Sodium in PDB 8oyw: De Novo Designed Rhomboid Protease-Like Fold RPF_9

The structure of De Novo Designed Rhomboid Protease-Like Fold RPF_9, PDB code: 8oyw was solved by M.Pacesa, B.E.Correia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.72, 66.68, 73.39, 90, 90, 90
R / Rfree (%)	19.8 / 21.6

The binding sites of Sodium atom in the De Novo Designed Rhomboid Protease-Like Fold RPF_9 (pdb code 8oyw). 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 Rhomboid Protease-Like Fold RPF_9, PDB code: 8oyw:

Sodium binding site 1 out of 1 in the De Novo Designed Rhomboid Protease-Like Fold RPF_9


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 Rhomboid Protease-Like Fold RPF_9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:55.1 occ:1.00 O A:HOH372 2.1 49.3 1.0 O A:HOH312 2.2 52.3 1.0 O A:HOH301 2.2 49.3 1.0 O A:HOH364 2.2 49.3 1.0 OD2 A:ASP63 3.9 40.7 1.0 O A:HOH303 3.9 58.6 1.0 OD1 A:ASP63 4.0 39.9 1.0 OD1 A:ASP58 4.1 55.7 1.0 O A:HOH313 4.1 31.4 1.0 HB3 A:SER60 4.1 44.9 1.0 OD2 A:ASP58 4.2 66.2 1.0 HG A:SER60 4.3 46.1 1.0 OG A:SER60 4.3 38.5 1.0 OE1 A:GLU148 4.4 36.8 0.5 CG A:ASP63 4.4 41.4 1.0 CG A:ASP58 4.4 54.9 1.0 O A:HOH441 4.5 53.5 1.0 CD A:GLU148 4.7 35.2 0.5 CB A:SER60 4.7 37.4 1.0 O A:ASP58 4.8 45.9 1.0 HG3 A:GLU148 4.8 41.5 0.5 H A:SER60 4.9 35.4 1.0 OE2 A:GLU148 5.0 32.5 0.5

C.A.Goverde, M.Pacesa, L.J.Dornfeld, S.Georgeon, S.Rosset, J.Dauparas, C.Schellhaas, S.Kozlov, D.Baker, S.Ovchinnikov, B.E.Correia. Computational Design of Soluble Analogues of Integral Membrane Protein Structures To Be Published.