Sodium in PDB 3r57: Human Cyclophilin D Complexed with A Fragment

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

The structure of Human Cyclophilin D Complexed with A Fragment, PDB code: 3r57 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)	22.00 / 1.71
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.430, 57.430, 87.975, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 18.1

The binding sites of Sodium atom in the Human Cyclophilin D Complexed with A Fragment (pdb code 3r57). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Cyclophilin D Complexed with A Fragment, PDB code: 3r57:

Sodium binding site 1 out of 1 in the Human Cyclophilin D Complexed with A Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Cyclophilin D Complexed with A Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:20.0 occ:1.00 O A:HOH752 2.6 20.1 1.0 O A:ASN45 2.7 7.7 1.0 OG A:SER207 2.8 4.6 1.0 CB A:SER207 3.7 4.6 1.0 O A:SER207 3.7 5.3 1.0 C A:ASN45 3.8 7.6 1.0 C A:SER207 3.9 5.1 1.0 O A:HOH436 4.2 18.3 0.8 OXT A:SER207 4.2 5.2 1.0 C A:GLY44 4.2 9.5 1.0 O A:HOH606 4.3 11.3 1.0 N A:LEU47 4.3 5.9 1.0 O A:GLY44 4.4 9.6 1.0 CG A:LEU47 4.4 7.6 1.0 CA A:SER207 4.4 4.8 1.0 N A:ASN45 4.4 8.7 1.0 CA A:PRO46 4.5 6.7 1.0 C A:PRO46 4.6 6.3 1.0 N A:PRO46 4.6 7.0 1.0 CA A:GLY44 4.6 9.9 1.0 CB A:LEU47 4.7 6.2 1.0 CA A:ASN45 4.7 8.0 1.0 CD1 A:LEU47 5.0 8.0 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