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Sodium in PDB 7qy2: X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2

Enzymatic activity of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2, PDB code: 7qy2 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) 45.89 / 1.55
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.369, 131.369, 155.336, 90, 90, 120
R / Rfree (%) 16.5 / 18.8

Other elements in 7qy2:

The structure of X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Chlorine (Cl) 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 2 (pdb code 7qy2). 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 2, PDB code: 7qy2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7qy2

Go back to Sodium Binding Sites List in 7qy2
Sodium binding site 1 out of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:19.6
occ:1.00
 OG1 A:THR314 2.3 19.0 1.0
O A:THR314 2.4 18.7 1.0
O A:THR309 2.4 17.9 1.0
OG A:SER316 2.5 18.4 1.0
O A:SER311 2.5 19.5 1.0
O A:HOH864 2.5 19.2 1.0
HG1 A:THR314 2.8 22.8 1.0
HG A:SER316 2.9 22.1 1.0
C A:THR314 3.2 18.5 1.0
H A:THR314 3.4 23.1 1.0
C A:THR309 3.4 18.1 1.0
CB A:THR314 3.5 18.4 1.0
HB2 A:SER316 3.6 21.5 1.0
HA A:THR309 3.6 20.7 1.0
CB A:SER316 3.6 17.9 1.0
C A:SER311 3.7 19.0 1.0
O A:HOH947 3.7 23.4 1.0
CA A:THR314 3.7 18.6 1.0
H A:SER316 3.7 24.4 1.0
HB A:THR314 3.8 22.1 1.0
H A:SER311 3.9 22.7 1.0
HE1 A:MET534 3.9 24.8 1.0
N A:THR314 3.9 19.2 1.0
N A:SER311 4.0 18.9 1.0
N A:SER316 4.0 20.3 1.0
CA A:THR309 4.1 17.3 1.0
N A:LEU315 4.2 19.7 1.0
HE3 A:MET534 4.2 24.8 1.0
HB2 A:SER335 4.2 23.0 1.0
O A:TYR308 4.2 17.3 1.0
HE2 A:MET534 4.2 24.8 1.0
HB3 A:SER311 4.2 20.7 1.0
HB3 A:SER316 4.3 21.5 1.0
CE A:MET534 4.3 20.7 1.0
HA A:LEU315 4.3 25.2 1.0
CA A:SER311 4.3 17.8 1.0
C A:ASN310 4.4 19.2 1.0
CA A:SER316 4.4 18.8 1.0
HA A:ILE312 4.4 22.4 1.0
N A:ASN310 4.4 17.6 1.0
O A:SER335 4.4 18.5 1.0
HG1 A:THR309 4.5 22.5 1.0
HA A:ASN310 4.5 21.4 1.0
C A:LEU315 4.6 20.4 1.0
CA A:LEU315 4.6 21.0 1.0
HA A:THR314 4.6 22.3 1.0
OG1 A:THR309 4.7 18.8 1.0
HA A:SER316 4.7 22.5 1.0
CA A:ASN310 4.7 17.8 1.0
CG2 A:THR314 4.7 19.9 1.0
N A:ILE312 4.7 18.5 1.0
HG23 A:THR314 4.8 23.9 1.0
CB A:SER311 4.8 17.2 1.0
H A:LEU315 4.9 23.6 1.0
CA A:ILE312 4.9 18.7 1.0
C A:ILE312 4.9 19.6 1.0
O A:ASN310 4.9 19.8 1.0
HG21 A:THR314 5.0 23.9 1.0

Sodium binding site 2 out of 4 in 7qy2

Go back to Sodium Binding Sites List in 7qy2
Sodium binding site 2 out of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:28.9
occ:0.31
 O A:SER544 2.1 25.0 0.7
O A:SER544 2.2 24.4 0.3
O A:HOH905 2.4 28.9 1.0
OG A:SER544 3.0 22.7 0.3
C A:SER544 3.0 23.8 0.7
C A:SER544 3.1 23.6 0.3
HG A:SER544 3.2 27.3 0.3
HA3 A:GLY545 3.3 28.5 1.0
HB3 A:SER544 3.3 29.7 0.7
HB3 A:PRO508 3.6 23.9 1.0
HB2 A:PRO508 3.7 23.9 1.0
N A:GLY545 3.8 24.2 1.0
CB A:SER544 3.9 24.8 0.7
CA A:SER544 3.9 24.3 0.7
CB A:SER544 3.9 23.1 0.3
CA A:SER544 3.9 23.5 0.3
CA A:GLY545 4.0 23.8 1.0
CB A:PRO508 4.1 20.0 1.0
OG A:SER544 4.2 25.4 0.7
HB2 A:SER544 4.2 27.7 0.3
HA2 A:GLY545 4.2 28.5 1.0
H A:SER544 4.2 29.3 0.7
H A:SER544 4.3 28.4 0.3
N A:SER544 4.3 24.4 0.7
N A:SER544 4.3 23.6 0.3
HB3 A:ASP542 4.4 26.7 1.0
O A:ASP542 4.4 21.8 1.0
HG2 A:PRO508 4.6 24.2 1.0
H A:GLY545 4.6 29.0 0.3
H A:GLY545 4.6 29.0 0.7
OD1 A:ASP542 4.6 24.3 1.0
HE3 A:MET509 4.7 31.5 0.2
HB3 A:SER544 4.8 27.7 0.3
HA A:SER544 4.8 29.1 0.7
CG A:ASP542 4.8 23.1 1.0
HB2 A:SER544 4.8 29.7 0.7
HA A:SER544 4.8 28.2 0.3
HG A:SER544 4.8 30.4 0.7
CG A:PRO508 4.9 20.2 1.0

