Sodium in PDB 6z0l: Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix

The structure of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix, PDB code: 6z0l was solved by A.G.Mcewen, P.Poussin-Courmontagne, E.A.Naudin, W.F.Degrado, V.Torbeev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.77 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.669, 49.952, 53.043, 105.09, 92.49, 110.15
R / Rfree (%)	22.3 / 28.3

The structure of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix also contains other interesting chemical elements:

Cadmium

(Cd)

5 atoms

The binding sites of Sodium atom in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix (pdb code 6z0l). 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 Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix, PDB code: 6z0l:

Sodium binding site 1 out of 1 in the Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Het-N2 - De Novo Designed Three-Helix Heterodimer with Cysteine at the N2 Position of the Alpha-Helix within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:34.7 occ:1.00 NH1 D:ARG34 2.5 33.4 1.0 NH2 D:ARG6 2.6 38.1 1.0 O D:HOH208 2.8 34.9 1.0 OE1 D:GLU33 3.0 50.4 1.0 CZ D:ARG34 3.5 49.5 1.0 NH2 D:ARG34 3.7 50.8 1.0 CZ D:ARG6 3.7 52.5 1.0 CD D:GLU33 3.8 43.4 1.0 CG D:GLN30 4.1 42.7 1.0 OE2 D:GLU33 4.1 40.3 1.0 NH1 D:ARG6 4.2 53.2 1.0 NE2 D:GLN30 4.3 31.4 1.0 CD D:GLN30 4.4 38.2 1.0 NE D:ARG34 4.8 38.0 1.0 NE D:ARG6 4.8 53.3 1.0 CB D:GLN30 4.8 24.2 1.0

E.A.Naudin, A.G.Mcewen, S.K.Tan, P.Poussin-Courmontagne, J.L.Schmitt, C.Birck, W.F.Degrado, V.Torbeev. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of Alpha-Helix As Oxyanion-Binding Site. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 33635059
DOI: 10.1021/JACS.0C10053