Sodium in PDB 4q3a: Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+
Protein crystallography data
The structure of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+, PDB code: 4q3a
was solved by
F.Quitterer,
P.Beck,
A.Bacher,
M.Groll,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.20
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.490,
259.850,
48.660,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.9 /
20.4
|
Other elements in 4q3a:
The structure of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+
(pdb code 4q3a). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+, PDB code: 4q3a:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 4q3a
Go back to
Sodium Binding Sites List in 4q3a
Sodium binding site 1 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na902
b:39.4
occ:1.00
|
O
|
A:CYS206
|
2.6
|
33.7
|
1.0
|
O
|
A:THR204
|
2.8
|
26.5
|
1.0
|
O
|
A:PRO227
|
2.8
|
38.3
|
1.0
|
OE1
|
A:GLU202
|
2.9
|
26.6
|
1.0
|
OE2
|
A:GLU202
|
3.1
|
26.2
|
1.0
|
O
|
A:HOH1113
|
3.1
|
36.5
|
1.0
|
OG1
|
A:THR204
|
3.3
|
25.4
|
1.0
|
CD
|
A:GLU202
|
3.4
|
26.0
|
1.0
|
C
|
A:CYS206
|
3.6
|
35.0
|
1.0
|
C
|
A:THR204
|
3.7
|
26.5
|
1.0
|
N
|
A:CYS206
|
3.7
|
32.8
|
1.0
|
N
|
A:ALA229
|
3.9
|
37.9
|
1.0
|
C
|
A:GLY225
|
3.9
|
30.0
|
1.0
|
CA
|
A:ALA229
|
3.9
|
37.6
|
1.0
|
CA
|
A:GLY225
|
3.9
|
29.2
|
1.0
|
C
|
A:PRO227
|
4.1
|
38.9
|
1.0
|
CB
|
A:ALA229
|
4.1
|
36.6
|
1.0
|
N
|
A:ILE226
|
4.1
|
32.6
|
1.0
|
C
|
A:CYS228
|
4.2
|
39.6
|
1.0
|
CA
|
A:CYS206
|
4.2
|
34.5
|
1.0
|
O
|
A:GLY225
|
4.3
|
29.2
|
1.0
|
N
|
A:THR204
|
4.3
|
24.8
|
1.0
|
CA
|
A:THR204
|
4.3
|
25.4
|
1.0
|
C
|
A:PRO205
|
4.4
|
31.1
|
1.0
|
CB
|
A:THR204
|
4.4
|
25.7
|
1.0
|
N
|
A:PRO205
|
4.5
|
28.1
|
1.0
|
O
|
A:CYS228
|
4.6
|
37.4
|
1.0
|
OG1
|
A:THR209
|
4.6
|
31.0
|
1.0
|
C
|
A:ILE226
|
4.6
|
35.9
|
1.0
|
CA
|
A:PRO205
|
4.6
|
29.4
|
1.0
|
N
|
A:ALA207
|
4.7
|
36.0
|
1.0
|
OG1
|
A:THR223
|
4.7
|
28.1
|
1.0
|
N
|
A:PRO227
|
4.8
|
37.4
|
1.0
|
CA
|
A:ILE226
|
4.8
|
34.8
|
1.0
|
CA
|
A:CYS228
|
4.8
|
40.4
|
1.0
|
CG
|
A:GLU202
|
4.8
|
25.5
|
1.0
|
O
|
A:ILE226
|
4.8
|
37.1
|
1.0
|
N
|
A:CYS228
|
4.9
|
40.0
|
1.0
|
CG2
|
A:THR209
|
4.9
|
33.1
|
1.0
|
CA
|
A:ALA207
|
5.0
|
37.0
|
1.0
|
|
Sodium binding site 2 out
of 4 in 4q3a
Go back to
Sodium Binding Sites List in 4q3a
Sodium binding site 2 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na902
