Sodium in PDB 5u35: Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet

The structure of Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet, PDB code: 5u35 was solved by G.Oberdorfer, E.Marcos, B.Basanta, T.M.Chidyausiku, B.Sankaran, P.H.Zwart, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.27 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.010, 33.200, 86.590, 90.00, 91.78, 90.00
R / Rfree (%)	20.1 / 24.7

The structure of Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet (pdb code 5u35). 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 Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet, PDB code: 5u35:

Sodium binding site 1 out of 1 in the Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A De Novo Designed Protein with Curved Beta-Sheet within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:45.6 occ:1.00 O B:HOH302 2.6 52.6 1.0 O A:HOH348 2.7 42.8 1.0 OG B:SER101 3.2 31.8 1.0 OE2 B:GLU96 3.4 43.2 1.0 CE1 A:TYR106 3.6 29.3 1.0 CB B:SER101 3.7 26.6 1.0 NZ A:LYS112 3.9 58.0 1.0 CD1 A:TYR106 3.9 24.9 1.0 CB B:MET102 3.9 25.5 1.0 CE A:LYS112 4.0 52.2 1.0 CD B:GLU96 4.1 40.3 1.0 O B:SER101 4.3 24.0 1.0 O A:ILE107 4.3 23.3 0.7 C B:SER101 4.3 29.2 1.0 SD B:MET102 4.3 41.3 1.0 O A:ILE107 4.4 23.0 0.3 O B:HOH343 4.4 56.9 1.0 OE1 B:GLU96 4.6 37.3 1.0 CZ A:TYR106 4.6 32.5 1.0 N B:MET102 4.6 26.3 1.0 CA B:SER101 4.7 26.1 1.0 CG B:MET102 4.8 22.8 1.0 CA B:MET102 4.9 25.4 1.0 OH A:TYR106 5.0 31.5 1.0

E.Marcos, B.Basanta, T.M.Chidyausiku, Y.Tang, G.Oberdorfer, G.Liu, G.V.Swapna, R.Guan, D.A.Silva, J.Dou, J.H.Pereira, R.Xiao, B.Sankaran, P.H.Zwart, G.T.Montelione, D.Baker. Principles For Designing Proteins with Cavities Formed By Curved Beta Sheets. Science V. 355 201 2017.
ISSN: ESSN 1095-9203
PubMed: 28082595
DOI: 10.1126/SCIENCE.AAH7389