Sodium in PDB 7qy1: X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4
Enzymatic activity of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4
All present enzymatic activity of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4:
3.4.21.75;
Protein crystallography data
The structure of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4, PDB code: 7qy1
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)
|
36.73 /
1.45
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.191,
131.191,
155.28,
90,
90,
120
|
R / Rfree (%)
|
15 /
17.5
|
Other elements in 7qy1:
The structure of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4 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 4
(pdb code 7qy1). 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 4, PDB code: 7qy1:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7qy1
Go back to
Sodium Binding Sites List in 7qy1
Sodium binding site 1 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4
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 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:17.0
occ:1.00
|
OG1
|
A:THR314
|
2.4
|
16.3
|
1.0
|
O
|
A:THR309
|
2.4
|
16.4
|
1.0
|
O
|
A:THR314
|
2.4
|
17.5
|
1.0
|
O
|
A:SER311
|
2.5
|
17.4
|
1.0
|
OG
|
A:SER316
|
2.5
|
17.6
|
1.0
|
O
|
A:HOH865
|
2.5
|
18.9
|
1.0
|
C
|
A:THR314
|
3.2
|
17.0
|
1.0
|
C
|
A:THR309
|
3.4
|
15.2
|
1.0
|
H
|
A:THR314
|
3.5
|
21.4
|
1.0
|
CB
|
A:THR314
|
3.5
|
16.9
|
1.0
|
HA
|
A:THR309
|
3.6
|
19.1
|
1.0
|
HB2
|
A:SER316
|
3.6
|
21.0
|
1.0
|
CB
|
A:SER316
|
3.6
|
17.5
|
1.0
|
C
|
A:SER311
|
3.6
|
17.0
|
1.0
|
O
|
A:HOH943
|
3.7
|
20.9
|
1.0
|
CA
|
A:THR314
|
3.7
|
16.4
|
1.0
|
H
|
A:SER316
|
3.7
|
20.7
|
1.0
|
HB
|
A:THR314
|
3.8
|
20.2
|
1.0
|
HE1
|
A:MET534
|
3.8
|
21.7
|
1.0
|
H
|
A:SER311
|
3.9
|
20.8
|
1.0
|
N
|
A:SER311
|
4.0
|
17.3
|
1.0
|
N
|
A:THR314
|
4.0
|
17.8
|
1.0
|
N
|
A:SER316
|
4.0
|
17.2
|
1.0
|
CA
|
A:THR309
|
4.1
|
15.9
|
1.0
|
HB3
|
A:SER311
|
4.1
|
21.4
|
1.0
|
HE3
|
A:MET534
|
4.2
|
21.7
|
1.0
|
N
|
A:LEU315
|
4.2
|
16.0
|
1.0
|
HB2
|
A:SER335
|
4.2
|
21.2
|
1.0
|
HE2
|
A:MET534
|
4.2
|
21.7
|
1.0
|
O
|
A:TYR308
|
4.2
|
17.9
|
1.0
|
CE
|
A:MET534
|
4.3
|
18.1
|
1.0
|
HB3
|
A:SER316
|
4.3
|
21.0
|
1.0
|
HA
|
A:LEU315
|
4.3
|
20.7
|
1.0
|
CA
|
A:SER311
|
4.3
|
16.8
|
1.0
|
C
|
A:ASN310
|
4.3
|
17.7
|
1.0
|
CA
|
A:SER316
|
4.4
|
17.1
|
1.0
|
N
|
A:ASN310
|
4.4
|
16.5
|
1.0
|
O
|
A:SER335
|
4.4
|
18.1
|
1.0
|
HA
|
A:ILE312
|
4.4
|
18.8
|
1.0
|
HA
|
A:ASN310
|
4.5
|
20.1
|
1.0
|
HG1
|
A:THR309
|
4.6
|
22.6
|
1.0
|
CA
|
A:LEU315
|
4.6
|
17.3
|
1.0
|
C
|
A:LEU315
|
4.6
|
18.1
|
1.0
|
HA
|
A:THR314
|
4.7
|
