Sodium in PDB 6myk: Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris

The structure of Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris, PDB code: 6myk 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)	49.27 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.857, 86.684, 92.878, 90.00, 99.13, 90.00
R / Rfree (%)	19.4 / 21.9

The binding sites of Sodium atom in the Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris (pdb code 6myk). 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 Mutant E69A with Bis-Tris, PDB code: 6myk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris


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 Mutant E69A with Bis-Tris within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:30.7 occ:1.00 HG3 A:GLN5 2.7 15.1 1.0 OG A:SER94 2.7 8.9 1.0 O A:HOH414 2.7 18.4 1.0 O A:PRO95 2.8 14.5 1.0 O A:GLY124 3.0 10.3 1.0 O A:HOH308 3.1 19.9 1.0 OD1 A:ASN101 3.1 13.8 1.0 HG A:SER94 3.2 10.6 1.0 C A:SER94 3.2 9.5 1.0 HD2 A:PRO95 3.3 15.3 1.0 HA A:SER94 3.3 11.5 1.0 HA A:ALA125 3.4 11.3 1.0 N A:PRO95 3.4 12.7 1.0 HA A:GLN5 3.5 14.2 1.0 CG A:GLN5 3.5 12.6 1.0 O A:HOH376 3.5 33.8 1.0 CA A:SER94 3.5 9.6 1.0 O A:SER94 3.5 9.6 1.0 CB A:SER94 3.6 9.1 1.0 HG2 A:GLN5 3.6 15.1 1.0 C A:PRO95 3.7 14.2 1.0 C A:GLY124 3.7 10.7 1.0 CD A:PRO95 3.8 12.8 1.0 HB3 A:GLN5 3.9 14.2 1.0 HB3 A:SER94 4.0 11.0 1.0 HE21 A:GLN5 4.0 15.2 1.0 CB A:GLN5 4.1 11.8 1.0 CA A:PRO95 4.2 13.4 1.0 CG A:ASN101 4.2 13.9 1.0 CA A:ALA125 4.2 9.4 1.0 CA A:GLN5 4.2 11.8 1.0 HD21 A:ASN101 4.3 19.2 1.0 N A:ALA125 4.3 10.3 1.0 HG2 A:PRO95 4.4 16.7 1.0 HB2 A:SER94 4.4 11.0 1.0 H A:LEU126 4.5 11.3 1.0 HA2 A:GLY124 4.6 14.2 1.0 HD3 A:PRO95 4.6 15.3 1.0 ND2 A:ASN101 4.6 16.0 1.0 CD A:GLN5 4.6 12.5 1.0 CA A:GLY124 4.7 11.8 1.0 CG A:PRO95 4.7 13.9 1.0 NE2 A:GLN5 4.7 12.6 1.0 H A:TRP6 4.7 9.8 1.0 HA A:TRP96 4.8 21.2 1.0 C A:ALA125 4.8 9.1 1.0 HA A:PRO95 4.8 16.1 1.0 N A:LEU126 4.8 9.4 1.0 O A:SER98 4.8 28.7 1.0 N A:TRP96 4.8 15.8 1.0 H A:GLY124 4.9 14.8 1.0 O A:ALA4 4.9 11.2 1.0 N A:GLY124 5.0 12.4 1.0 N A:SER94 5.0 10.4 1.0 HB2 A:GLN5 5.0 14.2 1.0

Sodium binding site 2 out of 4 in the Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris


