Fluorine in PDB 2vk7: The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates

All present enzymatic activity of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates:
3.2.1.18;

The structure of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates, PDB code: 2vk7 was solved by S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.2
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.600, 97.400, 72.600, 90.00, 91.00, 90.00
R / Rfree (%)	13.1 / 15.9

The structure of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Fluorine atom in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates (pdb code 2vk7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates, PDB code: 2vk7:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ A:F2693 b:14.7 occ:1.00 F1 A:FSI2693 0.0 14.7 1.0 C3 A:FSI2693 1.3 9.7 1.0 C2 A:FSI2693 2.3 12.8 1.0 C4 A:FSI2693 2.3 10.1 1.0 O4 A:FSI2693 2.7 10.4 1.0 C1 A:FSI2693 2.8 9.6 1.0 C5 A:FSI2693 2.8 9.8 1.0 O1A A:FSI2693 2.8 9.7 1.0 OD1 A:ASP1291 2.9 14.6 1.0 O6 A:FSI2693 2.9 10.8 1.0 NH1 A:ARG1266 3.0 10.3 1.0 OD2 A:ASP1291 3.4 15.3 1.0 C6 A:FSI2693 3.4 9.6 1.0 CG A:ASP1291 3.5 12.2 1.0 O A:HOH3885 3.6 25.8 1.0 O A:HOH3126 3.7 27.9 1.0 CZ A:ARG1266 3.8 9.2 1.0 OH A:TYR1655 3.8 12.1 1.0 O1B A:FSI2693 3.9 10.9 1.0 NH2 A:ARG1266 4.0 9.3 1.0 N5 A:FSI2693 4.1 9.4 1.0 NH2 A:ARG1285 4.2 10.5 1.0 CD1 A:ILE1267 4.3 9.4 1.0 O7 A:FSI2693 4.3 11.3 1.0 O A:HOH3886 4.3 26.8 1.0 CZ A:TYR1655 4.4 10.2 1.0 NH1 A:ARG1285 4.5 10.9 1.0 C7 A:FSI2693 4.5 9.7 1.0 O A:HOH3121 4.7 17.5 1.0 CZ A:ARG1285 4.8 10.1 1.0 NE A:ARG1266 4.8 9.2 1.0 CE2 A:TYR1655 4.9 10.5 1.0 CB A:ASP1291 4.9 11.8 1.0 O10 A:FSI2693 4.9 9.5 1.0 C10 A:FSI2693 4.9 9.2 1.0 CE1 A:TYR1655 4.9 9.9 1.0

Fluorine binding site 2 out of 2 in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ B:F2692 b:14.6 occ:1.00 F1 B:FSI2692 0.0 14.6 1.0 C3 B:FSI2692 1.4 10.5 1.0 C2 B:FSI2692 2.3 13.7 1.0 C4 B:FSI2692 2.3 10.8 1.0 O4 B:FSI2692 2.8 10.9 1.0 C5 B:FSI2692 2.8 10.1 1.0 C1 B:FSI2692 2.8 10.7 1.0 O1B B:FSI2692 2.8 10.2 1.0 O6 B:FSI2692 2.9 12.4 1.0 OD1 B:ASP1291 2.9 15.6 1.0 NH1 B:ARG1266 3.0 10.8 1.0 O B:HOH3112 3.1 35.7 1.0 OD2 B:ASP1291 3.3 15.5 1.0 O B:HOH3111 3.4 25.5 1.0 C6 B:FSI2692 3.4 11.0 1.0 CG B:ASP1291 3.4 13.1 1.0 CZ B:ARG1266 3.7 9.3 1.0 OH B:TYR1655 3.8 12.3 1.0 O1A B:FSI2692 3.9 12.2 1.0 NH2 B:ARG1266 3.9 10.2 1.0 N5 B:FSI2692 4.1 10.2 1.0 O7 B:FSI2692 4.3 12.6 1.0 NH2 B:ARG1285 4.3 11.2 1.0 CD1 B:ILE1267 4.3 10.4 1.0 CZ B:TYR1655 4.4 10.1 1.0 O B:HOH3773 4.4 38.3 1.0 C7 B:FSI2692 4.5 11.2 1.0 NH1 B:ARG1285 4.5 11.3 1.0 O B:HOH3109 4.5 24.3 1.0 NE B:ARG1266 4.8 9.8 1.0 CB B:ASP1291 4.8 13.1 1.0 O10 B:FSI2692 4.8 11.6 1.0 CE2 B:TYR1655 4.9 10.1 1.0 C10 B:FSI2692 4.9 10.7 1.0 CZ B:ARG1285 4.9 10.2 1.0 CE1 B:TYR1655 4.9 9.6 1.0

S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor. The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates. J.Biol.Chem. V. 283 9080 2008.
ISSN: ISSN 0021-9258
PubMed: 18218621
DOI: 10.1074/JBC.M710247200