Chlorine 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:

Fluorine	(F)	8 atoms
Magnesium	(Mg)	2 atoms
Aluminium	(Al)	2 atoms

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

Chlorine binding site 1 out of 5 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2008 b:75.4 occ:1.00 N A:ASN337 3.6 42.2 1.0 O A:GLU335 4.0 38.9 1.0 CG A:LYS338 4.2 56.4 1.0 O A:HOH2272 4.2 68.6 1.0 CA A:ASN337 4.2 40.8 1.0 C A:ASN337 4.2 47.8 1.0 N A:LYS338 4.2 48.1 1.0 CB A:ASN337 4.3 46.1 1.0 CA A:TYR336 4.4 42.0 1.0 C A:TYR336 4.5 40.0 1.0 O A:HOH2136 4.6 51.2 1.0 O A:ASN337 4.8 45.6 1.0 C A:GLU335 4.9 45.0 1.0

Chlorine binding site 2 out of 5 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2009 b:76.6 occ:1.00 O A:HOH2225 2.5 76.7 1.0 ND1 A:HIS325 3.0 39.8 1.0 NZ A:LYS282 3.2 61.2 1.0 CE1 A:HIS325 3.8 38.7 1.0 O A:LEU324 3.8 46.2 1.0 CD A:LYS282 4.0 42.2 1.0 CE A:LYS282 4.0 52.8 1.0 CA A:HIS325 4.0 37.8 1.0 CG A:HIS325 4.0 36.8 1.0 CB A:HIS325 4.3 35.0 1.0 C A:LEU324 4.6 37.0 1.0 O A:HIS325 4.6 39.6 1.0 O A:THR406 4.8 37.1 1.0 N A:HIS325 4.8 34.9 1.0 C A:HIS325 4.9 41.8 1.0 CB A:THR406 4.9 49.0 1.0 NE2 A:HIS325 5.0 40.3 1.0

Chlorine binding site 3 out of 5 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2010 b:84.2 occ:1.00 NH2 A:ARG311 3.2 70.5 1.0 OG1 A:THR333 3.3 39.6 1.0 O A:ARG311 3.9 39.7 1.0 O A:THR333 3.9 42.4 1.0 NE A:ARG311 4.0 59.8 1.0 CZ A:ARG311 4.0 62.8 1.0 O A:HOH2242 4.0 63.4 1.0 C A:THR333 4.1 43.6 1.0 CB A:THR333 4.2 40.2 1.0 O A:HOH2184 4.3 51.7 1.0 N A:ASN334 4.4 39.8 1.0 CA A:ASN334 4.5 37.7 1.0 CD1 A:ILE447 4.6 58.2 1.0 C A:ARG311 4.8 38.8 1.0 CA A:THR333 4.8 43.5 1.0 CB A:ARG311 4.8 37.4 1.0 CA A:ARG311 4.9 39.1 1.0

Chlorine binding site 4 out of 5 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2008 b:72.5 occ:1.00 CD B:PRO111 4.8 61.9 1.0 CA B:GLY110 5.0 62.9 1.0

Chlorine binding site 5 out of 5 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2009 b:78.5 occ:1.00 NH1 B:ARG311 3.0 56.8 1.0 OE1 B:GLU451 3.1 73.1 1.0 N6 B:ADP2001 3.9 53.0 1.0 CD B:GLU451 4.0 68.0 1.0 CZ B:ARG311 4.0 63.3 1.0 CG B:GLU451 4.1 60.9 1.0 NH2 B:ARG311 4.2 57.9 1.0 CG2 B:ILE447 4.2 55.7 1.0 CZ3 B:TRP450 4.5 47.5 1.0 CE3 B:TRP450 4.7 39.3 1.0 C6 B:ADP2001 4.9 54.5 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