Atomistry » Sodium » PDB 6ycs-6yt4 » 6yd7
Atomistry »
  Sodium »
    PDB 6ycs-6yt4 »
      6yd7 »

Sodium in PDB 6yd7: X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba

Enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba, PDB code: 6yd7 was solved by S.O.Dahms, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.77 / 1.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.785, 131.785, 155.354, 90, 90, 120
R / Rfree (%) 15.4 / 17.1

Other elements in 6yd7:

The structure of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba (pdb code 6yd7). 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 in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba, PDB code: 6yd7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6yd7

Go back to Sodium Binding Sites List in 6yd7
Sodium binding site 1 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba


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 Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:19.5
occ:1.00
 O A:SER311 2.3 17.4 1.0
O A:THR309 2.3 17.9 1.0
O A:HOH858 2.4 16.4 1.0
OG1 A:THR314 2.4 17.6 1.0
O A:THR314 2.5 18.7 1.0
HB2 A:SER316 3.1 21.2 1.0
C A:THR314 3.3 21.0 1.0
H A:THR314 3.3 21.0 1.0
C A:THR309 3.4 20.0 1.0
H A:SER316 3.5 21.5 1.0
C A:SER311 3.5 17.1 1.0
CB A:THR314 3.6 18.0 1.0
HE1 A:MET534 3.7 23.8 1.0
HA A:THR309 3.8 20.5 1.0
O A:HOH859 3.8 28.8 1.0
CA A:THR314 3.8 18.9 1.0
H A:SER311 3.8 20.1 1.0
N A:SER311 3.8 16.7 1.0
N A:THR314 3.9 17.5 1.0
N A:SER316 3.9 17.9 1.0
CB A:SER316 3.9 17.6 1.0
HE3 A:MET534 4.0 23.8 1.0
HE2 A:MET534 4.0 23.8 1.0
HB3 A:SER311 4.0 21.0 1.0
HB3 A:SER316 4.0 21.2 1.0
CE A:MET534 4.1 19.8 1.0
O A:TYR308 4.1 18.6 1.0
HB A:THR314 4.1 21.7 1.0
CA A:SER311 4.1 17.3 1.0
C A:ASN310 4.2 20.6 1.0
CA A:THR309 4.2 17.0 1.0
HA A:ILE312 4.2 19.4 1.0
N A:LEU315 4.3 17.8 1.0
HA A:LEU315 4.3 22.1 1.0
HB2 A:SER335 4.3 23.0 1.0
N A:ASN310 4.3 16.8 1.0
HA A:ASN310 4.4 18.1 1.0
CA A:SER316 4.5 17.8 1.0
O A:SER335 4.5 16.6 1.0
CA A:ASN310 4.5 15.1 1.0
C A:LEU315 4.6 21.8 1.0
N A:ILE312 4.6 16.4 1.0
CB A:SER311 4.6 17.5 1.0
CA A:LEU315 4.6 18.4 1.0
HG23 A:THR314 4.6 24.3 1.0
O A:ASN310 4.7 19.9 1.0
CG2 A:THR314 4.7 20.2 1.0
CA A:ILE312 4.7 16.1 1.0
HA A:THR314 4.7 22.8 1.0
C A:ILE312 4.8 18.6 1.0
HA A:SER316 4.8 21.4 1.0
HG21 A:THR314 5.0 24.3 1.0
H A:LEU315 5.0 21.4 1.0

Sodium binding site 2 out of 3 in 6yd7

Go back to Sodium Binding Sites List in 6yd7
Sodium binding site 2 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba


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 Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:29.3
occ:1.00
 O A:SER279 2.3 23.1 1.0
O A:HOH826 2.4 26.9 1.0
O A:HOH1121 2.4 43.5 1.0
O A:HOH1095 2.5 40.0 1.0
O A:GLY284 2.5 27.2 1.0
O A:HOH804 3.1 50.9 1.0
HA2 A:GLY284 3.3 31.9 1.0
HA A:SER279 3.3 24.7 1.0
C A:SER279 3.4 24.1 1.0
C A:GLY284 3.5 25.1 1.0
HA3 A:GLY284 3.7 31.9 1.0
CA A:GLY284 3.7 26.6 1.0
CA A:SER279 3.9 20.5 1.0
O A:HOH1068 4.0 29.3 1.0
O A:VAL278 4.3 20.2 1.0
O A:HOH848 4.4 31.9 1.0
HB3 A:SER279 4.4 27.2 1.0
HA A:GLN280 4.4 27.1 1.0
O A:HOH1124 4.5 36.2 1.0
N A:GLN280 4.6 24.1 1.0
O A:HOH1111 4.6 40.7 1.0
N A:LEU285 4.7 24.9 1.0
CB A:SER279 4.7 22.6 1.0
HA A:LEU285 4.9 28.5 1.0
O A:HOH1162 4.9 45.6 1.0
CA A:GLN280 5.0 22.5 1.0

Sodium binding site 3 out of 3 in 6yd7

Go back to Sodium Binding Sites List in 6yd7
Sodium binding site 3 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba


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 Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Arg-Tle-Canavanine-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:34.4
occ:0.50
 O A:SER544 2.2 25.1 1.0
O A:HOH910 2.4 20.6 1.0
HA3 A:GLY545 3.1 30.8 1.0
C A:SER544 3.1 24.8 1.0
HB3 A:PRO508 3.4 30.8 1.0
HB3 A:SER544 3.5 27.9 1.0
HB2 A:PRO508 3.5 30.8 1.0
HG A:SER544 3.6 37.9 1.0
CA A:GLY545 3.9 25.6 1.0
CB A:PRO508 3.9 25.7 1.0
N A:GLY545 3.9 23.1 1.0
CB A:SER544 4.1 23.2 1.0
CA A:SER544 4.1 23.2 1.0
HA2 A:GLY545 4.2 30.8 1.0
OG A:SER544 4.3 31.6 1.0
H A:SER544 4.4 28.2 1.0
N A:SER544 4.4 23.4 1.0
HG2 A:PRO508 4.5 27.3 1.0
O A:ASP542 4.6 24.8 1.0
HB3 A:ASP542 4.6 27.0 1.0
H A:GLY545 4.7 27.8 1.0
CG A:PRO508 4.8 22.7 1.0
HG3 A:MET509 4.9 28.6 0.5
HA A:SER544 4.9 27.9 1.0
HB2 A:SER544 5.0 27.9 1.0
OD1 A:ASP542 5.0 23.2 1.0

Reference:

T.Van Lam Van, M.R.Heindl, C.Schlutt, E.Bottcher-Friebertshauser, R.Bartenschlager, G.Klebe, H.Brandstetter, S.O.Dahms, T.Steinmetzer. The Basicity Makes the Difference: Improved Canavanine-Derived Inhibitors of the Proprotein Convertase Furin Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.0C00651
Page generated: Tue Oct 8 15:07:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy