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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:

Chlorine (Cl) 3 atoms
Calcium (Ca) 3 atoms

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

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