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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:

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 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

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