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 Mutant E69A with Bis-Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:32.4 occ:1.00 OG B:SER94 2.6 19.0 1.0 HG3 B:GLN5 2.6 31.5 1.0 O B:GLY124 2.8 24.5 1.0 OD1 B:ASN101 2.8 21.1 1.0 O B:PRO95 2.8 24.4 1.0 C B:SER94 3.1 20.6 1.0 O B:HOH359 3.2 31.5 1.0 HA B:SER94 3.2 22.0 1.0 O B:SER94 3.4 22.0 1.0 CA B:SER94 3.5 18.3 1.0 N B:PRO95 3.5 21.7 1.0 CG B:GLN5 3.5 26.2 1.0 CB B:SER94 3.5 18.4 1.0 HD2 B:PRO95 3.5 27.0 1.0 HA B:ALA125 3.6 19.3 1.0 HG2 B:GLN5 3.6 31.5 1.0 HA B:GLN5 3.7 30.1 1.0 C B:GLY124 3.7 24.8 1.0 CG B:ASN101 3.8 20.7 1.0 C B:PRO95 3.8 24.9 1.0 HD21 B:ASN101 3.8 25.5 1.0 HE21 B:GLN5 3.8 33.5 1.0 HB3 B:SER94 4.0 22.1 1.0 HB3 B:GLN5 4.0 31.0 1.0 CD B:PRO95 4.0 22.5 1.0 ND2 B:ASN101 4.1 21.3 1.0 CB B:GLN5 4.2 25.8 1.0 CA B:PRO95 4.2 24.1 1.0 HB2 B:SER94 4.3 22.1 1.0 CA B:ALA125 4.3 16.1 1.0 N B:ALA125 4.4 18.6 1.0 CA B:GLN5 4.4 25.1 1.0 HG2 B:PRO95 4.5 31.1 1.0 NE2 B:GLN5 4.5 28.0 1.0 H B:LEU126 4.5 19.1 1.0 CD B:GLN5 4.5 26.9 1.0 H B:GLY124 4.6 36.8 1.0 CA B:GLY124 4.6 28.2 1.0 HA2 B:GLY124 4.7 33.8 1.0 C B:ALA125 4.7 16.8 1.0 N B:LEU126 4.8 15.9 1.0 HA B:TRP96 4.8 38.6 1.0 HD3 B:PRO95 4.8 27.0 1.0 CG B:PRO95 4.8 25.9 1.0 N B:GLY124 4.8 30.7 1.0 HA B:PRO95 4.8 28.9 1.0 N B:TRP96 4.9 30.9 1.0 N B:SER94 4.9 18.2 1.0 HD22 B:ASN101 5.0 25.5 1.0

Sodium binding site 3 out of 4 in the Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris


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 Mutant E69A with Bis-Tris within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:31.8 occ:1.00 OG C:SER94 2.6 18.7 1.0 O C:PRO95 2.7 29.7 1.0 HG3 C:GLN5 2.7 25.7 1.0 O C:GLY124 2.8 17.8 1.0 O C:HOH375 2.9 33.0 1.0 HG C:SER94 3.1 22.4 1.0 OD1 C:ASN101 3.1 22.1 1.0 O C:HOH314 3.3 17.5 1.0 C C:SER94 3.3 20.1 1.0 HA C:ALA125 3.4 15.0 1.0 HA C:SER94 3.5 22.6 1.0 HD2 C:PRO95 3.5 31.5 1.0 HA C:GLN5 3.5 23.1 1.0 N C:PRO95 3.5 26.2 1.0 CG C:GLN5 3.6 21.4 1.0 C C:GLY124 3.6 16.3 1.0 O C:SER94 3.6 20.5 1.0 C C:PRO95 3.7 29.7 1.0 CA C:SER94 3.7 18.9 1.0 CB C:SER94 3.7 18.8 1.0 HG2 C:GLN5 3.8 25.7 1.0 HE21 C:GLN5 3.9 28.2 1.0 HB3 C:GLN5 4.0 24.1 1.0 CD C:PRO95 4.0 26.3 1.0 CA C:ALA125 4.2 12.5 1.0 CB C:GLN5 4.2 20.1 1.0 CG C:ASN101 4.2 21.6 1.0 HB3 C:SER94 4.2 22.5 1.0 N C:ALA125 4.2 13.0 1.0 HD21 C:ASN101 4.2 26.8 1.0 CA C:PRO95 4.2 28.7 1.0 CA C:GLN5 4.3 19.2 1.0 HG2 C:PRO95 4.3 34.4 1.0 HA2 C:GLY124 4.4 20.2 1.0 HB2 C:SER94 4.4 22.5 1.0 CA C:GLY124 4.5 16.8 1.0 H C:LEU126 4.5 16.4 1.0 NE2 C:GLN5 4.6 23.5 1.0 ND2 C:ASN101 4.6 22.3 1.0 HA C:TRP96 4.6 41.1 1.0 CD C:GLN5 4.7 22.6 1.0 CG C:PRO95 4.7 28.7 1.0 H C:GLY124 4.7 21.0 1.0 C C:ALA125 4.7 12.4 1.0 N C:TRP96 4.8 32.2 1.0 HD3 C:PRO95 4.8 31.5 1.0 H C:TRP6 4.8 17.5 1.0 N C:LEU126 4.8 13.7 1.0 HA C:PRO95 4.8 34.4 1.0 N C:GLY124 4.8 17.5 1.0 H C:ALA125 4.9 15.6 1.0 O C:SER98 4.9 48.0 1.0

