Sodium in PDB 7qxy: X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
Enzymatic activity of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
All present enzymatic activity of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3:
3.4.21.75;
Protein crystallography data
The structure of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3, PDB code: 7qxy
was solved by
S.O.Dahms,
H.Brandstetter,
A.Pautsch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
114.03 /
1.48
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.672,
131.672,
155.354,
90,
90,
120
|
R / Rfree (%)
|
17.1 /
18.2
|
Other elements in 7qxy:
The structure of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
(pdb code 7qxy). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3, PDB code: 7qxy:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7qxy
Go back to
Sodium Binding Sites List in 7qxy
Sodium binding site 1 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:12.4
occ:1.00
|
O
|
A:THR309
|
2.3
|
12.4
|
1.0
|
O
|
A:HOH906
|
2.4
|
15.0
|
1.0
|
O
|
A:THR314
|
2.4
|
12.6
|
1.0
|
OG1
|
A:THR314
|
2.4
|
12.4
|
1.0
|
O
|
A:SER311
|
2.5
|
12.2
|
1.0
|
OG
|
A:SER316
|
2.6
|
18.6
|
1.0
|
C
|
A:THR314
|
3.2
|
12.8
|
1.0
|
H
|
A:THR314
|
3.3
|
12.7
|
0.0
|
C
|
A:THR309
|
3.4
|
12.5
|
1.0
|
H
|
A:SER316
|
3.5
|
14.4
|
0.0
|
HB2
|
A:SER316
|
3.6
|
17.2
|
0.0
|
HA
|
A:THR309
|
3.6
|
13.1
|
0.0
|
CB
|
A:THR314
|
3.6
|
12.5
|
1.0
|
CB
|
A:SER316
|
3.6
|
15.5
|
1.0
|
C
|
A:SER311
|
3.7
|
11.5
|
1.0
|
O
|
A:HOH869
|
3.7
|
18.5
|
1.0
|
CA
|
A:THR314
|
3.8
|
12.1
|
1.0
|
HE1
|
A:MET534
|
3.8
|
14.1
|
0.0
|
N
|
A:SER316
|
3.9
|
13.1
|
1.0
|
H
|
A:SER311
|
4.0
|
12.8
|
0.0
|
N
|
A:SER311
|
4.0
|
12.0
|
1.0
|
N
|
A:THR314
|
4.0
|
11.8
|
1.0
|
HB
|
A:THR314
|
4.0
|
13.6
|
0.0
|
HB2
|
A:SER335
|
4.0
|
13.8
|
0.0
|
HG1
|
A:THR309
|
4.1
|
17.3
|
0.0
|
CA
|
A:THR309
|
4.1
|
12.2
|
1.0
|
HE3
|
A:MET534
|
4.1
|
14.0
|
0.0
|
HE2
|
A:MET534
|
4.1
|
14.1
|
0.0
|
HB3
|
A:SER311
|
4.1
|
13.9
|
0.0
|
N
|
A:LEU315
|
4.2
|
12.6
|
1.0
|
CE
|
A:MET534
|
4.2
|
12.9
|
1.0
|
O
|
A:TYR308
|
4.3
|
14.0
|
1.0
|
C
|
A:ASN310
|
4.3
|
12.4
|
1.0
|
HA
|
A:LEU315
|
4.3
|
14.4
|
0.0
|
CA
|
A:SER311
|
4.3
|
11.5
|
1.0
|
O
|
A:SER335
|
4.4
