Sodium in PDB 6ebn: Crystal Structure of Psilocybe Cubensis Noncanonical Aromatic Amino Acid Decarboxylase
Protein crystallography data
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
|
Sodium Binding Sites:
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 6ebn
Go back to
Sodium Binding Sites List in 6ebn
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 6ebn
Go back to
Sodium Binding Sites List in 6ebn
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 6ebn
Go back to
Sodium Binding Sites List in 6ebn
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 6ebn
Go back to
Sodium Binding Sites List in 6ebn
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
|
|
Reference:
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
Page generated: Tue Oct 8 08:22:50 2024
|