Fluorine in PDB 6jim: Viral Helicase Protein

The structure of Viral Helicase Protein, PDB code: 6jim was solved by Y.S.Law, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.32 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.888, 53.905, 100.718, 96.93, 94.07, 97.04
R / Rfree (%)	17.7 / 21.5

The structure of Viral Helicase Protein also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Aluminium	(Al)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Fluorine atom in the Viral Helicase Protein (pdb code 6jim). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Viral Helicase Protein, PDB code: 6jim:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F2004 b:28.4 occ:1.00 AL A:AL2003 1.8 25.5 1.0 F A:F2007 2.4 27.9 1.0 O A:HOH2126 2.5 25.3 1.0 O1B A:ADP2001 2.6 27.4 1.0 F A:F2006 2.6 26.8 1.0 NH2 A:ARG312 2.7 33.4 1.0 NH1 A:ARG416 2.8 24.7 1.0 O A:HOH2107 3.1 27.5 1.0 CA A:GLY384 3.2 25.1 1.0 NH1 A:ARG312 3.4 30.1 1.0 C A:GLY384 3.4 33.7 1.0 O A:GLY384 3.4 34.3 1.0 CZ A:ARG312 3.5 34.0 1.0 F A:F2005 3.5 29.0 1.0 MG A:MG2002 3.6 29.2 1.0 NH2 A:ARG416 3.6 28.4 1.0 CZ A:ARG416 3.6 29.9 1.0 N A:GLY384 3.7 26.2 1.0 PB A:ADP2001 3.8 27.8 1.0 O3B A:ADP2001 4.1 28.1 1.0 O1A A:ADP2001 4.2 30.5 1.0 N A:LEU385 4.2 31.3 1.0 OE2 A:GLU253 4.2 28.3 1.0 O3A A:ADP2001 4.3 28.2 1.0 O A:HOH2123 4.3 26.5 1.0 O A:LEU385 4.3 29.8 1.0 N A:GLY189 4.5 27.4 1.0 NE A:ARG312 4.7 32.3 1.0 OE1 A:GLN283 4.8 30.2 1.0 O A:HOH2106 4.8 28.9 1.0 PA A:ADP2001 4.9 30.0 1.0 C A:LEU385 4.9 29.8 1.0 NE A:ARG416 4.9 30.9 1.0 C A:GLN383 5.0 26.4 1.0

Fluorine binding site 2 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F2005 b:29.0 occ:1.00 AL A:AL2003 1.7 25.5 1.0 O1B A:ADP2001 2.5 27.4 1.0 F A:F2007 2.5 27.9 1.0 F A:F2006 2.6 26.8 1.0 O A:HOH2126 2.8 25.3 1.0 NZ A:LYS192 2.8 23.8 1.0 O A:HOH2139 3.0 32.2 1.0 NE2 A:GLN283 3.0 27.2 1.0 PB A:ADP2001 3.4 27.8 1.0 CE A:LYS192 3.4 28.2 1.0 F A:F2004 3.5 28.4 1.0 O2B A:ADP2001 3.8 29.2 1.0 CA A:PRO188 3.9 31.8 1.0 CD A:GLN283 3.9 33.7 1.0 OE1 A:GLN283 3.9 30.2 1.0 O A:HOH2106 3.9 28.9 1.0 O3B A:ADP2001 4.0 28.1 1.0 N A:GLY189 4.1 27.4 1.0 MG A:MG2002 4.1 29.2 1.0 OE2 A:GLU253 4.2 28.3 1.0 O A:VAL187 4.3 27.9 1.0 C A:PRO188 4.5 29.7 1.0 N A:PRO188 4.6 28.6 1.0 CB A:PRO188 4.6 25.7 1.0 CB A:ASP280 4.7 23.9 1.0 C A:VAL187 4.8 32.5 1.0 O3A A:ADP2001 4.8 28.2 1.0 OE1 A:GLU253 4.8 33.9 1.0 O A:GLY186 4.9 32.9 1.0 CD A:LYS192 4.9 31.9 1.0 NH2 A:ARG416 4.9 28.4 1.0 CD A:GLU253 4.9 34.4 1.0

Fluorine binding site 3 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F2006 b:26.8 occ:1.00 MG A:MG2002 1.8 29.2 1.0 AL A:AL2003 1.9 25.5 1.0 O A:HOH2106 2.3 28.9 1.0 O A:HOH2123 2.6 26.5 1.0 F A:F2005 2.6 29.0 1.0 O1B A:ADP2001 2.6 27.4 1.0 F A:F2004 2.6 28.4 1.0 O3B A:ADP2001 2.7 28.1 1.0 O A:HOH2126 2.7 25.3 1.0 OE2 A:GLU253 2.8 28.3 1.0 O A:HOH2107 2.8 27.5 1.0 PB A:ADP2001 3.0 27.8 1.0 O A:HOH2139 3.2 32.2 1.0 OG A:SER193 3.6 26.5 1.0 F A:F2007 3.7 27.9 1.0 CA A:GLY384 3.8 25.1 1.0 CD A:GLU253 3.8 34.4 1.0 O2B A:ADP2001 4.1 29.2 1.0 O3A A:ADP2001 4.3 28.2 1.0 OE1 A:GLU253 4.4 33.9 1.0 O A:GLY384 4.5 34.3 1.0 N A:GLY384 4.5 26.2 1.0 NZ A:LYS192 4.5 23.8 1.0 C A:GLY384 4.6 33.7 1.0 CE A:LYS192 4.6 28.2 1.0 O1A A:ADP2001 4.6 30.5 1.0 CB A:SER193 4.7 27.1 1.0 NH2 A:ARG312 4.8 33.4 1.0 OD1 A:ASP252 4.9 32.7 1.0 CG A:GLU253 4.9 25.6 1.0