|
13.2
|
1.0
|
CA
|
A:SER316
|
4.4
|
13.1
|
1.0
|
HA
|
A:ILE312
|
4.4
|
11.9
|
0.0
|
N
|
A:ASN310
|
4.4
|
11.4
|
1.0
|
HB3
|
A:SER316
|
4.5
|
17.1
|
0.0
|
HA
|
A:ASN310
|
4.5
|
11.9
|
0.0
|
C
|
A:LEU315
|
4.6
|
12.9
|
1.0
|
CA
|
A:ASN310
|
4.6
|
11.2
|
1.0
|
OG1
|
A:THR309
|
4.6
|
15.7
|
1.0
|
CA
|
A:LEU315
|
4.7
|
13.0
|
1.0
|
HA
|
A:SER316
|
4.7
|
14.3
|
0.0
|
N
|
A:ILE312
|
4.7
|
10.6
|
1.0
|
CB
|
A:SER311
|
4.8
|
12.9
|
1.0
|
CG2
|
A:THR314
|
4.8
|
12.7
|
1.0
|
O
|
A:ASN310
|
4.8
|
13.5
|
1.0
|
HA
|
A:THR314
|
4.8
|
13.2
|
0.0
|
HG23
|
A:THR314
|
4.9
|
13.8
|
0.0
|
CA
|
A:ILE312
|
4.9
|
11.2
|
1.0
|
C
|
A:ILE312
|
4.9
|
11.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7qxy
Go back to
Sodium Binding Sites List in 7qxy
Sodium binding site 2 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:26.8
occ:0.50
|
O
|
A:SER544
|
2.2
|
16.4
|
1.0
|
O
|
A:HOH961
|
2.3
|
16.8
|
1.0
|
HA3
|
A:GLY545
|
3.1
|
20.2
|
0.0
|
C
|
A:SER544
|
3.2
|
15.8
|
1.0
|
HB3
|
A:SER544
|
3.3
|
22.3
|
0.0
|
HB3
|
A:PRO508
|
3.4
|
20.3
|
0.0
|
HB2
|
A:PRO508
|
3.6
|
20.1
|
0.0
|
N
|
A:GLY545
|
3.9
|
15.9
|
1.0
|
CA
|
A:GLY545
|
3.9
|
15.7
|
1.0
|
CB
|
A:PRO508
|
4.0
|
15.9
|
1.0
|
CB
|
A:SER544
|
4.0
|
17.6
|
1.0
|
CA
|
A:SER544
|
4.1
|
15.1
|
1.0
|
HA2
|
A:GLY545
|
4.3
|
20.3
|
0.0
|
OG
|
A:SER544
|
4.3
|
22.1
|
1.0
|
H
|
A:SER544
|
4.4
|
18.1
|
0.0
|
N
|
A:SER544
|
4.4
|
14.5
|
1.0
|
HB3
|
A:ASP542
|
4.4
|
18.1
|
0.0
|
HG2
|
A:PRO508
|
4.5
|
19.9
|
0.0
|
O
|
A:ASP542
|
4.6
|
15.0
|
1.0
|
CG
|
A:PRO508
|
4.8
|
16.1
|
1.0
|
H
|
A:GLY545
|
4.8
|
20.1
|
0.0
|
HG2
|
A:MET509
|
4.9
|
26.8
|
0.0
|
OD1
|
A:ASP542
|
4.9
|
17.2
|
1.0
|
HG
|
A:SER544
|
5.0
|
27.8
|
0.0
|
|
Sodium binding site 3 out
of 4 in 7qxy
Go back to
Sodium Binding Sites List in 7qxy
Sodium binding site 3 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na606
b:48.2
occ:1.00
|
H
|
A:GLY265
|
2.8
|
16.1
|
0.0
|
HA
|
A:ASP264
|
2.9
|
17.1
|
0.0
|
OD1
|
A:ASP264
|
3.0
|
25.8
|
1.0
|
HZ3
|
A:TRP531
|
3.0
|
16.3
|
0.0
|
O
|
A:HOH904
|
3.2
|
25.7
|
1.0
|
O
|
A:HOH1073
|
3.3
|
38.1
|
1.0
|
N
|
A:GLY265
|
3.5
|
14.2
|
1.0
|
CA
|
A:ASP264
|
3.9
|
14.9
|
1.0
|
CZ3
|
A:TRP531
|
4.1
|
14.3
|
1.0
|
CG
|
A:ASP264
|
4.1
|
25.4
|
1.0
|
C
|
A:ASP264
