Sodium in PDB 6myi: Pleurotus Ostreatus Ostreolysina

The structure of Pleurotus Ostreatus Ostreolysina, PDB code: 6myi 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)	33.31 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.430, 100.335, 59.018, 90.00, 106.43, 90.00
R / Rfree (%)	14.2 / 16.1

The binding sites of Sodium atom in the Pleurotus Ostreatus Ostreolysina (pdb code 6myi). 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, PDB code: 6myi:
Jump to Sodium binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:22.8 occ:1.00 O A:HOH306 2.1 30.2 1.0 OD1 A:ASN101 2.5 16.1 1.0 OE1 A:GLN5 2.5 16.6 1.0 O A:PRO95 2.5 16.9 1.0 O A:GLY124 2.7 20.4 1.0 CD A:GLN5 3.3 15.6 1.0 CG A:ASN101 3.4 14.9 1.0 O A:LYS99 3.5 36.0 1.0 NE2 A:GLN5 3.6 17.9 1.0 C A:GLY124 3.6 19.1 1.0 C A:PRO95 3.7 15.2 1.0 ND2 A:ASN101 3.7 15.3 1.0 N A:PRO95 3.7 13.8 1.0 OG A:SER94 3.8 14.7 1.0 C A:SER94 3.9 13.0 1.0 CD A:PRO95 3.9 15.3 1.0 N A:GLY124 4.1 26.8 1.0 CA A:SER94 4.2 13.0 1.0 CA A:PRO95 4.3 15.2 1.0 O A:GLY97 4.4 38.7 1.0 CG A:PRO95 4.4 18.2 1.0 O A:SER94 4.4 13.2 1.0 CA A:GLY124 4.4 23.2 1.0 CG A:GLN5 4.4 15.0 1.0 N A:ALA125 4.5 16.4 1.0 CA A:ALA125 4.5 14.5 1.0 CB A:SER94 4.6 13.8 1.0 C A:LYS99 4.7 34.6 1.0 N A:TRP96 4.8 16.7 1.0 CB A:ASN101 4.8 13.8 1.0 CB A:PRO95 4.9 17.9 1.0 C A:SER123 4.9 28.8 1.0 C A:ALA125 5.0 14.0 1.0 N A:LEU126 5.0 12.8 1.0 O A:ASP122 5.0 34.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:42.1 occ:1.00 OD1 B:ASN101 2.6 21.4 1.0 O B:GLY124 2.8 31.0 1.0 O B:PRO95 2.9 28.1 1.0 O B:HOH359 3.1 35.4 1.0 OE1 B:GLN5 3.1 26.6 1.0 O B:LYS99 3.4 35.3 1.0 CG B:ASN101 3.5 18.0 1.0 ND2 B:ASN101 3.8 18.4 1.0 C B:GLY124 3.8 27.7 1.0 CD B:GLN5 4.0 24.4 1.0 CD B:PRO95 4.0 20.1 1.0 N B:GLY124 4.0 36.0 1.0 C B:PRO95 4.1 24.7 1.0 N B:PRO95 4.1 19.5 1.0 NE2 B:GLN5 4.2 25.0 1.0 OG B:SER94 4.3 21.2 1.0 CA B:GLY124 4.4 31.3 1.0 CG B:PRO95 4.4 21.4 1.0 N B:ASN101 4.5 17.8 1.0 C B:SER94 4.5 17.2 1.0 O B:GLY97 4.5 40.7 1.0 C B:LYS99 4.7 33.2 1.0 CA B:PRO95 4.7 21.3 1.0 CA B:SER94 4.7 17.6 1.0 CB B:ASN101 4.8 16.4 1.0 C B:THR100 4.8 20.7 1.0 CA B:ASN101 4.9 15.5 1.0 N B:ALA125 4.9 22.0 1.0 O B:ASP122 4.9 38.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:34.1 occ:1.00 OD1 C:ASN101 2.7 23.1 1.0 O C:LYS99 2.8 32.6 1.0 O C:PRO95 2.8 26.0 1.0 NE2 C:GLN5 3.3 24.9 1.0 O C:GLY124 3.5 27.6 1.0 O C:GLY97 3.6 34.4 1.0 CD C:PRO95 3.6 18.8 1.0 N C:PRO95 3.7 18.6 1.0 CG C:ASN101 3.8 19.2 1.0 C C:PRO95 3.9 23.5 1.0 N C:GLY124 3.9 35.4 1.0 CG C:PRO95 4.0 22.2 1.0 C C:LYS99 4.1 30.9 1.0 CD C:GLN5 4.1 24.9 1.0 C C:SER94 4.2 17.1 1.0 CA C:SER123 4.2 42.2 1.0 CA C:PRO95 4.3 21.4 1.0 ND2 C:ASN101 4.3 21.4 1.0 OE1 C:GLN5 4.3 27.5 1.0 OG C:SER94 4.3 18.3 1.0 O C:ASP122 4.5 40.5 1.0 C C:GLY124 4.5 27.1 1.0 CA C:SER94 4.5 16.4 1.0 N C:ASN101 4.5 19.6 1.0 C C:SER123 4.6 41.2 1.0 C C:THR100 4.6 22.4 1.0 CB C:PRO95 4.7 23.1 1.0 C C:GLY97 4.7 33.4 1.0 CA C:GLY124 4.8 31.3 1.0 CA C:THR100 4.8 26.9 1.0 O C:SER94 4.8 17.8 1.0 N C:LYS99 4.9 35.1 1.0 N C:THR100 4.9 28.0 1.0 CB C:SER123 4.9 45.1 1.0 CA C:ASN101 4.9 17.4 1.0 CB C:ASN101 4.9 17.4 1.0 O C:THR100 4.9 23.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:43.5 occ:1.00 OD1 D:ASN101 2.7 25.2 1.0 O D:PRO95 3.0 24.0 1.0 OE1 D:GLN5 3.1 26.2 1.0 O D:LYS99 3.2 36.9 1.0 O D:GLY124 3.3 25.8 1.0 CG D:ASN101 3.7 20.5 1.0 CD D:PRO95 3.7 21.3 1.0 O D:GLY97 3.8 40.1 1.0 N D:PRO95 3.8 20.4 1.0 N D:GLY124 3.9 33.7 1.0 CD D:GLN5 4.0 24.0 1.0 C D:PRO95 4.0 22.6 1.0 CG D:PRO95 4.1 24.1 1.0 ND2 D:ASN101 4.1 21.7 1.0 OG D:SER94 4.1 20.9 1.0 C D:SER94 4.2 18.6 1.0 C D:GLY124 4.2 24.8 1.0 NE2 D:GLN5 4.3 25.1 1.0 C D:LYS99 4.4 35.0 1.0 CA D:PRO95 4.5 22.5 1.0 CA D:SER94 4.5 17.4 1.0 O D:ASP122 4.5 39.5 1.0 CA D:GLY124 4.5 28.9 1.0 N D:ASN101 4.6 22.4 1.0 C D:THR100 4.7 27.1 1.0 C D:SER123 4.9 41.3 1.0 CB D:ASN101 4.9 19.5 1.0 O D:SER94 4.9 18.1 1.0 CB D:PRO95 4.9 24.6 1.0 CA D:ASN101 4.9 19.6 1.0 CA D:THR100 4.9 30.0 1.0 CA D:SER123 5.0 45.1 1.0 CB D:SER94 5.0 18.5 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