Chlorine in PDB 3rcg: Human Cyclophilin D Complexed with Dimethylformamide

All present enzymatic activity of Human Cyclophilin D Complexed with Dimethylformamide:
5.2.1.8;

The structure of Human Cyclophilin D Complexed with Dimethylformamide, PDB code: 3rcg was solved by L.Colliandre, H.Ahmed-Belkacem, Y.Bessin, J.M.Pawlotsky, J.F.Guichou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.85 / 0.97
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.374, 57.374, 87.384, 90.00, 90.00, 90.00
R / Rfree (%)	9 / 10.8

The binding sites of Chlorine atom in the Human Cyclophilin D Complexed with Dimethylformamide (pdb code 3rcg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Cyclophilin D Complexed with Dimethylformamide, PDB code: 3rcg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Cyclophilin D Complexed with Dimethylformamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Cyclophilin D Complexed with Dimethylformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl208 b:35.1 occ:0.30 CL A:CL208 0.0 35.1 0.3 CL A:CL208 0.9 11.0 0.3 H2 A:HOH558 1.8 12.1 0.7 O A:HOH558 2.1 12.1 0.7 H1 A:HOH556 2.4 11.4 0.7 HH22 A:ARG61 2.5 4.9 1.0 O A:HOH555 2.7 9.8 0.8 HH12 A:ARG61 2.8 5.7 1.0 H1 A:HOH555 2.9 9.8 0.8 H2 A:HOH555 2.9 9.9 0.8 H1 A:HOH558 3.1 12.0 0.7 O A:HOH556 3.2 11.3 0.7 H2 A:HOH556 3.2 11.3 0.7 O A:HOH565 3.3 12.1 0.5 O A:HOH308 3.3 7.9 0.7 NH2 A:ARG61 3.3 5.8 1.0 H2 A:HOH565 3.5 12.1 0.5 NH1 A:ARG61 3.6 6.7 1.0 H2 A:HOH308 3.6 7.8 0.7 O A:HOH574 3.6 11.5 0.5 H2 A:HOH565 3.7 8.5 0.4 H1 A:HOH565 3.8 12.1 0.5 CZ A:ARG61 3.9 5.0 1.0 H2 A:HOH400 3.9 15.4 0.3 HH21 A:ARG61 3.9 5.4 1.0 H2 A:HOH574 3.9 11.6 0.5 H1 A:HOH308 4.0 7.9 0.7 H2 A:HOH25 4.1 24.6 0.8 O A:HOH400 4.2 15.4 0.3 H1 A:HOH528 4.2 16.0 0.6 HH11 A:ARG61 4.3 6.3 1.0 O A:HOH565 4.3 8.6 0.4 HH A:TYR49 4.5 4.9 0.8 H1 A:HOH574 4.5 11.6 0.5 H1 A:HOH400 4.5 15.4 0.3 H1 A:HOH25 4.6 24.6 0.8 H1 A:HOH565 4.8 8.6 0.4 O A:HOH25 4.8 24.5 0.8 HD22 A:LEU206 4.8 5.0 1.0 H2 A:HOH548 4.9 11.2 0.4 OH A:TYR49 4.9 5.0 0.8 O A:HOH548 4.9 11.1 0.4 H1 A:HOH548 5.0 11.1 0.4 CZ A:TYR49 5.0 5.2 1.0

Chlorine binding site 2 out of 2 in the Human Cyclophilin D Complexed with Dimethylformamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Cyclophilin D Complexed with Dimethylformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl208 b:11.0 occ:0.30 CL A:CL208 0.0 11.0 0.3 CL A:CL208 0.9 35.1 0.3 HH22 A:ARG61 2.1 4.9 1.0 H1 A:HOH556 2.1 11.4 0.7 H2 A:HOH558 2.3 12.1 0.7 H2 A:HOH556 2.6 11.3 0.7 O A:HOH556 2.7 11.3 0.7 H2 A:HOH555 2.7 9.9 0.8 O A:HOH558 2.8 12.1 0.7 O A:HOH555 2.8 9.8 0.8 NH2 A:ARG61 2.9 5.8 1.0 H1 A:HOH555 2.9 9.8 0.8 HH12 A:ARG61 3.0 5.7 1.0 H1 A:HOH528 3.3 16.0 0.6 H2 A:HOH25 3.3 24.6 0.8 HH21 A:ARG61 3.4 5.4 1.0 NH1 A:ARG61 3.6 6.7 1.0 H1 A:HOH558 3.7 12.0 0.7 HH A:TYR49 3.7 4.9 0.8 CZ A:ARG61 3.7 5.0 1.0 H2 A:HOH400 4.0 15.4 0.3 O A:HOH565 4.0 12.1 0.5 O A:HOH308 4.0 7.9 0.7 H1 A:HOH25 4.0 24.6 0.8 H2 A:HOH565 4.0 12.1 0.5 O A:HOH25 4.1 24.5 0.8 OH A:TYR49 4.1 5.0 0.8 CZ A:TYR49 4.2 5.2 1.0 H2 A:HOH308 4.2 7.8 0.7 O A:HOH528 4.3 15.9 0.6 O A:HOH400 4.3 15.4 0.3 O A:HOH574 4.3 11.5 0.5 HH11 A:ARG61 4.4 6.3 1.0 H1 A:HOH565 4.4 12.1 0.5 H2 A:HOH565 4.4 8.5 0.4 CE1 A:TYR49 4.5 5.2 1.0 H1 A:HOH15 4.5 6.7 0.9 H2 A:HOH574 4.5 11.6 0.5 HE1 A:TYR49 4.6 4.7 1.0 H2 A:HOH528 4.6 16.0 0.6 CE2 A:TYR49 4.6 4.7 1.0 H1 A:HOH308 4.8 7.9 0.7 HE2 A:TYR49 4.8 4.6 1.0 HD22 A:LEU206 4.8 5.0 1.0 H1 A:HOH400 4.9 15.4 0.3 NE A:ARG61 5.0 4.3 1.0

A.Ahmed-Belkacem, L.Colliandre, N.Ahnou, Q.Nevers, M.Gelin, Y.Bessin, R.Brillet, O.Cala, D.Douguet, W.Bourguet, I.Krimm, J.M.Pawlotsky, J.F.Guichou. Fragment-Based Discovery of A New Family of Non-Peptidic Small-Molecule Cyclophilin Inhibitors with Potent Antiviral Activities. Nat Commun V. 7 12777 2016.
ISSN: ESSN 2041-1723
PubMed: 27652979
DOI: 10.1038/NCOMMS12777