Chlorine in PDB 5njv: Flavivirus NS5 Domain

The structure of Flavivirus NS5 Domain, PDB code: 5njv was solved by S.K.Talapatra, C.Chatrin, F.Kozielski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.53 / 2.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	125.920, 125.920, 125.854, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25.8

The binding sites of Chlorine atom in the Flavivirus NS5 Domain (pdb code 5njv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Flavivirus NS5 Domain, PDB code: 5njv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Flavivirus NS5 Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Flavivirus NS5 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:36.4 occ:1.00 O A:HOH501 3.0 28.6 1.0 N A:GLU149 3.1 32.6 1.0 CA A:GLY148 3.5 26.9 1.0 O A:HOH558 3.7 47.9 1.0 CG A:GLU149 3.7 40.3 1.0 C A:GLY148 3.8 28.9 1.0 CD A:ARG160 3.9 25.2 1.0 N A:GLY148 3.9 28.1 1.0 CB A:ARG160 3.9 23.9 1.0 CG2 A:ILE147 4.0 28.7 1.0 CG A:ARG160 4.1 29.5 1.0 CA A:GLU149 4.2 33.8 1.0 CB A:GLU149 4.2 37.7 1.0 CL A:CL303 4.4 37.6 1.0 NE A:ARG160 4.6 25.0 1.0 O A:GLU149 4.8 27.6 1.0 O A:HOH565 4.8 25.7 1.0 C A:ILE147 4.8 25.5 1.0 O A:ARG160 4.9 19.4 1.0 CA A:ARG160 4.9 20.0 1.0 CD A:GLU149 4.9 42.2 1.0 O A:GLY148 5.0 26.1 1.0

Chlorine binding site 2 out of 4 in the Flavivirus NS5 Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Flavivirus NS5 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:37.6 occ:1.00 N A:GLY148 3.2 28.1 1.0 O A:HOH431 3.2 36.6 1.0 N A:GLU149 3.6 32.6 1.0 C A:GLY148 3.7 28.9 1.0 CB A:GLU149 3.8 37.7 1.0 C8 A:SAM301 3.8 29.2 1.0 C5' A:SAM301 3.9 29.8 1.0 CA A:GLY148 3.9 26.9 1.0 CA A:GLU149 3.9 33.8 1.0 O4' A:SAM301 4.0 30.9 1.0 CA A:ILE147 4.0 25.0 1.0 C A:ILE147 4.1 25.5 1.0 O A:GLY148 4.1 26.1 1.0 C2' A:SAM301 4.2 34.5 1.0 C3' A:SAM301 4.2 28.4 1.0 CG2 A:ILE147 4.2 28.7 1.0 C4' A:SAM301 4.3 29.6 1.0 CL A:CL302 4.4 36.4 1.0 N9 A:SAM301 4.5 27.7 1.0 C1' A:SAM301 4.6 25.4 1.0 CG A:GLU149 4.6 40.3 1.0 O A:ASP146 4.6 33.0 1.0 CB A:ILE147 4.7 21.0 1.0 N7 A:SAM301 4.7 32.7 1.0

Chlorine binding site 3 out of 4 in the Flavivirus NS5 Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Flavivirus NS5 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:57.5 occ:1.00 O B:HOH549 2.4 39.4 1.0 N B:LEU8 2.9 31.6 1.0 CA B:THR7 3.4 38.7 1.0 CG B:LEU8 3.5 37.0 1.0 CB B:THR7 3.6 34.1 1.0 C B:THR7 3.7 31.3 1.0 O B:HOH527 3.8 24.6 1.0 CB B:LEU8 3.8 32.8 1.0 CA B:LEU8 4.0 29.3 1.0 CG2 B:THR7 4.2 33.3 1.0 CD1 B:LEU8 4.2 34.0 1.0 OG B:SER234 4.6 31.6 1.0 CD2 B:LEU8 4.7 36.1 1.0 O B:GLU6 4.7 43.6 1.0 N B:THR7 4.8 40.2 1.0 OG1 B:THR7 4.8 30.9 1.0 O B:THR7 4.9 34.7 1.0 CE B:MET192 4.9 29.4 1.0

Chlorine binding site 4 out of 4 in the Flavivirus NS5 Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Flavivirus NS5 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl303 b:34.8 occ:1.00 N B:GLY148 3.1 21.4 1.0 O B:HOH454 3.4 35.1 1.0 C5' B:SAM301 3.5 30.1 1.0 C B:GLY148 3.7 24.8 1.0 N B:GLU149 3.8 29.0 1.0 C8 B:SAM301 3.9 32.7 1.0 O4' B:SAM301 3.9 26.8 1.0 CA B:ILE147 3.9 22.0 1.0 C3' B:SAM301 4.0 24.8 1.0 C2' B:SAM301 4.0 33.4 1.0 O B:GLY148 4.0 27.5 1.0 CA B:GLY148 4.0 27.3 1.0 C B:ILE147 4.0 21.4 1.0 C4' B:SAM301 4.1 25.9 1.0 CA B:GLU149 4.2 24.9 1.0 CG2 B:ILE147 4.2 20.4 1.0 CB B:GLU149 4.3 28.2 1.0 C1' B:SAM301 4.4 22.7 1.0 O B:ASP146 4.5 24.7 1.0 N9 B:SAM301 4.5 31.7 1.0 CB B:ILE147 4.6 21.1 1.0 O B:HOH575 4.7 19.5 1.0 N7 B:SAM301 4.9 26.6 1.0 SD B:SAM301 4.9 37.4 1.0

C.Chatrin, S.K.Talapatra, B.Canard, F.Kozielski. The Structure of the Binary Methyltransferase-Sah Complex From Zika Virus Reveals A Novel Conformation For the Mechanism of Mrna Capping. Oncotarget V. 9 3160 2018.
ISSN: ESSN 1949-2553
PubMed: 29423037
DOI: 10.18632/ONCOTARGET.23223