Sodium in PDB 6suy: Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene

The structure of Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene, PDB code: 6suy was solved by J.M.Alex, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 1.75
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.489, 102.489, 72.180, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 17.9

The structure of Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene (pdb code 6suy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene, PDB code: 6suy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:26.3 occ:1.00 O33 A:LVT202 2.3 44.3 1.0 O5 A:LVT202 2.3 28.6 1.0 O24 A:LVT202 2.3 49.9 1.0 O21 A:LVT202 2.4 28.9 1.0 O1 A:LVT202 2.4 27.5 1.0 O17 A:LVT202 2.4 26.7 1.0 O19 A:LVT202 2.8 46.9 1.0 O23 A:LVT202 3.0 51.9 1.0 C22 A:LVT202 3.1 47.9 1.0 C31 A:LVT202 3.1 41.5 1.0 C20 A:LVT202 3.1 38.4 1.0 C24 A:LVT202 3.1 33.1 1.0 C19 A:LVT202 3.3 34.2 1.0 C23 A:LVT202 3.3 35.2 1.0 C18 A:LVT202 3.4 44.0 1.0 C21 A:LVT202 3.4 46.1 1.0 C26 A:LVT202 3.4 23.5 1.0 C44 A:LVT202 3.5 24.2 1.0 C5 A:LVT202 3.5 27.6 1.0 C14 A:LVT202 3.5 24.3 1.0 C25 A:LVT202 4.3 22.6 1.0 C27 A:LVT202 4.3 22.9 1.0 O34 A:LVT202 4.3 44.5 1.0 O28 A:LVT202 4.3 51.6 1.0 C17 A:LVT202 4.3 23.8 1.0 C42 A:LVT202 4.3 22.2 1.0 C43 A:LVT202 4.3 23.1 1.0 C1 A:LVT202 4.3 22.7 1.0 C4 A:LVT202 4.3 25.0 1.0 C15 A:LVT202 4.3 23.7 1.0 C45 A:LVT202 4.3 22.5 1.0 C13 A:LVT202 4.4 25.3 1.0 C16 A:LVT202 4.4 26.4 1.0 C6 A:LVT202 4.4 26.2 1.0 O22 A:LVT202 4.4 48.0 1.0 O20 A:LVT202 4.5 46.0 1.0

Sodium binding site 2 out of 2 in the Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Yeast Cytochrome C in Complex with An Octa-Anionic Calix[4]Arene within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:26.1 occ:1.00 O22 B:LVT202 2.2 41.3 1.0 O1 B:LVT202 2.3 28.6 1.0 O19 B:LVT202 2.3 40.9 1.0 O17 B:LVT202 2.4 27.3 1.0 O24 B:LVT202 2.4 47.4 1.0 O21 B:LVT202 2.5 30.5 1.0 O5 B:LVT202 2.5 28.6 1.0 C21 B:LVT202 3.0 41.7 1.0 C18 B:LVT202 3.0 40.4 1.0 C19 B:LVT202 3.0 34.0 1.0 C23 B:LVT202 3.1 34.4 1.0 C24 B:LVT202 3.2 33.9 1.0 C22 B:LVT202 3.3 44.1 1.0 C20 B:LVT202 3.4 36.5 1.0 C44 B:LVT202 3.5 26.2 1.0 C26 B:LVT202 3.5 24.7 1.0 C14 B:LVT202 3.5 25.3 1.0 C5 B:LVT202 3.6 25.3 1.0 O23 B:LVT202 4.1 45.8 1.0 O20 B:LVT202 4.2 42.8 1.0 C43 B:LVT202 4.3 25.2 1.0 C42 B:LVT202 4.3 24.6 1.0 C45 B:LVT202 4.3 25.2 1.0 C1 B:LVT202 4.3 25.1 1.0 C27 B:LVT202 4.3 23.6 1.0 C17 B:LVT202 4.3 22.0 1.0 C4 B:LVT202 4.3 23.8 1.0 C25 B:LVT202 4.4 22.7 1.0 C31 B:LVT202 4.4 42.3 1.0 C6 B:LVT202 4.4 25.4 1.0 C15 B:LVT202 4.4 24.5 1.0 C16 B:LVT202 4.4 23.8 1.0 C13 B:LVT202 4.4 24.6 1.0 O28 B:LVT202 4.5 46.7 1.0 O34 B:LVT202 4.8 45.5 1.0

J.M.Alex, G.Brancatelli, S.Volpi, C.Bonaccorso, A.Casnati, S.Geremia, P.B.Crowley. Probing the Determinants of Porosity in Protein Frameworks: Co-Crystals of Cytochrome C and An Octa-Anionic Calix[4]Arene. Org.Biomol.Chem. V. 18 211 2020.
ISSN: ESSN 1477-0539
PubMed: 31808772
DOI: 10.1039/C9OB02275A