Sodium in PDB 4q3b: Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+
Protein crystallography data
The structure of Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+, PDB code: 4q3b
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)
|
10.00 /
1.90
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.640,
261.170,
48.740,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.3 /
22.2
|
Other elements in 4q3b:
The structure of Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+
(pdb code 4q3b). 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-D-Lysine and Nad+, PDB code: 4q3b:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 4q3b
Go back to
Sodium Binding Sites List in 4q3b
Sodium binding site 1 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na902
b:35.2
occ:1.00
|
O
|
A:PRO227
|
2.7
|
29.6
|
1.0
|
O
|
A:CYS206
|
2.7
|
29.8
|
1.0
|
O
|
A:HOH1061
|
2.9
|
30.2
|
1.0
|
O
|
A:THR204
|
2.9
|
24.9
|
1.0
|
OE1
|
A:GLU202
|
3.0
|
22.7
|
1.0
|
OE2
|
A:GLU202
|
3.2
|
22.6
|
1.0
|
CD
|
A:GLU202
|
3.4
|
22.7
|
1.0
|
N
|
A:CYS206
|
3.7
|
29.8
|
1.0
|
C
|
A:CYS206
|
3.8
|
30.7
|
1.0
|
C
|
A:THR204
|
3.8
|
25.5
|
1.0
|
N
|
A:ALA229
|
3.8
|
29.1
|
1.0
|
C
|
A:GLY225
|
3.8
|
25.9
|
1.0
|
CA
|
A:ALA229
|
3.9
|
29.3
|
1.0
|
CA
|
A:GLY225
|
3.9
|
25.0
|
1.0
|
CB
|
A:ALA229
|
3.9
|
29.1
|
1.0
|
CG2
|
A:THR204
|
3.9
|
26.7
|
1.0
|
C
|
A:PRO227
|
4.0
|
30.1
|
1.0
|
N
|
A:ILE226
|
4.0
|
27.1
|
1.0
|
C
|
A:CYS228
|
4.1
|
30.5
|
1.0
|
O
|
A:GLY225
|
4.1
|
25.5
|
1.0
|
CB
|
A:THR204
|
4.3
|
26.3
|
1.0
|
CA
|
A:CYS206
|
4.4
|
31.3
|
1.0
|
N
|
A:THR204
|
4.4
|
23.8
|
1.0
|
CA
|
A:THR204
|
4.4
|
25.2
|
1.0
|
C
|
A:ILE226
|
4.4
|
29.4
|
1.0
|
C
|
A:PRO205
|
4.5
|
28.7
|
1.0
|
O
|
A:CYS228
|
4.5
|
29.4
|
1.0
|
CA
|
A:ILE226
|
4.6
|
28.6
|
1.0
|
N
|
A:PRO227
|
4.6
|
30.4
|
1.0
|
N
|
A:PRO205
|
4.6
|
26.5
|
1.0
|
OG1
|
A:THR223
|
4.6
|
22.4
|
1.0
|
O
|
A:ILE226
|
4.7
|
28.4
|
1.0
|
CA
|
A:PRO205
|
4.7
|
27.2
|
1.0
|
CA
|
A:CYS228
|
4.7
|
30.7
|
1.0
|
OG1
|
A:THR209
|
4.7
|
29.7
|
1.0
|
N
|
A:ALA207
|
4.8
|
31.1
|
1.0
|
N
|
A:CYS228
|
4.8
|
30.7
|
1.0
|
CG
|
A:GLU202
|
4.9
|
22.4
|
1.0
|
CA
|
A:PRO227
|
4.9
|
30.4
|
1.0
|
N
|
A:GLY225
|
5.0
|
24.1
|
1.0
|
|
Sodium binding site 2 out
of 4 in 4q3b
Go back to
Sodium Binding Sites List in 4q3b