Sodium binding site 3 out of 4 in 7qy2

Go back to Sodium Binding Sites List in 7qy2
Sodium binding site 3 out of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:45.4
occ:1.00
 O A:HOH1024 2.2 44.2 1.0
O A:HOH965 2.3 39.2 1.0
O A:THR413 2.3 22.8 1.0
O A:HOH818 2.3 23.6 1.0
O A:HOH1086 2.5 47.6 1.0
O A:HOH1113 2.7 51.6 1.0
O A:HOH953 3.4 46.0 1.0
C A:THR413 3.5 22.8 1.0
HA A:ASN414 3.6 26.0 1.0
O A:HOH1002 4.0 38.9 1.0
HB A:THR413 4.1 31.3 1.0
O A:ASN414 4.2 22.0 1.0
CA A:ASN414 4.2 21.6 1.0
C A:ASN414 4.3 22.0 1.0
O A:HOH983 4.3 40.7 1.0
N A:ASN414 4.3 21.0 1.0
HA A:THR511 4.4 24.5 1.0
H A:THR413 4.5 28.5 1.0
O A:GLY510 4.5 24.5 1.0
O A:MET509 4.5 22.2 0.2
CA A:THR413 4.5 23.8 1.0
O A:MET509 4.7 23.1 0.8
HG22 A:THR413 4.7 32.8 1.0
CB A:THR413 4.7 26.1 1.0
N A:THR413 4.7 23.8 1.0
OG1 A:THR511 4.7 22.0 1.0
C A:GLY510 4.8 22.7 1.0
HA2 A:GLY415 4.8 28.6 1.0
HA3 A:GLY510 4.9 26.6 1.0
O A:HOH1157 4.9 62.4 1.0
HB1 A:ALA412 4.9 31.3 1.0
O A:HOH962 4.9 26.5 1.0
N A:GLY415 4.9 21.9 1.0

Sodium binding site 4 out of 4 in 7qy2

Go back to Sodium Binding Sites List in 7qy2
Sodium binding site 4 out of 4 in the X-Ray Structure of Furin in Complex with the Dichlorophenylpyridine- Based Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:23.6
occ:0.90
 O A:HOH774 2.3 27.2 1.0
O A:HOH1023 2.4 26.4 1.0
O A:HOH874 2.5 35.1 1.0
O A:HOH921 2.6 25.8 1.0
OD2 A:ASP258 2.6 20.2 1.0
HA2 A:GLY294 2.8 21.6 1.0
OD1 A:ASP258 3.0 19.9 1.0
CG A:ASP258 3.1 19.8 1.0
HA A:TRP254 3.4 23.4 1.0
H A:GLY255 3.4 24.6 1.0
H A:ASN295 3.6 22.9 1.0
N A:GLY255 3.7 20.5 1.0
CA A:GLY294 3.7 18.0 1.0
O A:HOH784 3.8 27.8 1.0
HA3 A:GLY294 3.9 21.6 1.0
O A:HOH808 4.0 18.2 1.0
O A:PRO256 4.0 20.5 1.0
HA3 A:GLY255 4.1 24.3 1.0
OD2 A:ASP306 4.2 19.0 1.0
CA A:TRP254 4.2 19.5 1.0
C A:TRP254 4.2 20.6 1.0
N A:ASN295 4.3 19.1 1.0
CA A:GLY255 4.4 20.2 1.0
HE3 A:TRP254 4.4 22.6 1.0
CB A:ASP258 4.5 20.8 1.0
C A:GLY294 4.5 19.1 1.0
CA A:CA604 4.6 18.6 1.0
N A:GLY294 4.6 19.8 1.0
C A:GLY255 4.6 20.3 1.0
O A:SER253 4.7 20.0 1.0
O A:HOH916 4.7 17.9 1.0
HB2 A:ASP258 4.7 24.9 1.0
HB3 A:TRP254 4.7 24.7 1.0
O A:GLY255 4.9 19.9 1.0
HD2 A:PRO256 4.9 27.5 1.0
OE2 A:GLU331 4.9 19.3 1.0
H A:GLY294 5.0 23.7 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 08:25:36 2024

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