Fluorine in PDB 3dzg: Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex

All present enzymatic activity of Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex:
3.2.2.5;

The structure of Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex, PDB code: 3dzg was solved by Q.Liu, I.A.Kriksunov, H.Jiang, R.Graeff, H.Lin, H.C.Lee, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.689, 52.812, 65.381, 106.06, 91.95, 95.12
R / Rfree (%)	17.4 / 21.1

The binding sites of Fluorine atom in the Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex (pdb code 3dzg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex, PDB code: 3dzg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:22.0 occ:1.00 F2 A:RF5301 0.0 22.0 1.0 C2 A:RF5301 1.4 17.8 1.0 C3 A:RF5301 2.3 18.9 1.0 C1 A:RF5301 2.4 16.2 1.0 O3 A:RF5301 3.0 20.0 1.0 CB A:LEU145 3.1 26.8 1.0 OE2 A:GLU226 3.2 28.2 1.0 O A:HOH303 3.2 15.1 1.0 CD2 A:LEU145 3.3 30.9 1.0 O4 A:RF5301 3.5 16.1 1.0 C4 A:RF5301 3.6 14.7 1.0 CG A:LEU145 3.8 28.4 1.0 CD2 A:PHE196 3.9 27.6 1.0 CD A:GLU226 3.9 28.8 1.0 OE1 A:GLU226 4.2 30.1 1.0 N1 A:NCA302 4.2 25.8 1.0 CE2 A:PHE196 4.3 29.3 1.0 CA A:LEU145 4.3 27.1 1.0 OG A:SER193 4.3 31.1 1.0 N A:LEU145 4.4 26.1 1.0 CD2 A:LEU124 4.4 29.9 1.0 CD1 A:LEU145 4.6 29.8 1.0 C5 A:RF5301 4.7 14.9 1.0 C2 A:NCA302 4.8 23.5 1.0 CG A:PHE196 4.8 26.3 1.0 OE2 A:GLU146 4.9 32.0 1.0 NE1 A:TRP125 4.9 27.7 1.0 CB A:SER193 4.9 29.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human CD38 Extracellular Domain, Ara-F-Ribose-5'- Phosphate/Nicotinamide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:26.5 occ:1.00 F2 B:RF5301 0.0 26.5 1.0 C2 B:RF5301 1.4 25.5 1.0 C3 B:RF5301 2.3 26.5 1.0 C1 B:RF5301 2.4 25.1 1.0 O3 B:RF5301 3.0 24.0 1.0 OE2 B:GLU226 3.1 29.5 1.0 CB B:LEU145 3.2 28.2 1.0 O B:HOH456 3.2 21.1 1.0 CD2 B:LEU145 3.3 30.5 1.0 O4 B:RF5301 3.4 22.6 1.0 C4 B:RF5301 3.5 26.1 1.0 CG B:LEU145 3.8 28.5 1.0 CD2 B:PHE196 3.9 25.4 1.0 CD B:GLU226 3.9 28.7 1.0 OE1 B:GLU226 4.1 28.5 1.0 N1 B:NCA302 4.2 26.7 1.0 CD2 B:LEU124 4.3 29.2 1.0 OG B:SER193 4.3 30.1 1.0 CE2 B:PHE196 4.3 25.8 1.0 CA B:LEU145 4.4 28.1 1.0 N B:LEU145 4.4 27.0 1.0 CD1 B:LEU145 4.6 29.2 1.0 C5 B:RF5301 4.6 27.9 1.0 OE2 B:GLU146 4.7 33.2 1.0 C2 B:NCA302 4.8 23.4 1.0 NE1 B:TRP125 4.8 28.7 1.0 CB B:SER193 4.9 28.9 1.0 CG B:PHE196 4.9 23.6 1.0

Q.Liu, I.A.Kriksunov, H.Jiang, R.Graeff, H.Lin, H.C.Lee, Q.Hao. Covalent and Noncovalent Intermediates of An Nad Utilizing Enzyme, Human CD38. Chem.Biol. V. 15 1068 2008.
ISSN: ISSN 1074-5521
PubMed: 18940667
DOI: 10.1016/J.CHEMBIOL.2008.08.007