Fluorine in PDB 5y6m: Zika Virus Helicase in Complex with Adp-ALF3

The structure of Zika Virus Helicase in Complex with Adp-ALF3, PDB code: 5y6m was solved by X.Y.Yang, C.Chen, H.L.Tian, H.Chi, Z.Y.Mu, T.Q.Zhang, K.L.Yang, Q.Zhao, X.H.Liu, Z.F.Wang, X.Y.Ji, H.T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.29 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.638, 69.152, 57.819, 90.00, 94.14, 90.00
R / Rfree (%)	17.7 / 22.3

The structure of Zika Virus Helicase in Complex with Adp-ALF3 also contains other interesting chemical elements:

Aluminium	(Al)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Fluorine atom in the Zika Virus Helicase in Complex with Adp-ALF3 (pdb code 5y6m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Zika Virus Helicase in Complex with Adp-ALF3, PDB code: 5y6m:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Zika Virus Helicase in Complex with Adp-ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Zika Virus Helicase in Complex with Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:45.3 occ:1.00 F1 A:AF3703 0.0 45.3 1.0 AL A:AF3703 1.7 47.7 1.0 NZ A:LYS200 2.5 31.6 1.0 F3 A:AF3703 3.0 46.0 1.0 F2 A:AF3703 3.0 47.0 1.0 CB A:ALA317 3.2 28.2 1.0 CE A:LYS200 3.3 31.4 1.0 N A:ALA317 3.6 23.0 1.0 O2B A:ADP702 3.6 32.5 1.0 CA A:PRO196 3.8 25.7 1.0 O A:HOH900 3.9 36.9 1.0 CA A:ALA317 4.0 25.5 1.0 NE2 A:GLN455 4.2 26.9 1.0 O A:HOH852 4.3 35.3 1.0 OE1 A:GLN455 4.3 26.7 1.0 CB A:PRO196 4.3 22.1 1.0 N A:PRO196 4.3 27.5 1.0 PB A:ADP702 4.4 31.3 1.0 OE1 A:GLU286 4.4 35.0 1.0 CG A:PRO196 4.5 24.0 1.0 O A:LEU194 4.5 28.8 1.0 O1B A:ADP702 4.5 26.2 1.0 O A:HIS195 4.5 29.0 1.0 MN A:MN701 4.6 44.4 1.0 CD A:LYS200 4.6 28.3 1.0 C A:THR316 4.6 22.7 1.0 C A:HIS195 4.7 27.4 1.0 CD A:GLN455 4.7 28.4 1.0 O3B A:ADP702 4.8 31.9 1.0 N A:GLY197 4.8 25.9 1.0 CD A:PRO196 4.9 26.1 1.0 OE2 A:GLU286 4.9 37.6 1.0 C A:PRO196 4.9 27.1 1.0 CA A:THR316 4.9 24.9 1.0

Fluorine binding site 2 out of 3 in the Zika Virus Helicase in Complex with Adp-ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Zika Virus Helicase in Complex with Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:47.0 occ:1.00 F2 A:AF3703 0.0 47.0 1.0 AL A:AF3703 1.7 47.7 1.0 MN A:MN701 2.4 44.4 1.0 O2B A:ADP702 2.5 32.5 1.0 O A:HOH1052 2.6 43.3 1.0 O A:HOH900 2.7 36.9 1.0 F3 A:AF3703 2.9 46.0 1.0 OE2 A:GLU286 2.9 37.6 1.0 F1 A:AF3703 3.0 45.3 1.0 O3B A:ADP702 3.2 31.9 1.0 O A:HOH804 3.3 34.7 1.0 PB A:ADP702 3.4 31.3 1.0 O A:HOH852 3.7 35.3 1.0 CD A:GLU286 3.8 34.4 1.0 NZ A:LYS200 3.9 31.6 1.0 OE1 A:GLU286 4.0 35.0 1.0 NH2 A:ARG462 4.0 37.4 1.0 O A:HOH877 4.2 42.2 1.0 O1B A:ADP702 4.5 26.2 1.0 O3A A:ADP702 4.6 26.6 1.0 NH1 A:ARG462 4.7 35.9 1.0 CA A:GLY415 4.7 69.5 1.0 O2A A:ADP702 4.8 36.3 1.0 CZ A:ARG462 4.8 35.6 1.0 OG1 A:THR201 4.8 36.5 1.0 N A:GLY415 4.9 70.8 1.0 NH2 A:ARG459 4.9 30.9 1.0 NH1 A:ARG459 4.9 34.7 1.0

Fluorine binding site 3 out of 3 in the Zika Virus Helicase in Complex with Adp-ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Zika Virus Helicase in Complex with Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:46.0 occ:1.00 F3 A:AF3703 0.0 46.0 1.0 AL A:AF3703 1.7 47.7 1.0 NH2 A:ARG462 2.2 37.4 1.0 F2 A:AF3703 2.9 47.0 1.0 NH2 A:ARG459 3.0 30.9 1.0 O A:HOH900 3.0 36.9 1.0 F1 A:AF3703 3.0 45.3 1.0 O2B A:ADP702 3.2 32.5 1.0 CB A:PRO196 3.2 22.1 1.0 CZ A:ARG462 3.5 35.6 1.0 CA A:PRO196 3.5 25.7 1.0 O A:HOH1052 3.7 43.3 1.0 CZ A:ARG459 3.8 31.9 1.0 NH1 A:ARG459 3.8 34.7 1.0 OE1 A:GLN455 3.9 26.7 1.0 N A:GLY197 4.0 25.9 1.0 NH1 A:ARG462 4.0 35.9 1.0 CG A:PRO196 4.1 24.0 1.0 C A:PRO196 4.2 27.1 1.0 NE A:ARG462 4.4 33.6 1.0 O A:GLY458 4.6 19.1 1.0 PB A:ADP702 4.6 31.3 1.0 N A:PRO196 4.7 27.5 1.0 NZ A:LYS200 4.8 31.6 1.0 CD A:GLN455 4.9 28.4 1.0

X.Yang, C.Chen, H.Tian, H.Chi, Z.Mu, T.Zhang, K.Yang, Q.Zhao, X.Liu, Z.Wang, X.Ji, H.Yang. Mechanism of Atp Hydrolysis By the Zika Virus Helicase. Faseb J. V. 32 5250 2018.
ISSN: ESSN 1530-6860
PubMed: 29913559
DOI: 10.1096/FJ.201701140R