Fluorine binding site 4 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:F2007 b:27.9 occ:1.00 AL A:AL2003 1.7 25.5 1.0 F A:F2004 2.4 28.4 1.0 F A:F2005 2.5 29.0 1.0 O1B A:ADP2001 2.6 27.4 1.0 O A:HOH2126 2.7 25.3 1.0 NH2 A:ARG416 2.8 28.4 1.0 NH1 A:ARG312 3.1 30.1 1.0 N A:GLY189 3.1 27.4 1.0 CA A:PRO188 3.2 31.8 1.0 CB A:PRO188 3.3 25.7 1.0 NE2 A:GLN283 3.5 27.2 1.0 NH1 A:ARG416 3.6 24.7 1.0 CZ A:ARG416 3.6 29.9 1.0 C A:PRO188 3.6 29.7 1.0 F A:F2006 3.7 26.8 1.0 OE1 A:GLN283 3.7 30.2 1.0 NH2 A:ARG312 3.8 33.4 1.0 CZ A:ARG312 3.9 34.0 1.0 CD A:GLN283 4.0 33.7 1.0 PB A:ADP2001 4.1 27.8 1.0 CA A:GLY189 4.2 25.3 1.0 CG A:PRO188 4.4 27.2 1.0 N A:PRO188 4.5 28.6 1.0 NZ A:LYS192 4.8 23.8 1.0 OG1 A:THR415 4.8 27.1 1.0 O A:PRO188 4.8 35.2 1.0 O3A A:ADP2001 4.9 28.2 1.0 NE A:ARG416 4.9 30.9 1.0 O2B A:ADP2001 4.9 29.2 1.0 O A:THR415 4.9 30.3 1.0

Fluorine binding site 5 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:F2004 b:29.8 occ:1.00 AL B:AL2003 1.7 28.6 1.0 F B:F2007 2.5 29.4 1.0 F B:F2006 2.6 30.4 1.0 NH2 B:ARG312 2.6 32.9 1.0 O3B B:ADP2001 2.6 27.5 1.0 O B:HOH2113 2.7 26.3 1.0 NH1 B:ARG416 2.8 30.8 1.0 O B:HOH2114 3.1 24.9 1.0 CA B:GLY384 3.2 25.1 1.0 O B:GLY384 3.4 32.4 1.0 C B:GLY384 3.4 32.2 1.0 CZ B:ARG312 3.4 38.6 1.0 NH1 B:ARG312 3.4 33.3 1.0 F B:F2005 3.6 30.3 1.0 CZ B:ARG416 3.6 31.3 1.0 NH2 B:ARG416 3.6 26.2 1.0 N B:GLY384 3.7 28.3 1.0 PB B:ADP2001 3.7 29.2 1.0 MG B:MG2002 3.8 26.5 1.0 O1B B:ADP2001 3.9 25.0 1.0 O2A B:ADP2001 4.1 39.0 1.0 N B:LEU385 4.2 30.4 1.0 O B:HOH2117 4.3 28.2 1.0 O3A B:ADP2001 4.3 30.6 1.0 OE2 B:GLU253 4.3 35.1 1.0 O B:LEU385 4.4 29.6 1.0 N B:GLY189 4.4 30.9 1.0 NE B:ARG312 4.6 33.2 1.0 PA B:ADP2001 4.8 30.3 1.0 C B:LEU385 4.9 27.7 1.0 NE2 B:GLN283 4.9 25.6 1.0 NE B:ARG416 4.9 27.9 1.0 CA B:GLY189 4.9 28.1 1.0 C B:GLN383 5.0 31.2 1.0

