Sodium in PDB 6myj: Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin

The structure of Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin, PDB code: 6myj was solved by D.R.Tomchick, A.Radhakrishnan, S.Endapally, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.56 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.425, 100.565, 58.813, 90.00, 106.29, 90.00
R / Rfree (%)	15.5 / 16.8

The binding sites of Sodium atom in the Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin (pdb code 6myj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin, PDB code: 6myj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:40.1 occ:1.00 OD1 A:ASN101 2.6 18.4 1.0 O A:PRO95 2.8 22.3 1.0 OE1 A:GLN5 3.0 24.2 1.0 HD2 A:PRO95 3.0 21.4 1.0 O A:GLY124 3.2 24.3 1.0 O A:LYS99 3.3 34.8 1.0 H A:GLY124 3.4 35.8 1.0 HG2 A:PRO95 3.5 31.5 1.0 HG A:SER94 3.6 23.9 1.0 CG A:ASN101 3.6 17.8 1.0 HD21 A:ASN101 3.7 23.5 1.0 CD A:PRO95 3.7 17.8 1.0 N A:PRO95 3.7 17.4 1.0 CD A:GLN5 3.8 22.0 1.0 HA A:SER94 3.8 17.8 1.0 C A:PRO95 3.9 19.9 1.0 HE22 A:GLN5 3.9 29.3 1.0 O A:GLY97 3.9 39.4 1.0 OG A:SER94 4.0 19.9 1.0 ND2 A:ASN101 4.0 19.6 1.0 C A:SER94 4.1 16.4 1.0 CG A:PRO95 4.1 26.2 1.0 N A:GLY124 4.1 29.9 1.0 NE2 A:GLN5 4.2 24.4 1.0 C A:GLY124 4.2 22.4 1.0 HA A:SER123 4.2 62.2 1.0 CA A:PRO95 4.3 20.2 1.0 CA A:SER94 4.4 14.8 1.0 C A:LYS99 4.5 34.2 1.0 HD3 A:PRO95 4.6 21.4 1.0 HA A:ASN101 4.6 20.2 1.0 O A:ASP122 4.6 32.0 1.0 CA A:GLY124 4.7 24.7 1.0 N A:ASN101 4.7 19.5 1.0 O A:SER94 4.7 16.8 1.0 HA A:THR100 4.7 33.6 1.0 C A:THR100 4.7 24.6 1.0 HG3 A:GLN5 4.8 21.2 1.0 CB A:PRO95 4.8 27.9 1.0 HA2 A:GLY124 4.8 29.6 1.0 CB A:SER94 4.8 14.8 1.0 CB A:ASN101 4.8 16.0 1.0 H A:ASN101 4.8 23.4 1.0 HG3 A:PRO95 4.9 31.5 1.0 HD22 A:ASN101 4.9 23.5 1.0 CG A:GLN5 4.9 17.7 1.0 HE21 A:GLN5 4.9 29.3 1.0 CA A:ASN101 4.9 16.8 1.0 HB2 A:PRO95 4.9 33.5 1.0 C A:SER123 5.0 45.9 1.0 H A:GLY97 5.0 33.2 1.0

