Sodium in PDB 6ebn: Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase

The structure of Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase, PDB code: 6ebn was solved by M.P.Torrens-Spence, L.Chun-Ting, T.Pluskal, Y.K.Chung, J.K.Weng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.79 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	238.723, 143.570, 71.408, 90.00, 92.78, 90.00
R / Rfree (%)	17 / 19.7

The binding sites of Sodium atom in the Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase (pdb code 6ebn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase, PDB code: 6ebn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase


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 Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:17.6 occ:1.00 OD1 A:ASP971 2.2 35.0 1.0 O A:SER632 2.3 32.1 1.0 O A:GLN629 2.3 36.3 1.0 OE1 A:GLU638 2.4 42.6 1.0 O A:HOH1508 2.5 33.6 1.0 O A:HOH1451 2.5 29.8 1.0 OD2 A:ASP971 2.5 38.8 1.0 CG A:ASP971 2.7 36.8 1.0 OE2 A:GLU638 2.7 40.3 1.0 CD A:GLU638 2.8 42.1 1.0 C A:SER632 3.4 31.0 1.0 C A:GLN629 3.5 32.4 1.0 CB A:ASP971 4.2 35.6 1.0 N A:SER632 4.2 33.9 1.0 CA A:GLN629 4.2 31.6 1.0 CG A:GLU638 4.2 49.6 1.0 N A:VAL633 4.3 28.8 1.0 CA A:VAL633 4.3 26.9 1.0 OG A:SER632 4.3 36.0 1.0 CA A:SER632 4.4 30.8 1.0 N A:ARG630 4.5 30.0 1.0 C A:ARG630 4.6 33.4 1.0 CA A:ARG630 4.6 28.5 1.0 O A:HOH1487 4.7 44.1 1.0 N A:THR634 4.7 30.7 1.0 CB A:GLN629 4.7 36.4 1.0 O A:ARG630 4.7 31.8 1.0 OG1 A:THR643 4.8 38.4 1.0 O A:HOH1224 4.9 44.8 1.0 CB A:SER632 5.0 35.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1111 b:38.6 occ:1.00 O A:MET930 2.2 56.0 1.0 OE2 A:GLU824 2.3 70.5 1.0 O A:HOH1588 2.3 59.3 1.0 OD2 A:ASP825 2.4 59.5 1.0 O A:HOH1507 2.4 45.6 1.0 OD1 A:ASP825 2.4 59.7 1.0 O A:HOH1443 2.4 52.3 1.0 CG A:ASP825 2.7 60.4 1.0 CD A:GLU824 3.3 68.0 1.0 C A:MET930 3.4 59.7 1.0 CG A:GLU824 3.8 62.9 1.0 CB A:ASP825 4.2 51.3 1.0 N A:ASP931 4.2 63.6 1.0 CA A:ASP931 4.2 63.0 1.0 CB A:MET930 4.4 60.5 1.0 CA A:MET930 4.4 56.4 1.0 OE1 A:GLU824 4.4 66.7 1.0 OD2 A:ASP931 4.6 73.4 1.0 O A:HOH1525 4.6 59.1 1.0 OG A:SER820 4.7 49.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1109 b:24.4 occ:1.00 OE1 B:GLU638 2.2 51.8 1.0 O B:SER632 2.3 39.0 1.0 O B:GLN629 2.3 35.2 1.0 OD1 B:ASP971 2.4 46.8 1.0 O B:HOH1399 2.6 36.5 1.0 OE2 B:GLU638 2.6 54.6 1.0 OD2 B:ASP971 2.6 51.0 1.0 O B:HOH1425 2.7 37.4 1.0 CD B:GLU638 2.7 52.8 1.0 CG B:ASP971 2.9 47.0 1.0 C B:SER632 3.5 39.0 1.0 C B:GLN629 3.5 42.3 1.0 CG B:GLU638 4.1 54.9 1.0 N B:SER632 4.2 39.6 1.0 CA B:VAL633 4.3 36.9 1.0 N B:VAL633 4.3 37.5 1.0 CA B:GLN629 4.3 42.7 1.0 CB B:ASP971 4.4 50.7 1.0 OG B:SER632 4.4 36.0 1.0 CA B:SER632 4.4 39.0 1.0 N B:ARG630 4.5 38.3 1.0 O B:HOH1333 4.6 47.7 1.0 C B:ARG630 4.6 40.4 1.0 CA B:ARG630 4.7 37.1 1.0 O B:HOH1262 4.7 60.9 1.0 OG1 B:THR643 4.7 40.9 1.0 O B:ARG630 4.8 40.4 1.0 N B:THR634 4.8 40.6 1.0 O B:HOH1325 4.8 58.1 1.0 CB B:GLN629 4.9 41.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1110 b:40.5 occ:1.00 O B:HOH1521 2.0 49.2 1.0 OE2 B:GLU824 2.3 63.5 1.0 OD1 B:ASP825 2.3 57.4 1.0 O B:MET930 2.4 58.2 1.0 OD2 B:ASP825 2.8 55.9 1.0 O B:HOH1615 2.8 60.9 1.0 O B:HOH1272 2.9 64.4 1.0 CG B:ASP825 2.9 55.3 1.0 CD B:GLU824 3.4 66.6 1.0 C B:MET930 3.6 57.0 1.0 CG B:GLU824 3.9 63.9 1.0 CA B:ASP931 4.2 63.3 1.0 N B:ASP931 4.3 54.6 1.0 CB B:ASP825 4.4 50.3 1.0 OD2 B:ASP931 4.4 71.2 1.0 OE1 B:GLU824 4.5 69.5 1.0 CB B:MET930 4.6 70.6 1.0 CA B:MET930 4.6 64.4 1.0 CD B:PRO932 4.9 55.1 1.0

M.P.Torrens-Spence, C.T.Liu, T.Pluskal, Y.K.Chung, J.K.Weng. Monoamine Biosynthesis Via A Noncanonical Calcium-Activatable Aromatic Amino Acid Decarboxylase in Psilocybin Mushroom. Acs Chem. Biol. V. 13 3343 2018.
ISSN: ESSN 1554-8937
PubMed: 30484626
DOI: 10.1021/ACSCHEMBIO.8B00821