Fluorine binding site 6 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:F2005 b:30.3 occ:1.00 AL B:AL2003 1.9 28.6 1.0 F B:F2006 2.5 30.4 1.0 F B:F2007 2.7 29.4 1.0 O3B B:ADP2001 2.7 27.5 1.0 O B:HOH2128 2.8 33.5 1.0 O B:HOH2113 2.8 26.3 1.0 NZ B:LYS192 2.8 30.2 1.0 OE1 B:GLN283 2.9 32.7 1.0 CE B:LYS192 3.4 27.8 1.0 PB B:ADP2001 3.6 29.2 1.0 F B:F2004 3.6 29.8 1.0 CD B:GLN283 3.7 32.5 1.0 NE2 B:GLN283 3.8 25.6 1.0 O2B B:ADP2001 3.8 33.8 1.0 CA B:PRO188 3.9 31.4 1.0 O B:HOH2136 4.0 30.9 1.0 O1B B:ADP2001 4.1 25.0 1.0 MG B:MG2002 4.1 26.5 1.0 N B:GLY189 4.2 30.9 1.0 OE2 B:GLU253 4.2 35.1 1.0 O B:VAL187 4.3 28.6 1.0 CB B:ASP280 4.5 26.6 1.0 C B:PRO188 4.6 34.4 1.0 N B:PRO188 4.6 32.0 1.0 CB B:PRO188 4.7 31.2 1.0 C B:VAL187 4.7 33.2 1.0 OE1 B:GLU253 4.7 32.4 1.0 O B:GLY186 4.8 30.6 1.0 CD B:LYS192 4.9 31.1 1.0 CD B:GLU253 4.9 30.5 1.0 OD1 B:ASP280 5.0 33.6 1.0 NH2 B:ARG416 5.0 26.2 1.0 O3A B:ADP2001 5.0 30.6 1.0

Fluorine binding site 7 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:F2006 b:30.4 occ:1.00 AL B:AL2003 1.8 28.6 1.0 MG B:MG2002 1.9 26.5 1.0 F B:F2005 2.5 30.3 1.0 O B:HOH2136 2.6 30.9 1.0 F B:F2004 2.6 29.8 1.0 O3B B:ADP2001 2.6 27.5 1.0 O B:HOH2113 2.6 26.3 1.0 O1B B:ADP2001 2.6 25.0 1.0 O B:HOH2117 2.7 28.2 1.0 O B:HOH2114 2.8 24.9 1.0 OE2 B:GLU253 2.9 35.1 1.0 PB B:ADP2001 3.0 29.2 1.0 O B:HOH2128 3.2 33.5 1.0 F B:F2007 3.6 29.4 1.0 OG B:SER193 3.7 29.6 1.0 CA B:GLY384 3.8 25.1 1.0 CD B:GLU253 3.9 30.5 1.0 O2B B:ADP2001 4.0 33.8 1.0 O3A B:ADP2001 4.3 30.6 1.0 OE1 B:GLU253 4.4 32.4 1.0 NZ B:LYS192 4.4 30.2 1.0 O B:GLY384 4.5 32.4 1.0 N B:GLY384 4.5 28.3 1.0 C B:GLY384 4.6 32.2 1.0 O2A B:ADP2001 4.6 39.0 1.0 CE B:LYS192 4.6 27.8 1.0 NH2 B:ARG312 4.7 32.9 1.0 CB B:SER193 4.8 28.0 1.0 NE2 B:GLN283 4.9 25.6 1.0 OE1 B:GLN283 5.0 32.7 1.0 CG B:GLU253 5.0 29.1 1.0

Fluorine binding site 8 out of 8 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:F2007 b:29.4 occ:1.00 AL B:AL2003 1.8 28.6 1.0 F B:F2004 2.5 29.8 1.0 F B:F2005 2.7 30.3 1.0 O3B B:ADP2001 2.7 27.5 1.0 NH2 B:ARG416 2.7 26.2 1.0 O B:HOH2113 2.8 26.3 1.0 N B:GLY189 3.1 30.9 1.0 CA B:PRO188 3.1 31.4 1.0 NH1 B:ARG312 3.1 33.3 1.0 CB B:PRO188 3.2 31.2 1.0 OE1 B:GLN283 3.5 32.7 1.0 C B:PRO188 3.6 34.4 1.0 CZ B:ARG416 3.6 31.3 1.0 F B:F2006 3.6 30.4 1.0 NH1 B:ARG416 3.6 30.8 1.0 NE2 B:GLN283 3.7 25.6 1.0 NH2 B:ARG312 3.8 32.9 1.0 CZ B:ARG312 3.9 38.6 1.0 CD B:GLN283 3.9 32.5 1.0 CA B:GLY189 4.2 28.1 1.0 PB B:ADP2001 4.2 29.2 1.0 CG B:PRO188 4.3 28.0 1.0 N B:PRO188 4.4 32.0 1.0 OG1 B:THR415 4.7 26.2 1.0 O B:PRO188 4.8 34.5 1.0 NZ B:LYS192 4.8 30.2 1.0 NE B:ARG416 4.9 27.9 1.0 O2B B:ADP2001 4.9 33.8 1.0 O3A B:ADP2001 5.0 30.6 1.0 O B:VAL187 5.0 28.6 1.0 O B:THR415 5.0 34.4 1.0

Y.S.Law, A.Utt, Y.B.Tan, J.Zheng, S.Wang, M.W.Chen, P.R.Griffin, A.Merits, D.Luo. Structural Insights Into Rna Recognition By the Chikungunya Virus NSP2 Helicase. Proc.Natl.Acad.Sci.Usa V. 116 9558 2019.
ISSN: ESSN 1091-6490
PubMed: 31000599
DOI: 10.1073/PNAS.1900656116