Sodium in PDB 8b4v: X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine

All present enzymatic activity of X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine:
3.4.21.75;

The structure of X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine, PDB code: 8b4v was solved by S.O.Dahms, H.Brandstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.77 / 1.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.952, 131.952, 155.351, 90, 90, 120
R / Rfree (%)	15.4 / 16.6

The structure of X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine (pdb code 8b4v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine, PDB code: 8b4v:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine


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 (PCSK3) in Complex with Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:17.9 occ:1.00 O A:THR309 2.3 16.1 1.0 OG1 A:THR314 2.4 17.4 1.0 O A:THR314 2.4 17.7 1.0 O A:HOH908 2.4 16.9 1.0 O A:SER311 2.4 17.5 1.0 OG A:SER316 2.5 22.2 1.0 C A:THR314 3.2 18.1 1.0 C A:THR309 3.4 16.5 1.0 H A:THR314 3.5 20.0 1.0 HB2 A:SER316 3.5 25.4 1.0 CB A:THR314 3.6 15.9 1.0 CB A:SER316 3.6 21.1 1.0 C A:SER311 3.6 16.7 1.0 H A:SER316 3.6 22.4 1.0 HA A:THR309 3.6 18.3 1.0 O A:HOH907 3.7 21.6 1.0 CA A:THR314 3.8 17.9 1.0 HE1 A:MET534 3.9 19.8 1.0 H A:SER311 3.9 19.3 1.0 HB A:THR314 3.9 19.1 1.0 N A:SER311 3.9 16.1 1.0 N A:SER316 4.0 18.6 1.0 N A:THR314 4.0 16.6 1.0 CA A:THR309 4.1 15.2 1.0 HE3 A:MET534 4.1 19.8 1.0 HB3 A:SER311 4.1 21.9 1.0 HE2 A:MET534 4.1 19.8 1.0 HB2 A:SER335 4.2 20.2 1.0 N A:LEU315 4.2 16.9 1.0 CE A:MET534 4.3 16.5 1.0 O A:TYR308 4.3 18.0 1.0 C A:ASN310 4.3 18.3 1.0 CA A:SER311 4.3 16.7 1.0 HB3 A:SER316 4.3 25.4 1.0 N A:ASN310 4.4 17.3 1.0 HA A:ILE312 4.4 18.7 1.0 HA A:LEU315 4.4 24.4 1.0 CA A:SER316 4.4 16.8 1.0 O A:SER335 4.4 17.0 1.0 HA A:ASN310 4.4 18.0 1.0 CA A:ASN310 4.6 15.0 1.0 C A:LEU315 4.6 19.6 1.0 CA A:LEU315 4.6 20.3 1.0 OG1 A:THR309 4.7 24.9 1.0 N A:ILE312 4.7 15.7 1.0 HA A:THR314 4.7 21.5 1.0 HA A:SER316 4.7 20.1 1.0 CB A:SER311 4.7 18.2 1.0 HG1 A:THR309 4.8 30.0 1.0 CG2 A:THR314 4.8 17.1 1.0 O A:ASN310 4.8 18.4 1.0 HG23 A:THR314 4.8 20.6 1.0 CA A:ILE312 4.9 15.6 1.0 H A:LEU315 4.9 20.3 1.0 C A:ILE312 4.9 17.9 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine


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 (PCSK3) in Complex with Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:28.4 occ:0.38 O A:SER544 2.1 22.1 1.0 O A:HOH896 2.3 21.4 1.0 C A:SER544 3.0 20.2 1.0 HB3 A:SER544 3.1 26.6 1.0 HA3 A:GLY545 3.4 25.6 1.0 CB A:SER544 3.7 22.1 1.0 HB3 A:PRO508 3.8 25.8 1.0 HB2 A:PRO508 3.8 25.8 1.0 CA A:SER544 3.8 19.7 1.0 N A:GLY545 3.9 21.4 1.0 OG A:SER544 4.0 27.3 1.0 CA A:GLY545 4.1 21.3 1.0 H A:SER544 4.1 24.3 1.0 N A:SER544 4.2 20.2 1.0 CB A:PRO508 4.2 21.5 1.0 HB3 A:ASP542 4.3 22.7 1.0 HA2 A:GLY545 4.4 25.6 1.0 HG A:SER544 4.4 32.7 1.0 O A:ASP542 4.4 21.7 1.0 OD1 A:ASP542 4.5 21.8 1.0 HG2 A:PRO508 4.6 22.9 1.0 HB2 A:SER544 4.6 26.6 1.0 H A:GLY545 4.6 25.7 1.0 CG A:ASP542 4.7 20.4 1.0 HA A:SER544 4.7 23.7 1.0 HE3 A:MET509 4.9 42.4 0.4 CG A:PRO508 5.0 19.1 1.0 HG3 A:MET509 5.0 25.0 0.4

Sodium binding site 3 out of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Benzamidine


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 (PCSK3) in Complex with Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:30.1 occ:0.55 O A:HOH938 2.1 32.6 1.0 O A:HOH1035 2.2 39.3 1.0 O A:GLY265 2.4 20.5 1.0 O A:HOH777 2.5 38.6 1.0 OD1 A:ASP264 2.5 30.4 1.0 O A:HOH1157 2.9 37.7 1.0 CG A:ASP264 3.3 30.0 1.0 O A:HOH1172 3.3 36.4 1.0 H A:GLY265 3.4 24.2 1.0 OD2 A:ASP264 3.4 38.4 1.0 HB2 A:ALA267 3.5 25.4 1.0 C A:GLY265 3.6 21.7 1.0 H A:ALA267 3.8 23.5 1.0 N A:GLY265 4.0 20.1 1.0 N A:ALA267 4.0 19.5 1.0 HA A:PRO266 4.2 21.6 1.0 OH A:TYR308 4.3 21.2 1.0 CB A:ALA267 4.3 21.2 1.0 C A:PRO266 4.3 18.7 1.0 CA A:GLY265 4.4 21.8 1.0 HH A:TYR308 4.5 25.5 1.0 O A:HOH1082 4.5 34.9 1.0 N A:PRO266 4.5 19.1 1.0 CA A:PRO266 4.6 18.0 1.0 HB3 A:ALA267 4.6 25.4 1.0 O A:HOH783 4.6 19.4 1.0 CB A:ASP264 4.6 24.6 1.0 CA A:ALA267 4.6 18.7 1.0 HA A:ALA267 4.6 22.4 1.0 HE1 A:TYR308 4.7 24.5 1.0 HB3 A:ASP264 4.8 29.5 1.0 HA A:ASP264 4.8 23.0 1.0 HA2 A:GLY265 4.9 26.2 1.0 O A:PRO266 4.9 19.5 1.0 C A:ASP264 4.9 20.2 1.0

S.O.Dahms, H.Brandstetter. Aminoisoindol-Based Furin Inhibitors To Be Published.