Sodium in PDB 5ibc: Caspase 3 V266I

All present enzymatic activity of Caspase 3 V266I:
3.4.22.56;

The structure of Caspase 3 V266I, PDB code: 5ibc was solved by J.J.Maciag, S.H.Mackenzie, M.B.Tucker, J.L.Schipper, P.D.Swartz, A.C.Clark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.98 / 1.66
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.591, 84.325, 96.617, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.8

The structure of Caspase 3 V266I also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Caspase 3 V266I (pdb code 5ibc). 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 Caspase 3 V266I, PDB code: 5ibc:

Sodium binding site 1 out of 1 in the Caspase 3 V266I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Caspase 3 V266I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:19.4 occ:1.00 O A:TRP206 2.8 11.8 1.0 OE1 A:GLN161 2.9 12.2 1.0 N A:PHE215 2.9 11.7 1.0 NE2 A:GLN261 3.0 13.0 1.0 OG A:SER205 3.2 12.9 1.0 CB A:PHE215 3.3 12.1 1.0 N A:TRP214 3.4 10.9 1.0 CD A:GLN161 3.6 12.4 1.0 NE2 A:GLN161 3.7 13.2 1.0 CA A:PHE215 3.7 11.1 1.0 CB A:TRP214 3.7 14.5 1.0 CB A:SER213 3.7 13.5 1.0 C A:TRP214 3.8 10.3 1.0 CA A:TRP214 3.8 12.2 1.0 C A:TRP206 3.9 10.9 1.0 CD A:GLN261 3.9 10.9 1.0 N A:TRP206 3.9 11.4 1.0 C A:SER213 4.0 11.1 1.0 OE1 A:GLN261 4.0 14.0 1.0 OG A:SER213 4.1 12.3 1.0 CB A:SER198 4.2 12.6 1.0 CA A:SER213 4.3 12.4 1.0 CA A:TRP206 4.4 12.5 1.0 CG A:TRP214 4.5 12.7 1.0 OG A:SER198 4.6 14.0 1.0 CB A:SER205 4.6 11.2 1.0 CG A:PHE215 4.7 10.3 1.0 C A:SER205 4.7 10.5 1.0 N A:ILE216 4.8 9.9 1.0 C A:PHE215 4.8 11.2 1.0 O A:SER213 4.8 12.4 1.0 O A:SER198 4.9 13.6 1.0 CB A:TRP206 4.9 11.6 1.0 N A:ARG207 5.0 11.4 1.0 CG A:GLN161 5.0 10.7 1.0 O A:TRP214 5.0 12.9 1.0

J.J.Maciag, S.H.Mackenzie, M.B.Tucker, J.L.Schipper, P.Swartz, A.C.Clark. Tunable Allosteric Library of Caspase-3 Identifies Coupling Between Conserved Water Molecules and Conformational Selection. Proc.Natl.Acad.Sci.Usa V. 113 E6080 2016.
ISSN: ESSN 1091-6490
PubMed: 27681633
DOI: 10.1073/PNAS.1603549113