Sodium binding site 2 out of 4 in the Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:31.6 occ:1.00 O B:SER123 2.6 35.6 1.0 OD1 B:ASN101 2.7 16.3 1.0 O B:PRO95 2.8 18.5 1.0 O B:LYS99 2.9 27.9 1.0 HE22 B:GLN5 2.9 23.6 1.0 HD2 B:PRO95 3.0 17.8 1.0 HA B:SER123 3.1 50.4 1.0 NE2 B:GLN5 3.3 19.6 1.0 C B:SER123 3.3 34.3 1.0 HG2 B:PRO95 3.3 23.8 1.0 O B:GLY124 3.4 25.0 1.0 HE21 B:GLN5 3.5 23.6 1.0 O B:GLY97 3.7 31.9 1.0 CD B:PRO95 3.7 14.8 1.0 CA B:SER123 3.7 42.0 1.0 N B:PRO95 3.8 14.2 1.0 CG B:ASN101 3.8 15.2 1.0 C B:PRO95 3.9 18.4 1.0 O B:ASP122 3.9 28.0 1.0 CG B:PRO95 3.9 19.8 1.0 HG B:SER123 3.9 83.4 1.0 HD21 B:ASN101 4.0 21.4 1.0 HA B:SER94 4.0 14.7 1.0 CD B:GLN5 4.0 21.2 1.0 HG B:SER94 4.0 18.2 1.0 C B:LYS99 4.1 29.2 1.0 C B:SER94 4.2 13.5 1.0 N B:GLY124 4.3 30.9 1.0 ND2 B:ASN101 4.3 17.8 1.0 OE1 B:GLN5 4.3 26.5 1.0 CA B:PRO95 4.3 16.9 1.0 C B:GLY124 4.4 24.8 1.0 OG B:SER94 4.4 15.2 1.0 HA B:THR100 4.4 29.7 1.0 OG B:SER123 4.5 69.5 1.0 HD3 B:PRO95 4.5 17.8 1.0 CA B:SER94 4.6 12.3 1.0 N B:ASN101 4.6 15.6 1.0 C B:THR100 4.6 17.5 1.0 HA B:ASN101 4.6 15.4 1.0 H B:ASN101 4.6 18.7 1.0 CB B:PRO95 4.7 22.5 1.0 CB B:SER123 4.7 59.7 1.0 HG3 B:PRO95 4.7 23.8 1.0 N B:SER123 4.7 32.3 1.0 CA B:GLY124 4.7 27.1 1.0 HA2 B:GLY124 4.7 32.5 1.0 C B:ASP122 4.8 33.1 1.0 C B:GLY97 4.8 32.0 1.0 HB2 B:PRO95 4.8 27.0 1.0 HG3 B:GLN5 4.8 25.6 1.0 O B:SER94 4.9 14.1 1.0 CA B:THR100 4.9 24.7 1.0 N B:LYS99 4.9 24.9 1.0 H B:GLY124 4.9 37.1 1.0 HB3 B:LYS99 4.9 38.6 1.0 N B:THR100 4.9 22.3 1.0 CA B:ASN101 5.0 12.9 1.0 CB B:ASN101 5.0 12.2 1.0

Sodium binding site 3 out of 4 in the Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:38.4 occ:1.00 OD1 C:ASN101 2.6 16.3 1.0 O C:GLY124 2.8 27.0 1.0 O C:PRO95 2.9 25.1 1.0 OE1 C:GLN5 3.0 28.5 1.0 HD2 C:PRO95 3.2 20.1 1.0 HD21 C:ASN101 3.4 21.5 1.0 CG C:ASN101 3.4 16.1 1.0 O C:LYS99 3.6 31.7 1.0 HE22 C:GLN5 3.7 30.6 1.0 H C:GLY124 3.7 42.4 1.0 HG C:SER94 3.8 21.5 1.0 HG2 C:PRO95 3.8 22.9 1.0 ND2 C:ASN101 3.8 17.9 1.0 CD C:GLN5 3.8 26.6 1.0 C C:GLY124 3.9 27.7 1.0 CD C:PRO95 3.9 16.8 1.0 N C:PRO95 4.0 16.3 1.0 HA C:SER94 4.0 18.1 1.0 C C:PRO95 4.0 18.2 1.0 NE2 C:GLN5 4.1 25.5 1.0 OG C:SER94 4.2 17.9 1.0 N C:GLY124 4.3 35.3 1.0 C C:SER94 4.3 14.7 1.0 CG C:PRO95 4.4 19.1 1.0 H C:ASN101 4.4 20.0 1.0 HA C:ALA125 4.5 21.0 1.0 O C:HOH304 4.5 29.4 1.0 N C:ASN101 4.5 16.6 1.0 CA C:PRO95 4.6 18.3 1.0 CA C:SER94 4.6 15.1 1.0 CA C:GLY124 4.6 28.9 1.0 HD22 C:ASN101 4.6 21.5 1.0 HA C:ASN101 4.6 18.6 1.0 O C:GLY97 4.7 39.0 1.0 CB C:ASN101 4.7 15.4 1.0 HA2 C:GLY124 4.7 34.7 1.0 HD3 C:PRO95 4.8 20.1 1.0 HA C:SER123 4.8 45.0 1.0 HA C:TRP96 4.8 31.7 1.0 C C:LYS99 4.8 26.8 1.0 HE21 C:GLN5 4.9 30.6 1.0 CA C:ASN101 4.9 15.5 1.0 C C:THR100 4.9 18.6 1.0 N C:ALA125 4.9 20.1 1.0 HA C:THR100 4.9 29.5 1.0

