Sodium in PDB 6yd2: X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba

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

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

Protein crystallography data

The structure of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba, PDB code: 6yd2 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) 43.05 / 1.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.506, 131.506, 155.243, 90, 90, 120
R / Rfree (%) 15.8 / 17.7

Other elements in 6yd2:

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

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

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba (pdb code 6yd2). 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-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba, PDB code: 6yd2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6yd2

Go back to Sodium Binding Sites List in 6yd2
Sodium binding site 1 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-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-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:21.9
occ:1.00
 O A:SER311 2.3 21.1 1.0
O A:HOH795 2.4 20.4 1.0
O A:THR309 2.4 21.8 1.0
O A:THR314 2.4 19.3 1.0
OG1 A:THR314 2.4 21.3 1.0
HB2 A:SER316 3.1 28.8 1.0
C A:THR314 3.2 20.9 1.0
H A:THR314 3.3 27.3 1.0
H A:SER316 3.4 25.2 1.0
C A:THR309 3.4 20.0 1.0
C A:SER311 3.5 23.2 1.0
CB A:THR314 3.6 21.1 1.0
O A:HOH841 3.6 32.5 1.0
CA A:THR314 3.7 23.2 1.0
HA A:THR309 3.8 24.5 1.0
HE1 A:MET534 3.8 24.7 1.0
H A:SER311 3.9 23.9 1.0
N A:SER316 3.9 21.0 1.0
N A:SER311 3.9 19.9 1.0
N A:THR314 3.9 22.8 1.0
CB A:SER316 3.9 24.0 1.0
HE3 A:MET534 3.9 24.7 1.0
HE2 A:MET534 4.0 24.7 1.0
HB3 A:SER316 4.0 28.8 1.0
HB3 A:SER311 4.0 26.3 1.0
HB A:THR314 4.1 25.2 1.0
CE A:MET534 4.1 20.6 1.0
O A:TYR308 4.2 22.9 1.0
C A:ASN310 4.2 21.1 1.0
CA A:THR309 4.2 20.4 1.0
CA A:SER311 4.2 19.1 1.0
N A:LEU315 4.2 20.4 1.0
HA A:ILE312 4.2 21.5 1.0
HA A:LEU315 4.2 26.3 1.0
HB2 A:SER335 4.3 26.8 1.0
N A:ASN310 4.4 18.6 1.0
HA A:ASN310 4.5 23.9 1.0
O A:SER335 4.5 20.3 1.0
CA A:SER316 4.5 21.9 1.0
C A:LEU315 4.5 22.3 1.0
CA A:LEU315 4.6 21.9 1.0
N A:ILE312 4.6 20.9 1.0
CA A:ASN310 4.6 19.9 1.0
CB A:SER311 4.6 21.9 1.0
HG23 A:THR314 4.7 25.3 1.0
HA A:THR314 4.7 27.9 1.0
O A:ASN310 4.7 23.0 1.0
CA A:ILE312 4.7 17.9 1.0
C A:ILE312 4.7 21.5 1.0
CG2 A:THR314 4.7 21.1 1.0
HA A:SER316 4.8 26.3 1.0
H A:LEU315 4.9 24.4 1.0

Sodium binding site 2 out of 3 in 6yd2

Go back to Sodium Binding Sites List in 6yd2
Sodium binding site 2 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-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-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:33.0
occ:1.00
 O A:SER279 2.3 25.9 1.0
O A:HOH809 2.4 25.6 1.0
O A:HOH1094 2.4 38.2 1.0
O A:HOH1070 2.5 42.4 1.0
O A:GLY284 2.6 27.9 1.0
O A:HOH883 3.2 51.9 1.0
HA A:SER279 3.3 28.1 1.0
HA2 A:GLY284 3.3 35.0 1.0
C A:SER279 3.4 25.1 1.0
C A:GLY284 3.5 26.8 1.0
CA A:GLY284 3.7 29.1 1.0
HA3 A:GLY284 3.7 35.0 1.0
CA A:SER279 3.9 23.4 1.0
O A:HOH1034 4.0 34.0 1.0
O A:VAL278 4.3 24.1 1.0
HB3 A:SER279 4.3 31.6 1.0
HA A:GLN280 4.3 31.6 1.0
O A:HOH762 4.4 33.6 1.0
O A:HOH1104 4.5 34.7 1.0
N A:GLN280 4.6 27.0 1.0
O A:HOH1080 4.6 39.2 1.0
CB A:SER279 4.7 26.4 1.0
N A:LEU285 4.7 25.8 1.0
HA A:LEU285 4.9 33.1 1.0
CA A:GLN280 5.0 26.3 1.0
N A:SER279 5.0 21.9 1.0

Sodium binding site 3 out of 3 in 6yd2

Go back to Sodium Binding Sites List in 6yd2
Sodium binding site 3 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-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-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:34.7
occ:0.50
 O A:SER544 2.1 26.6 1.0
O A:HOH871 2.3 23.8 1.0
HA3 A:GLY545 3.1 31.0 1.0
C A:SER544 3.1 27.3 1.0
HB3 A:PRO508 3.4 30.6 1.0
HB2 A:PRO508 3.5 30.6 1.0
HB3 A:SER544 3.6 29.3 1.0
HG A:SER544 3.6 40.2 1.0
CA A:GLY545 3.9 25.8 1.0
N A:GLY545 3.9 26.6 1.0
CB A:PRO508 3.9 25.5 1.0
CA A:SER544 4.1 23.4 1.0
CB A:SER544 4.1 24.4 1.0
HA2 A:GLY545 4.1 31.0 1.0
OG A:SER544 4.2 33.5 1.0
H A:SER544 4.4 28.7 1.0
N A:SER544 4.5 23.9 1.0
HG2 A:PRO508 4.5 30.0 1.0
HB3 A:ASP542 4.6 28.2 1.0
O A:ASP542 4.6 26.3 1.0
H A:GLY545 4.7 32.0 1.0
CG A:PRO508 4.8 25.0 1.0
O A:HOH711 4.9 33.8 1.0
HA A:SER544 4.9 28.0 1.0
OD1 A:ASP542 5.0 24.4 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: Wed Mar 3 15:30:42 2021

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