Sodium binding site 2 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na902
b:38.5
occ:1.00
|
O
|
B:PRO227
|
2.7
|
28.8
|
1.0
|
O
|
B:CYS206
|
2.8
|
32.4
|
1.0
|
OE1
|
B:GLU202
|
2.8
|
26.4
|
1.0
|
O
|
B:THR204
|
3.0
|
25.5
|
1.0
|
O
|
B:HOH1009
|
3.0
|
25.6
|
1.0
|
OE2
|
B:GLU202
|
3.2
|
25.4
|
1.0
|
CD
|
B:GLU202
|
3.3
|
25.4
|
1.0
|
OG1
|
B:THR204
|
3.3
|
26.6
|
1.0
|
N
|
B:ALA229
|
3.7
|
31.6
|
1.0
|
C
|
B:CYS206
|
3.7
|
34.3
|
1.0
|
N
|
B:CYS206
|
3.8
|
32.2
|
1.0
|
C
|
B:GLY225
|
3.8
|
26.3
|
1.0
|
C
|
B:THR204
|
3.8
|
26.2
|
1.0
|
CA
|
B:ALA229
|
3.9
|
32.4
|
1.0
|
CA
|
B:GLY225
|
3.9
|
25.3
|
1.0
|
C
|
B:PRO227
|
4.0
|
29.9
|
1.0
|
CB
|
B:ALA229
|
4.0
|
31.5
|
1.0
|
N
|
B:ILE226
|
4.0
|
27.3
|
1.0
|
C
|
B:CYS228
|
4.1
|
31.9
|
1.0
|
O
|
B:GLY225
|
4.2
|
26.6
|
1.0
|
CA
|
B:CYS206
|
4.3
|
34.3
|
1.0
|
O
|
B:CYS228
|
4.4
|
31.6
|
1.0
|
N
|
B:THR204
|
4.4
|
25.1
|
1.0
|
C
|
B:ILE226
|
4.5
|
28.7
|
1.0
|
C
|
B:PRO205
|
4.5
|
30.2
|
1.0
|
CB
|
B:THR204
|
4.5
|
26.3
|
1.0
|
CA
|
B:THR204
|
4.5
|
25.7
|
1.0
|
N
|
B:PRO227
|
4.6
|
29.6
|
1.0
|
OG1
|
B:THR223
|
4.6
|
23.4
|
1.0
|
N
|
B:PRO205
|
4.7
|
27.5
|
1.0
|
CA
|
B:ILE226
|
4.7
|
28.2
|
1.0
|
CA
|
B:CYS228
|
4.7
|
31.8
|
1.0
|
OG1
|
B:THR209
|
4.7
|
33.7
|
1.0
|
CA
|
B:PRO205
|
4.7
|
28.3
|
1.0
|
O
|
B:ILE226
|
4.7
|
28.0
|
1.0
|
N
|
B:ALA207
|
4.7
|
34.6
|
1.0
|
CG
|
B:GLU202
|
4.8
|
25.3
|
1.0
|
N
|
B:CYS228
|
4.8
|
31.2
|
1.0
|
CA
|
B:PRO227
|
4.9
|
29.7
|
1.0
|
|
Sodium binding site 3 out
of 4 in 4q3b
Go back to
Sodium Binding Sites List in 4q3b
Sodium binding site 3 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na902
b:47.6
occ:1.00
|
O
|
C:PRO227
|
2.4
|
39.6
|
1.0
|
O
|
C:CYS206
|
2.6
|
42.0
|
1.0
|
O
|
C:HOH1017
|
2.9
|
38.2
|
1.0
|
O
|
C:THR204
|
3.0
|
38.5
|
1.0
|
OE1
|
C:GLU202
|
3.2
|
40.3
|
1.0
|
OE2
|
C:GLU202
|
3.3
|
41.2
|
1.0
|
CD
|
C:GLU202
|
3.6
|
41.0
|
1.0
|
C
|
C:CYS206
|
3.6
|
41.9
|
1.0
|
C
|
C:PRO227
|
3.6
|
40.7
|
1.0
|
N
|
C:ALA229
|
3.7
|
43.3
|
1.0
|
CA
|
C:ALA229
|
3.7
|
43.4
|
1.0
|
N
|
C:CYS206
|
3.8
|
40.6
|
1.0
|
C
|
C:GLY225
|
3.8
|
36.9
|
1.0
|
CB
|
C:ALA229
|
3.9
|
43.0
|
1.0
|
C
|
C:THR204
|
3.9
|
39.7
|
1.0
|
C
|
C:CYS228
|
4.0
|
43.7
|
1.0
|
N
|
C:ILE226
|
4.0
|
38.2
|
1.0
|
CA
|
C:GLY225
|
4.0
|
36.1
|
1.0
|
O
|
C:GLY225
|
4.0
|
38.1
|
1.0
|
CA
|
C:CYS206
|
4.3
|
42.5
|
1.0