|
4.2
|
14.5
|
1.0
|
O
|
A:GLY265
|
4.2
|
14.5
|
1.0
|
O
|
A:HOH1343
|
4.2
|
36.3
|
1.0
|
HA3
|
A:GLY265
|
4.3
|
16.2
|
0.0
|
O
|
A:HOH997
|
4.4
|
33.6
|
1.0
|
CA
|
A:GLY265
|
4.4
|
14.5
|
1.0
|
O
|
A:HOH1348
|
4.4
|
56.0
|
1.0
|
HH2
|
A:TRP531
|
4.5
|
16.1
|
0.0
|
C
|
A:GLY265
|
4.6
|
14.3
|
1.0
|
CB
|
A:ASP264
|
4.6
|
18.0
|
1.0
|
O
|
A:HOH926
|
4.6
|
57.6
|
1.0
|
O
|
A:HOH1219
|
4.7
|
57.1
|
1.0
|
O
|
A:VAL263
|
4.7
|
15.7
|
1.0
|
O
|
A:HOH1071
|
4.8
|
36.8
|
1.0
|
CH2
|
A:TRP531
|
4.8
|
14.4
|
1.0
|
N
|
A:ASP264
|
4.9
|
14.4
|
1.0
|
O
|
A:HOH1335
|
4.9
|
48.5
|
1.0
|
HE3
|
A:TRP531
|
5.0
|
15.6
|
0.0
|
|
Sodium binding site 4 out
of 4 in 7qxy
Go back to
Sodium Binding Sites List in 7qxy
Sodium binding site 4 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na607
b:38.3
occ:1.00
|
O
|
A:HOH990
|
2.2
|
39.9
|
1.0
|
O
|
A:HOH1164
|
2.2
|
47.6
|
1.0
|
O
|
A:HOH918
|
2.3
|
18.5
|
1.0
|
O
|
A:HOH885
|
2.3
|
33.0
|
1.0
|
O
|
A:THR413
|
2.4
|
18.2
|
1.0
|
C
|
A:THR413
|
3.6
|
18.2
|
1.0
|
HA
|
A:ASN414
|
3.7
|
20.5
|
0.0
|
O
|
A:HOH1138
|
3.7
|
46.3
|
1.0
|
O
|
A:HOH1161
|
3.9
|
35.3
|
1.0
|
HB
|
A:THR413
|
4.0
|
27.9
|
0.0
|
O
|
A:HOH1178
|
4.1
|
30.6
|
1.0
|
O
|
A:ASN414
|
4.2
|
17.2
|
1.0
|
HA
|
A:THR511
|
4.3
|
18.2
|
0.0
|
C
|
A:ASN414
|
4.3
|
17.1
|
1.0
|
O
|
A:GLY510
|
4.3
|
15.7
|
1.0
|
CA
|
A:ASN414
|
4.3
|
16.3
|
1.0
|
H
|
A:THR413
|
4.3
|
23.9
|
0.0
|
N
|
A:ASN414
|
4.4
|
16.7
|
1.0
|
O
|
A:MET509
|
4.5
|
18.5
|
0.5
|
O
|
A:MET509
|
4.6
|
17.8
|
0.5
|
CA
|
A:THR413
|
4.6
|
18.6
|
1.0
|
C
|
A:GLY510
|
4.7
|
15.9
|
1.0
|
HG22
|
A:THR413
|
4.7
|
28.3
|
0.0
|
OG1
|
A:THR511
|
4.7
|
16.3
|
1.0
|
N
|
A:THR413
|
4.8
|
18.5
|
1.0
|
CB
|
A:THR413
|
4.8
|
21.4
|
1.0
|
HA3
|
A:GLY510
|
4.8
|
21.6
|
0.0
|
HA2
|
A:GLY415
|
4.8
|
23.0
|
0.0
|
O
|
A:HOH1068
|
4.8
|
22.3
|
1.0
|
HB1
|
A:ALA412
|
4.9
|
25.0
|
0.0
|
N
|
A:GLY415
|
4.9
|
16.9
|
1.0
|
|
Reference:
S.O.Dahms,
G.Schnapp,
M.Winter,
F.H.Buttner,
M.Schleputz,
C.Gnamm,
A.Pautsch,
H.Brandstetter.
Dichlorophenylpyridine-Based Molecules Inhibit Furin Through An Induced-Fit Mechanism. Acs Chem.Biol. V. 17 816 2022.
ISSN: ESSN 1554-8937
PubMed: 35377598
DOI: 10.1021/ACSCHEMBIO.2C00103
Page generated: Wed Oct 9 08:25:00 2024
|