19.7
|
1.0
|
CA
|
A:ASN310
|
4.7
|
16.8
|
1.0
|
HA
|
A:SER316
|
4.7
|
20.6
|
1.0
|
OG1
|
A:THR309
|
4.7
|
18.8
|
1.0
|
CG2
|
A:THR314
|
4.7
|
18.0
|
1.0
|
N
|
A:ILE312
|
4.7
|
16.7
|
1.0
|
CB
|
A:SER311
|
4.8
|
17.8
|
1.0
|
HG23
|
A:THR314
|
4.8
|
21.6
|
1.0
|
H
|
A:LEU315
|
4.8
|
19.2
|
1.0
|
O
|
A:ASN310
|
4.9
|
17.9
|
1.0
|
C
|
A:ILE312
|
4.9
|
16.4
|
1.0
|
CA
|
A:ILE312
|
4.9
|
15.7
|
1.0
|
HG21
|
A:THR314
|
5.0
|
21.6
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7qy1
Go back to
Sodium Binding Sites List in 7qy1
Sodium binding site 2 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4
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 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na606
b:33.2
occ:0.34
|
O
|
A:SER544
|
2.1
|
22.8
|
0.7
|
O
|
A:SER544
|
2.2
|
22.6
|
0.3
|
O
|
A:HOH981
|
2.4
|
23.1
|
1.0
|
OG
|
A:SER544
|
3.0
|
18.5
|
0.3
|
C
|
A:SER544
|
3.0
|
22.5
|
0.7
|
C
|
A:SER544
|
3.1
|
22.2
|
0.3
|
HG
|
A:SER544
|
3.3
|
22.2
|
0.3
|
HA3
|
A:GLY545
|
3.3
|
27.1
|
1.0
|
HB3
|
A:SER544
|
3.3
|
28.6
|
0.7
|
HB3
|
A:PRO508
|
3.6
|
23.3
|
1.0
|
HB2
|
A:PRO508
|
3.7
|
23.3
|
1.0
|
N
|
A:GLY545
|
3.8
|
23.1
|
1.0
|
CB
|
A:SER544
|
3.9
|
19.4
|
0.3
|
CA
|
A:GLY545
|
3.9
|
22.6
|
1.0
|
CA
|
A:SER544
|
3.9
|
20.6
|
0.3
|
CA
|
A:SER544
|
4.0
|
22.1
|
0.7
|
CB
|
A:SER544
|
4.0
|
23.9
|
0.7
|
HB2
|
A:SER544
|
4.1
|
23.3
|
0.3
|
CB
|
A:PRO508
|
4.1
|
19.4
|
1.0
|
H
|
A:SER544
|
4.2
|
26.1
|
0.7
|
OG
|
A:SER544
|
4.2
|
25.8
|
0.7
|
HA2
|
A:GLY545
|
4.2
|
27.1
|
1.0
|
H
|
A:SER544
|
4.2
|
25.1
|
0.3
|
N
|
A:SER544
|
4.3
|
21.8
|
0.7
|
N
|
A:SER544
|
4.3
|
20.9
|
0.3
|
HB3
|
A:ASP542
|
4.5
|
24.2
|
1.0
|
O
|
A:ASP542
|
4.5
|
21.1
|
1.0
|
HG2
|
A:PRO508
|
4.5
|
24.4
|
1.0
|
H
|
A:GLY545
|
4.6
|
27.8
|
0.3
|
H
|
A:GLY545
|
4.6
|
27.8
|
0.7
|
OD1
|
A:ASP542
|
4.6
|
23.3
|
1.0
|
HE3
|
A:MET509
|
4.6
|
27.4
|
0.2
|
HB3
|
A:SER544
|
4.7
|
23.3
|
0.3
|
HA
|
A:SER544
|
4.8
|
26.5
|
0.7
|
HA
|
A:SER544
|
4.8
|
24.8
|
0.3
|
CG
|
A:PRO508
|
4.8
|
20.4
|
1.0
|
CG
|
A:ASP542
|
4.8
|
22.0
|
1.0
|
HB2
|
A:SER544
|
4.8
|
28.6
|
0.7
|
HG
|
A:SER544
|
4.8
|
30.9
|
0.7
|
|
Sodium binding site 3 out
of 4 in 7qy1
Go back to
Sodium Binding Sites List in 7qy1
Sodium binding site 3 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4
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 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na607
b:39.7
occ:1.00
|
O
|
A:HOH1045
|
2.2
|
45.9
|
1.0
|
O
|
A:HOH867
|
2.3
|
22.9
|
1.0
|
O
|
A:THR413
|
2.3
|
21.9
|
1.0
|
O
|
A:HOH907
|
2.4
|
36.7
|
1.0
|
O
|
A:HOH1090
|
2.5
|
48.9
|
1.0
|
O
|
A:HOH1104
|
3.1
|
50.3
|
1.0
|
O
|
A:HOH983
|