b:36.3
occ:1.00
|
O
|
B:PRO227
|
2.7
|
38.9
|
1.0
|
O
|
B:THR204
|
2.8
|
26.7
|
1.0
|
O
|
B:CYS206
|
2.8
|
35.3
|
1.0
|
O
|
B:HOH1058
|
3.0
|
35.4
|
1.0
|
OE1
|
B:GLU202
|
3.0
|
28.6
|
1.0
|
OE2
|
B:GLU202
|
3.2
|
27.4
|
1.0
|
CD
|
B:GLU202
|
3.5
|
28.0
|
1.0
|
OG1
|
B:THR204
|
3.6
|
28.2
|
1.0
|
N
|
B:CYS206
|
3.7
|
34.1
|
1.0
|
C
|
B:GLY225
|
3.7
|
30.6
|
1.0
|
C
|
B:CYS206
|
3.7
|
36.2
|
1.0
|
C
|
B:THR204
|
3.7
|
27.9
|
1.0
|
CA
|
B:GLY225
|
3.8
|
29.3
|
1.0
|
N
|
B:ILE226
|
3.8
|
32.6
|
1.0
|
C
|
B:PRO227
|
4.0
|
39.0
|
1.0
|
N
|
B:ALA229
|
4.0
|
39.3
|
1.0
|
CB
|
B:ALA229
|
4.1
|
38.1
|
1.0
|
O
|
B:GLY225
|
4.1
|
30.3
|
1.0
|
CA
|
B:ALA229
|
4.1
|
38.9
|
1.0
|
C
|
B:CYS228
|
4.3
|
40.3
|
1.0
|
CA
|
B:CYS206
|
4.3
|
35.9
|
1.0
|
C
|
B:PRO205
|
4.3
|
32.4
|
1.0
|
C
|
B:ILE226
|
4.4
|
35.9
|
1.0
|
N
|
B:THR204
|
4.4
|
27.3
|
1.0
|
CA
|
B:ILE226
|
4.5
|
34.9
|
1.0
|
CA
|
B:THR204
|
4.5
|
27.7
|
1.0
|
CA
|
B:PRO205
|
4.5
|
30.6
|
1.0
|
N
|
B:PRO205
|
4.5
|
29.6
|
1.0
|
N
|
B:PRO227
|
4.5
|
37.1
|
1.0
|
OG1
|
B:THR223
|
4.6
|
27.7
|
1.0
|
CB
|
B:THR204
|
4.6
|
28.4
|
1.0
|
O
|
B:CYS228
|
4.7
|
39.2
|
1.0
|
N
|
B:ALA207
|
4.7
|
37.1
|
1.0
|
O
|
B:ILE226
|
4.7
|
35.9
|
1.0
|
CA
|
B:CYS228
|
4.8
|
42.0
|
1.0
|
OG1
|
B:THR209
|
4.8
|
35.8
|
1.0
|
N
|
B:CYS228
|
4.8
|
40.4
|
1.0
|
CA
|
B:PRO227
|
4.9
|
38.2
|
1.0
|
N
|
B:GLY225
|
4.9
|
28.2
|
1.0
|
CG
|
B:GLU202
|
5.0
|
27.6
|
1.0
|
|
Sodium binding site 3 out
of 4 in 4q3a
Go back to
Sodium Binding Sites List in 4q3a
Sodium binding site 3 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na902
b:50.4
occ:1.00
|
O
|
C:CYS206
|
2.7
|
41.3
|
1.0
|
O
|
C:PRO227
|
2.7
|
50.8
|
1.0
|
O
|
C:THR204
|
2.9
|
38.5
|
1.0
|
O
|
C:HOH1039
|
3.1
|
40.4
|
1.0
|
OE1
|
C:GLU202
|
3.1
|
43.9
|
1.0
|
OE2
|
C:GLU202
|
3.1
|
43.1
|
1.0
|
CD
|
C:GLU202
|
3.5
|
43.3
|
1.0
|
OG1
|
C:THR204
|
3.5
|
40.3
|
1.0
|
N
|
C:CYS206
|
3.5
|
41.8
|
1.0
|
C
|
C:CYS206
|
3.6
|
43.3
|
1.0
|
C
|
C:THR204
|
3.7
|
39.0
|
1.0
|
C
|
C:GLY225
|
3.8
|
43.1
|
1.0
|
N
|
C:ALA229
|
3.9
|
54.2
|
1.0
|
C
|
C:PRO227
|
3.9
|
51.6
|
1.0
|
CA
|
C:ALA229
|
3.9
|
53.8
|
1.0
|
CA
|
C:GLY225
|
4.0
|
41.4
|
1.0
|
CB
|
C:ALA229
|
4.0
|
53.3
|
1.0
|
N
|
C:ILE226
|
4.0
|
45.1
|
1.0
|
CA
|
C:CYS206
|
4.2
|
42.6
|
1.0
|
O
|
C:GLY225
|
4.2
|
42.9
|
1.0
|
C
|
C:CYS228
|
4.2
|
55.2
|
1.0
|
C
|
C:PRO205
|
4.2
|
41.3
|
1.0
|
C
|
C:ILE226
|
4.4
|
47.3
|
1.0
|
