Sodium in PDB 8uc5: Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I)

All present enzymatic activity of Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I):
5.2.1.8;

The structure of Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I), PDB code: 8uc5 was solved by D.F.Kreitler, A.M.Rangwala, M.A.Seeliger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.33 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.667, 56.643, 101.172, 90, 123.72, 90
R / Rfree (%)	14.4 / 17.5

The structure of Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I) (pdb code 8uc5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I), PDB code: 8uc5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I) within 5.0Å range: probe atom residue distance (Å) B Occ X:Na207 b:30.0 occ:1.00 OD1 X:ASP160 2.4 18.7 1.0 O X:HOH416 2.5 35.7 1.0 O X:CYS161 2.6 14.1 1.0 OH X:TYR7 2.7 19.2 1.0 CG X:ASP160 3.2 20.7 1.0 OD2 X:ASP160 3.3 24.7 1.0 C X:CYS161 3.6 12.4 1.0 CZ X:TYR7 3.8 17.3 1.0 N X:CYS161 4.0 13.2 1.0 O X:HOH409 4.2 29.0 1.0 NZ X:LYS49 4.2 21.9 1.0 CA X:GLY162 4.4 14.6 1.0 N X:GLY162 4.5 12.6 1.0 CA X:CYS161 4.5 12.9 1.0 CE2 X:TYR7 4.6 16.2 1.0 CB X:ASP160 4.6 17.1 1.0 CE1 X:TYR7 4.7 15.7 1.0 C X:ASP160 4.9 12.6 1.0 CA X:ASP160 5.0 13.6 1.0

Sodium binding site 2 out of 2 in the Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:30.0 occ:1.00 O A:HOH319 2.3 41.9 1.0 OD1 A:ASP160 2.5 20.0 1.0 O A:CYS161 2.6 15.0 1.0 OH A:TYR7 2.6 23.9 1.0 CG A:ASP160 3.2 20.9 1.0 OD2 A:ASP160 3.3 26.2 1.0 C A:CYS161 3.6 12.7 1.0 CZ A:TYR7 3.7 19.7 1.0 N A:CYS161 4.0 13.2 1.0 O A:HOH368 4.2 29.4 1.0 CA A:GLY162 4.3 14.4 1.0 N A:GLY162 4.4 13.5 1.0 CE2 A:TYR7 4.4 18.5 1.0 CA A:CYS161 4.5 13.3 1.0 NZ A:LYS49 4.5 25.3 1.0 CB A:ASP160 4.6 16.7 1.0 CE1 A:TYR7 4.7 18.1 1.0 O A:HOH390 4.8 22.9 1.0 C A:ASP160 5.0 14.5 1.0

D.F.Kreitler, M.A.Seeliger, A.M.Rangwala. Apo X-Ray Crystal Structure of Cyclophilin D with A Surface Entropy Reduction Mutation (K175I) To Be Published.