|
C
|
C:ILE226
|
4.3
|
40.2
|
1.0
|
N
|
C:PRO227
|
4.4
|
40.5
|
1.0
|
O
|
C:CYS228
|
4.4
|
43.0
|
1.0
|
CG2
|
C:THR204
|
4.4
|
41.2
|
1.0
|
CA
|
C:CYS228
|
4.5
|
42.9
|
1.0
|
C
|
C:PRO205
|
4.5
|
40.3
|
1.0
|
N
|
C:CYS228
|
4.5
|
42.0
|
1.0
|
CA
|
C:ILE226
|
4.5
|
38.9
|
1.0
|
N
|
C:ALA207
|
4.6
|
42.2
|
1.0
|
CB
|
C:THR204
|
4.6
|
40.4
|
1.0
|
CA
|
C:PRO227
|
4.6
|
41.0
|
1.0
|
O
|
C:ILE226
|
4.6
|
41.4
|
1.0
|
CA
|
C:THR204
|
4.7
|
39.6
|
1.0
|
N
|
C:THR204
|
4.7
|
38.0
|
1.0
|
OG1
|
C:THR223
|
4.7
|
36.4
|
1.0
|
CA
|
C:PRO205
|
4.7
|
39.9
|
1.0
|
N
|
C:PRO205
|
4.7
|
40.4
|
1.0
|
CA
|
C:ALA207
|
4.8
|
43.0
|
1.0
|
OG1
|
C:THR209
|
5.0
|
45.8
|
1.0
|
|
Sodium binding site 4 out
of 4 in 4q3b
Go back to
Sodium Binding Sites List in 4q3b
Sodium binding site 4 out
of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na902
b:43.6
occ:1.00
|
O
|
D:PRO227
|
2.6
|
46.4
|
1.0
|
O
|
D:CYS206
|
2.8
|
37.1
|
1.0
|
OE1
|
D:GLU202
|
2.9
|
39.0
|
1.0
|
O
|
D:THR204
|
3.0
|
35.4
|
1.0
|
O
|
D:HOH1008
|
3.0
|
37.6
|
1.0
|
OE2
|
D:GLU202
|
3.2
|
37.6
|
1.0
|
CD
|
D:GLU202
|
3.4
|
38.6
|
1.0
|
N
|
D:ALA229
|
3.7
|
44.9
|
1.0
|
C
|
D:GLY225
|
3.8
|
41.5
|
1.0
|
N
|
D:CYS206
|
3.8
|
37.6
|
1.0
|
C
|
D:CYS206
|
3.8
|
38.8
|
1.0
|
C
|
D:THR204
|
3.8
|
36.0
|
1.0
|
C
|
D:PRO227
|
3.8
|
46.8
|
1.0
|
CA
|
D:ALA229
|
3.9
|
44.1
|
1.0
|
CA
|
D:GLY225
|
3.9
|
39.9
|
1.0
|
N
|
D:ILE226
|
4.0
|
42.0
|
1.0
|
CB
|
D:ALA229
|
4.0
|
43.9
|
1.0
|
C
|
D:CYS228
|
4.1
|
46.8
|
1.0
|
O
|
D:GLY225
|
4.2
|
42.4
|
1.0
|
CB
|
D:THR204
|
4.4
|
38.9
|
1.0
|
CA
|
D:CYS206
|
4.4
|
38.8
|
1.0
|
C
|
D:ILE226
|
4.4
|
42.9
|
1.0
|
N
|
D:THR204
|
4.5
|
36.2
|
1.0
|
CA
|
D:THR204
|
4.5
|
36.5
|
1.0
|
C
|
D:PRO205
|
4.5
|
36.7
|
1.0
|
O
|
D:CYS228
|
4.5
|
43.8
|
1.0
|
N
|
D:PRO227
|
4.6
|
45.0
|
1.0
|
CA
|
D:ILE226
|
4.6
|
43.4
|
1.0
|
CG2
|
D:THR204
|
4.6
|
39.2
|
1.0
|
CA
|
D:CYS228
|
4.6
|
49.0
|
1.0
|
OG1
|
D:THR223
|
4.6
|
41.1
|
1.0
|
N
|
D:CYS228
|
4.7
|
48.2
|
1.0
|
N
|
D:PRO205
|
4.7
|
36.5
|
1.0
|
CA
|
D:PRO205
|
4.7
|
36.0
|
1.0
|
OG1
|
D:THR209
|
4.7
|
41.3
|
1.0
|
O
|
D:ILE226
|
4.7
|
40.5
|
1.0
|
N
|
D:ALA207
|
4.8
|
37.9
|
1.0
|
CA
|
D:PRO227
|
4.8
|
46.6
|
1.0
|
CG
|
D:GLU202
|
4.9
|
39.0
|
1.0
|
N
|
D:GLY225
|
5.0
|
39.0
|
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 17:53:46 2024
|