N
|
C:THR204
|
4.5
|
39.4
|
1.0
|
CA
|
C:THR204
|
4.5
|
39.1
|
1.0
|
N
|
C:PRO205
|
4.5
|
39.9
|
1.0
|
CA
|
C:PRO205
|
4.5
|
40.1
|
1.0
|
CB
|
C:THR204
|
4.6
|
40.4
|
1.0
|
N
|
C:PRO227
|
4.6
|
49.0
|
1.0
|
O
|
C:CYS228
|
4.6
|
56.6
|
1.0
|
OG1
|
C:THR223
|
4.6
|
39.7
|
1.0
|
O
|
C:ILE226
|
4.6
|
46.8
|
1.0
|
CA
|
C:ILE226
|
4.6
|
46.7
|
1.0
|
N
|
C:ALA207
|
4.6
|
44.4
|
1.0
|
CA
|
C:CYS228
|
4.7
|
54.8
|
1.0
|
N
|
C:CYS228
|
4.8
|
53.9
|
1.0
|
OG1
|
C:THR209
|
4.8
|
50.9
|
1.0
|
CG
|
C:GLU202
|
4.9
|
43.1
|
1.0
|
CA
|
C:PRO227
|
4.9
|
50.4
|
1.0
|
|
Sodium binding site 4 out
of 4 in 4q3a
Go back to
Sodium Binding Sites List in 4q3a
Sodium binding site 4 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na902
b:53.1
occ:1.00
|
O
|
D:CYS206
|
2.6
|
39.0
|
1.0
|
O
|
D:PRO227
|
2.8
|
56.5
|
1.0
|
O
|
D:THR204
|
3.0
|
37.8
|
1.0
|
O
|
D:HOH1007
|
3.0
|
43.2
|
1.0
|
OE1
|
D:GLU202
|
3.0
|
41.2
|
1.0
|
OE2
|
D:GLU202
|
3.2
|
42.6
|
1.0
|
CD
|
D:GLU202
|
3.4
|
43.7
|
1.0
|
C
|
D:CYS206
|
3.7
|
40.0
|
1.0
|
N
|
D:ALA229
|
3.7
|
57.5
|
1.0
|
N
|
D:CYS206
|
3.7
|
39.0
|
1.0
|
C
|
D:GLY225
|
3.8
|
49.9
|
1.0
|
C
|
D:THR204
|
3.8
|
39.5
|
1.0
|
CA
|
D:ALA229
|
3.9
|
56.8
|
1.0
|
CA
|
D:GLY225
|
3.9
|
48.6
|
1.0
|
CB
|
D:ALA229
|
3.9
|
57.9
|
1.0
|
C
|
D:PRO227
|
3.9
|
57.5
|
1.0
|
N
|
D:ILE226
|
4.0
|
52.9
|
1.0
|
C
|
D:CYS228
|
4.2
|
58.0
|
1.0
|
O
|
D:GLY225
|
4.2
|
49.5
|
1.0
|
CB
|
D:THR204
|
4.3
|
43.3
|
1.0
|
CA
|
D:CYS206
|
4.3
|
38.7
|
1.0
|
CA
|
D:THR204
|
4.4
|
41.1
|
1.0
|
C
|
D:ILE226
|
4.4
|
54.1
|
1.0
|
N
|
D:THR204
|
4.5
|
40.3
|
1.0
|
C
|
D:PRO205
|
4.5
|
38.9
|
1.0
|
N
|
D:PRO227
|
4.6
|
55.2
|
1.0
|
OG1
|
D:THR223
|
4.6
|
51.2
|
1.0
|
O
|
D:CYS228
|
4.6
|
56.4
|
1.0
|
N
|
D:PRO205
|
4.6
|
39.6
|
1.0
|
CA
|
D:ILE226
|
4.7
|
54.7
|
1.0
|
O
|
D:ILE226
|
4.7
|
53.5
|
1.0
|
CA
|
D:CYS228
|
4.7
|
59.8
|
1.0
|
CA
|
D:PRO205
|
4.7
|
39.1
|
1.0
|
N
|
D:ALA207
|
4.7
|
40.3
|
1.0
|
N
|
D:CYS228
|
4.8
|
60.0
|
1.0
|
OG1
|
D:THR209
|
4.8
|
45.6
|
1.0
|
CG
|
D:GLU202
|
4.9
|
44.7
|
1.0
|
CA
|
D:PRO227
|
4.9
|
56.6
|
1.0
|
N
|
D:GLY225
|
5.0
|
46.8
|
1.0
|
|
Reference:
F.Quitterer,
P.Beck,
A.Bacher,
M.Groll.
The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed By Pyrrolysine Synthase (Pyld). Angew.Chem.Int.Ed.Engl. V. 53 8150 2014.
ISSN: ISSN 1433-7851
PubMed: 24916332
DOI: 10.1002/ANIE.201402595
Page generated: Mon Oct 7 17:53:34 2024
|