Chlorine in PDB 7axd: Crystal Structure of the Hpxr-Lbd in Complex with Fipronil

The structure of Crystal Structure of the Hpxr-Lbd in Complex with Fipronil, PDB code: 7axd was solved by M.Granell, V.Delfosse, W.Bourguet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.15 / 2.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.012, 92.012, 86.555, 90, 90, 90
R / Rfree (%)	19.5 / 23.7

The structure of Crystal Structure of the Hpxr-Lbd in Complex with Fipronil also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil (pdb code 7axd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil, PDB code: 7axd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:66.8 occ:0.71 CL A:S6W501 0.0 66.8 0.7 C5 A:S6W501 1.7 69.2 0.8 C A:S6W501 2.6 62.3 0.9 C4 A:S6W501 2.7 66.8 0.9 N A:S6W501 2.8 63.5 1.0 OG A:SER247 3.2 60.5 1.0 C6 A:S6W501 3.2 74.9 1.0 O A:MET243 3.4 57.4 1.0 N1 A:S6W501 3.5 70.2 0.7 N3 A:S6W501 3.6 74.5 1.0 CG A:MET246 3.7 44.2 1.0 CE A:MET243 3.9 76.2 1.0 C1 A:S6W501 3.9 68.6 0.9 C3 A:S6W501 3.9 71.0 0.8 CB A:MET246 3.9 39.4 1.0 N A:SER247 3.9 55.1 1.0 C7 A:S6W501 4.0 72.6 0.7 C8 A:S6W501 4.2 64.4 0.8 C A:MET243 4.2 54.5 1.0 CA A:MET243 4.3 62.5 1.0 CA A:SER247 4.3 48.7 1.0 CB A:MET243 4.3 57.6 1.0 CB A:SER247 4.3 38.9 1.0 C2 A:S6W501 4.4 73.3 1.0 C A:MET246 4.4 51.7 1.0 CZ A:PHE288 4.5 64.5 1.0 CE2 A:PHE288 4.6 59.4 1.0 SD A:MET243 4.8 85.9 1.0 CA A:MET246 4.8 49.6 1.0 F5 A:S6W501 4.8 61.2 0.6 O2 A:IPA505 4.9 80.7 1.0 F A:S6W501 5.0 70.4 0.5

Chlorine binding site 2 out of 2 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:85.0 occ:0.90 CL1 A:S6W501 0.0 85.0 0.9 C3 A:S6W501 1.7 71.0 0.8 C2 A:S6W501 2.7 73.3 1.0 C4 A:S6W501 2.7 66.8 0.9 N A:S6W501 3.0 63.5 1.0 OE1 A:GLN285 3.2 51.4 1.0 NE2 A:GLN285 3.3 66.8 1.0 CE A:MET323 3.4 79.8 0.8 N1 A:S6W501 3.5 70.2 0.7 CD A:GLN285 3.6 57.5 1.0 C6 A:S6W501 3.7 74.9 1.0 C1 A:S6W501 3.9 68.6 0.9 C5 A:S6W501 3.9 69.2 0.8 CD2 A:PHE288 4.1 53.4 1.0 NE2 A:HIS327 4.2 45.8 1.0 C3 A:IPA505 4.2 74.2 1.0 N3 A:S6W501 4.2 74.5 1.0 CG A:PHE288 4.3 46.8 1.0 SD A:MET323 4.3 81.3 0.2 C8 A:S6W501 4.3 64.4 0.8 C2 A:IPA505 4.3 82.4 1.0 O2 A:IPA505 4.4 80.7 1.0 C A:S6W501 4.4 62.3 0.9 C7 A:S6W501 4.5 72.6 0.7 CB A:PHE288 4.5 40.0 1.0 CE2 A:PHE288 4.6 59.4 1.0 SD A:MET323 4.8 96.1 0.8 CE1 A:HIS327 4.8 46.3 1.0 CE A:MET323 4.8 84.4 0.2 CE2 A:TRP299 4.9 62.5 1.0 NE1 A:TRP299 4.9 52.1 1.0 CZ2 A:TRP299 4.9 50.1 1.0 CD1 A:PHE288 4.9 56.6 1.0

V.Delfosse, T.Huet, D.Harrus, M.Granell, M.Bourguet, C.Gardia-Parege, B.Chiavarina, M.Grimaldi, S.Le Mevel, P.Blanc, D.Huang, J.Gruszczyk, B.Demeneix, S.Cianferani, J.B.Fini, P.Balaguer, W.Bourguet. Mechanistic Insights Into the Synergistic Activation of the Rxr-Pxr Heterodimer By Endocrine Disruptor Mixtures. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33361153
DOI: 10.1073/PNAS.2020551118