Sodium binding site 4 out of 4 in the Pleurotus Ostreatus Ostreolysina Mutant E69A with Bis-Tris


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 Mutant E69A with Bis-Tris within 5.0Å range: probe atom residue distance (Å) B Occ D:Na204 b:32.0 occ:1.00 OG D:SER94 2.4 16.5 1.0 O D:HOH390 2.7 34.5 1.0 OD1 D:ASN101 2.8 21.7 1.0 HG3 D:GLN5 2.9 29.1 1.0 O D:PRO95 3.0 21.0 1.0 O D:GLY124 3.0 31.5 1.0 HA D:SER94 3.0 17.9 1.0 C D:SER94 3.1 14.4 1.0 CA D:SER94 3.3 14.9 1.0 CB D:SER94 3.3 15.8 1.0 HA D:ALA125 3.4 30.1 1.0 N D:PRO95 3.4 17.6 1.0 HD2 D:PRO95 3.4 21.7 1.0 O D:SER94 3.4 15.0 1.0 HA D:GLN5 3.6 30.0 1.0 HB3 D:SER94 3.7 18.9 1.0 O D:HOH301 3.7 33.4 1.0 CG D:GLN5 3.8 24.2 1.0 CG D:ASN101 3.8 20.4 1.0 HD21 D:ASN101 3.8 24.7 1.0 C D:PRO95 3.9 20.6 1.0 HG2 D:GLN5 3.9 29.1 1.0 CD D:PRO95 3.9 18.1 1.0 HB3 D:GLN5 4.0 29.4 1.0 C D:GLY124 4.0 32.1 1.0 HB2 D:SER94 4.1 18.9 1.0 H D:LEU126 4.2 29.4 1.0 ND2 D:ASN101 4.2 20.6 1.0 CA D:PRO95 4.2 19.1 1.0 CB D:GLN5 4.2 24.5 1.0 CA D:ALA125 4.2 25.1 1.0 CA D:GLN5 4.4 25.0 1.0 HE21 D:GLN5 4.4 31.1 1.0 HG2 D:PRO95 4.5 24.1 1.0 N D:ALA125 4.5 29.1 1.0 N D:LEU126 4.6 24.5 1.0 HD3 D:PRO95 4.6 21.7 1.0 H D:TRP6 4.7 28.5 1.0 N D:SER94 4.7 15.1 1.0 CG D:PRO95 4.7 20.1 1.0 C D:ALA125 4.7 24.4 1.0 HA D:PRO95 4.8 22.9 1.0 H D:GLY124 4.9 49.9 1.0 CD D:GLN5 4.9 25.4 1.0 NE2 D:GLN5 5.0 25.9 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