Sodium binding site 4 out of 4 in the Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pleurotus Ostreatus Ostreolysina Plus Sphingomyelin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:19.9 occ:1.00 OD1 D:ASN101 2.4 13.3 1.0 O D:PRO95 2.5 15.3 1.0 OE1 D:GLN5 2.5 13.5 1.0 O D:GLY124 2.7 18.9 1.0 HD21 D:ASN101 3.3 16.0 1.0 CD D:GLN5 3.3 14.6 1.0 HG D:SER94 3.3 13.9 1.0 HE22 D:GLN5 3.4 17.9 1.0 HD2 D:PRO95 3.4 15.3 1.0 CG D:ASN101 3.4 11.8 1.0 O D:LYS99 3.5 43.7 1.0 C D:PRO95 3.6 13.8 1.0 NE2 D:GLN5 3.6 14.9 1.0 C D:GLY124 3.6 16.6 1.0 H D:GLY124 3.6 27.2 1.0 ND2 D:ASN101 3.7 13.3 1.0 HA D:SER94 3.7 10.6 1.0 N D:PRO95 3.7 11.1 1.0 HA D:ALA125 3.8 15.2 1.0 OG D:SER94 3.8 11.6 1.0 C D:SER94 3.9 10.2 1.0 HG2 D:PRO95 3.9 21.0 1.0 CD D:PRO95 3.9 12.8 1.0 N D:GLY124 4.1 22.7 1.0 CA D:SER94 4.2 8.9 1.0 CA D:PRO95 4.3 12.6 1.0 HG3 D:GLN5 4.3 14.3 1.0 HE21 D:GLN5 4.4 17.9 1.0 CG D:PRO95 4.4 17.5 1.0 CA D:GLY124 4.4 18.6 1.0 O D:SER94 4.4 10.9 1.0 CG D:GLN5 4.4 12.0 1.0 N D:ALA125 4.5 13.9 1.0 HA D:TRP96 4.5 20.3 1.0 O D:GLY97 4.5 44.6 1.0 CA D:ALA125 4.5 12.6 1.0 HA D:SER123 4.5 45.5 1.0 HD22 D:ASN101 4.6 16.0 1.0 HA2 D:GLY124 4.6 22.3 1.0 CB D:SER94 4.6 10.9 1.0 C D:LYS99 4.7 34.1 1.0 N D:TRP96 4.7 15.3 1.0 H D:LEU126 4.7 12.5 1.0 HB2 D:LYS99 4.8 59.0 1.0 CB D:ASN101 4.8 11.8 1.0 HD3 D:PRO95 4.8 15.3 1.0 HA D:ASN101 4.9 13.0 1.0 H D:LYS99 4.9 59.4 1.0 CB D:PRO95 4.9 16.2 1.0 HB3 D:GLN5 4.9 14.5 1.0 O D:ASP122 5.0 38.7 1.0 C D:SER123 5.0 29.1 1.0 H D:GLY97 5.0 27.0 1.0 C D:ALA125 5.0 10.9 1.0 N D:LEU126 5.0 10.4 1.0

S.Endapally, D.Frias, M.Grzemska, A.Gay, D.R.Tomchick, A.Radhakrishnan. Molecular Discrimination Between Two Conformations of Sphingomyelin in Plasma Membranes. Cell V. 176 1040 2019.
ISSN: ISSN 1097-4172
PubMed: 30712872
DOI: 10.1016/J.CELL.2018.12.042