191 4.7 33.2 1.0
C25 B:TKF1204 4.7 35.2 0.7
C B:SER241 4.8 36.6 1.0
CE1 B:PHE193 4.9 39.3 1.0
O B:HOH1394 4.9 38.6 1.0
CA B:VAL242 4.9 31.6 1.0
O B:VAL242 5.0 27.8 1.0
CD1 B:ILE351 5.0 37.7 1.0

Fluorine binding site 6 out of 6 in 8dtj

Go back to Fluorine Binding Sites List in 8dtj
Fluorine binding site 6 out of 6 in the Human Nampt in Complex with Small Molecule Activator Zn-43-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Nampt in Complex with Small Molecule Activator Zn-43-S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1204

b:44.5
occ:0.72
 F31 B:TKF1204 0.0 44.5 0.7
C28 B:TKF1204 1.4 35.7 0.7
F30 B:TKF1204 2.1 41.4 0.7
F29 B:TKF1204 2.1 42.4 0.7
C27 B:TKF1204 2.4 36.2 0.7
C26 B:TKF1204 2.8 35.4 0.7
CD1 B:ILE351 3.0 37.7 1.0
CG B:HIS191 3.3 37.7 1.0
ND1 B:HIS191 3.4 34.0 1.0
CZ B:PHE193 3.6 40.5 1.0
CB B:HIS191 3.6 33.2 1.0
C32 B:TKF1204 3.7 39.6 0.7
CD2 B:HIS191 3.7 32.4 1.0
CE1 B:PHE193 3.8 39.3 1.0
CE1 B:HIS191 3.8 39.1 1.0
O B:HOH1394 4.0 38.6 1.0
NE2 B:HIS191 4.0 38.4 1.0
C25 B:TKF1204 4.2 35.2 0.7
O B:HOH1473 4.2 38.8 1.0
CG1 B:ILE351 4.5 30.4 1.0
CE2 B:PHE193 4.8 44.4 1.0
C33 B:TKF1204 4.8 41.1 0.7

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: Fri Aug 2 17:36:31 2024

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