Sodium in PDB 6naf: De Novo Designed Homo-Trimeric Amantadine-Binding Protein

The structure of De Novo Designed Homo-Trimeric Amantadine-Binding Protein, PDB code: 6naf was solved by B.Selvaraj, J.Park, M.J.Cuneo, D.A.A.Myles, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.92
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	50.610, 50.610, 68.820, 90.00, 90.00, 120.00
R / Rfree (%)	27.7 / 31.8

The binding sites of Sodium atom in the De Novo Designed Homo-Trimeric Amantadine-Binding Protein (pdb code 6naf). 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 De Novo Designed Homo-Trimeric Amantadine-Binding Protein, PDB code: 6naf:

Sodium binding site 1 out of 1 in the De Novo Designed Homo-Trimeric Amantadine-Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of De Novo Designed Homo-Trimeric Amantadine-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:30.0 occ:0.33 D1 A:DOD212 2.1 17.5 1.0 O A:DOD212 2.5 17.5 1.0 OD1 A:ASN47 2.6 15.7 1.0 DD21 A:ASN47 3.0 19.1 0.6 CG A:ASN47 3.1 18.4 1.0 D2 A:DOD212 3.1 17.5 1.0 ND2 A:ASN47 3.3 19.1 1.0 HA A:ASN47 3.6 15.1 1.0 DD22 A:ASN50 3.9 10.7 0.7 HD21 A:ASN47 4.0 19.1 0.0 DD22 A:ASN47 4.1 19.1 1.0 CB A:ASN47 4.2 13.2 1.0 CA A:ASN47 4.4 15.1 1.0 ND2 A:ASN50 4.6 10.7 1.0 HB3 A:ASN47 4.6 13.2 1.0 HB3 A:ASN50 4.7 13.7 1.0 HB2 A:ASN50 4.8 13.7 1.0 OD1 A:ASN46 4.9 17.0 1.0

J.Park, B.Selvaraj, A.C.Mcshan, S.E.Boyken, K.Y.Wei, G.Oberdorfer, W.Degrado, N.G.Sgourakis, M.J.Cuneo, D.A.Myles, D.Baker. De Novo Design of A Homo-Trimeric Amantadine-Binding Protein. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31854299
DOI: 10.7554/ELIFE.47839