3.4
|
39.0
|
1.0
|
C
|
A:THR413
|
3.5
|
20.6
|
1.0
|
HA
|
A:ASN414
|
3.6
|
24.6
|
1.0
|
O
|
A:HOH984
|
4.0
|
32.7
|
1.0
|
HB
|
A:THR413
|
4.1
|
27.9
|
1.0
|
O
|
A:ASN414
|
4.2
|
22.6
|
1.0
|
O
|
A:HOH1008
|
4.3
|
39.1
|
1.0
|
CA
|
A:ASN414
|
4.3
|
20.5
|
1.0
|
C
|
A:ASN414
|
4.3
|
21.5
|
1.0
|
N
|
A:ASN414
|
4.4
|
20.1
|
1.0
|
HA
|
A:THR511
|
4.4
|
23.2
|
1.0
|
H
|
A:THR413
|
4.4
|
26.2
|
1.0
|
O
|
A:GLY510
|
4.5
|
23.0
|
1.0
|
O
|
A:MET509
|
4.5
|
22.0
|
0.2
|
CA
|
A:THR413
|
4.6
|
20.4
|
1.0
|
O
|
A:MET509
|
4.6
|
24.3
|
0.8
|
HG22
|
A:THR413
|
4.6
|
29.9
|
1.0
|
O
|
A:HOH1168
|
4.7
|
69.3
|
1.0
|
N
|
A:THR413
|
4.7
|
21.8
|
1.0
|
CB
|
A:THR413
|
4.7
|
23.3
|
1.0
|
OG1
|
A:THR511
|
4.8
|
20.9
|
1.0
|
C
|
A:GLY510
|
4.8
|
21.7
|
1.0
|
HA3
|
A:GLY510
|
4.8
|
26.9
|
1.0
|
HA2
|
A:GLY415
|
4.9
|
26.4
|
1.0
|
O
|
A:HOH951
|
4.9
|
27.9
|
1.0
|
HB1
|
A:ALA412
|
5.0
|
30.6
|
1.0
|
N
|
A:GLY415
|
5.0
|
21.0
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7qy1
Go back to
Sodium Binding Sites List in 7qy1
Sodium binding site 4 out
of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 4
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 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na608
b:20.9
occ:0.86
|
O
|
A:HOH817
|
2.2
|
21.7
|
1.0
|
O
|
A:HOH934
|
2.4
|
24.7
|
1.0
|
O
|
A:HOH1029
|
2.4
|
20.4
|
1.0
|
OD2
|
A:ASP258
|
2.5
|
18.9
|
1.0
|
O
|
A:HOH889
|
2.6
|
25.6
|
1.0
|
HA2
|
A:GLY294
|
2.9
|
21.6
|
1.0
|
OD1
|
A:ASP258
|
2.9
|
17.4
|
1.0
|
CG
|
A:ASP258
|
3.0
|
16.8
|
1.0
|
H
|
A:GLY255
|
3.4
|
22.6
|
1.0
|
HA
|
A:TRP254
|
3.4
|
20.2
|
1.0
|
H
|
A:ASN295
|
3.7
|
20.6
|
1.0
|
CA
|
A:GLY294
|
3.7
|
18.0
|
1.0
|
N
|
A:GLY255
|
3.8
|
18.8
|
1.0
|
HA3
|
A:GLY294
|
3.8
|
21.6
|
1.0
|
O
|
A:HOH761
|
3.8
|
22.6
|
1.0
|
O
|
A:HOH789
|
4.0
|
18.3
|
1.0
|
O
|
A:PRO256
|
4.0
|
16.9
|
1.0
|
O
|
A:HOH1074
|
4.1
|
45.0
|
1.0
|
OD2
|
A:ASP306
|
4.1
|
17.5
|
1.0
|
HA3
|
A:GLY255
|
4.2
|
23.3
|
1.0
|
CA
|
A:TRP254
|
4.2
|
16.8
|
1.0
|
C
|
A:TRP254
|
4.2
|
18.8
|
1.0
|
N
|
A:ASN295
|
4.3
|
17.2
|
1.0
|
HE3
|
A:TRP254
|
4.4
|
19.3
|
1.0
|
CA
|
A:GLY255
|
4.4
|
19.4
|
1.0
|
CB
|
A:ASP258
|
4.5
|
20.6
|
1.0
|
CA
|
A:CA604
|
4.6
|
17.2
|
1.0
|
O
|
A:HOH921
|
4.6
|
17.1
|
1.0
|
C
|
A:GLY294
|
4.6
|
18.1
|
1.0
|
N
|
A:GLY294
|
4.6
|
18.8
|
1.0
|
HB2
|
A:ASP258
|
4.7
|
24.7
|
1.0
|
C
|
A:GLY255
|
4.7
|
18.2
|
1.0
|
O
|
A:SER253
|
4.7
|
18.9
|
1.0
|
HB3
|
A:TRP254
|
4.9
|
22.1
|
1.0
|
HD2
|
A:PRO256
|
4.9
|
24.5
|
1.0
|
OE2
|
A:GLU331
|
4.9
|
16.9
|
1.0
|
O
|
A:GLY255
|
4.9
|
20.8
|
1.0
|
H
|
A:GLY294
|
5.0
|
22.5
|
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 08:25:32 2024
|