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Sodium in PDB 6yd4: X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Canavanine- Amba

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

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-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-Canavanine-Tle-Canavanine- Amba, PDB code: 6yd4 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) 45.98 / 1.70
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.685, 131.685, 155.499, 90, 90, 120
R / Rfree (%) 15.3 / 16.9

Other elements in 6yd4:

The structure of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-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-Canavanine-Tle-Canavanine- Amba (pdb code 6yd4). 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-Canavanine-Tle-Canavanine- Amba, PDB code: 6yd4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6yd4

Go back to Sodium Binding Sites List in 6yd4
Sodium binding site 1 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-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-Canavanine-Tle-Canavanine- Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:20.5
occ:1.00
 O A:SER311 2.3 19.9 1.0
O A:THR309 2.3 19.5 1.0
OG1 A:THR314 2.4 19.7 1.0
O A:HOH835 2.4 18.4 1.0
O A:THR314 2.5 20.5 1.0
HB2 A:SER316 3.1 24.9 1.0
C A:THR314 3.3 19.4 1.0
H A:THR314 3.3 24.5 1.0
C A:THR309 3.4 21.4 1.0
C A:SER311 3.4 18.6 1.0
H A:SER316 3.5 23.8 1.0
CB A:THR314 3.6 18.6 1.0
O A:HOH797 3.7 28.2 1.0
HE1 A:MET534 3.8 23.4 1.0
CA A:THR314 3.8 19.2 1.0
HA A:THR309 3.8 25.1 1.0
N A:SER311 3.8 18.8 1.0
H A:SER311 3.8 22.5 1.0
N A:THR314 3.9 20.4 1.0
CB A:SER316 3.9 20.7 1.0
HB3 A:SER316 3.9 24.9 1.0
HE2 A:MET534 4.0 23.4 1.0
N A:SER316 4.0 19.9 1.0
HE3 A:MET534 4.0 23.4 1.0
HB3 A:SER311 4.0 23.9 1.0
O A:TYR308 4.1 21.1 1.0
HB A:THR314 4.1 22.4 1.0
CE A:MET534 4.1 19.5 1.0
CA A:SER311 4.1 17.3 1.0
C A:ASN310 4.1 18.2 1.0
CA A:THR309 4.2 20.9 1.0
HA A:ILE312 4.2 20.5 1.0
HB2 A:SER335 4.3 23.1 1.0
N A:LEU315 4.3 19.5 1.0
N A:ASN310 4.3 19.5 1.0
HA A:LEU315 4.3 25.2 1.0
HA A:ASN310 4.4 22.6 1.0
O A:SER335 4.5 20.4 1.0
CA A:SER316 4.5 19.9 1.0
N A:ILE312 4.5 18.2 1.0
CA A:ASN310 4.5 18.8 1.0
CB A:SER311 4.6 19.9 1.0
C A:LEU315 4.6 22.6 1.0
CA A:LEU315 4.6 21.0 1.0
O A:ASN310 4.7 20.1 1.0
HG23 A:THR314 4.7 23.9 1.0
CA A:ILE312 4.7 17.1 1.0
HA A:THR314 4.7 23.1 1.0
CG2 A:THR314 4.7 19.9 1.0
C A:ILE312 4.7 18.8 1.0
HA A:SER316 4.8 23.9 1.0
HA A:SER311 5.0 20.8 1.0
N A:TYR313 5.0 20.0 1.0

Sodium binding site 2 out of 3 in 6yd4

Go back to Sodium Binding Sites List in 6yd4
Sodium binding site 2 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-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-Canavanine-Tle-Canavanine- Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:31.3
occ:1.00
 O A:SER279 2.3 24.7 1.0
O A:HOH844 2.4 28.8 1.0
O A:HOH1122 2.4 45.6 1.0
O A:HOH1105 2.5 40.2 1.0
O A:GLY284 2.5 25.7 1.0
O A:HOH809 3.1 52.3 1.0
HA2 A:GLY284 3.3 32.2 1.0
HA A:SER279 3.3 26.1 1.0
C A:SER279 3.4 25.9 1.0
C A:GLY284 3.4 24.9 1.0
CA A:GLY284 3.7 26.8 1.0
HA3 A:GLY284 3.7 32.2 1.0
CA A:SER279 3.9 21.7 1.0
O A:HOH1076 4.0 34.5 1.0
O A:VAL278 4.3 22.6 1.0
HA A:GLN280 4.4 31.6 1.0
HB3 A:SER279 4.4 28.9 1.0
O A:HOH784 4.4 33.3 1.0
O A:HOH1131 4.5 36.1 1.0
O A:HOH1109 4.6 43.3 1.0
N A:GLN280 4.6 27.7 1.0
N A:LEU285 4.7 24.9 1.0
CB A:SER279 4.7 24.1 1.0
HA A:LEU285 4.9 33.1 1.0
N A:SER279 5.0 21.1 1.0
CA A:GLN280 5.0 26.4 1.0

Sodium binding site 3 out of 3 in 6yd4

Go back to Sodium Binding Sites List in 6yd4
Sodium binding site 3 out of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-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-Canavanine-Tle-Canavanine- Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:34.1
occ:0.50
 O A:SER544 2.2 25.8 1.0
O A:HOH888 2.4 23.0 1.0
HA3 A:GLY545 3.1 29.8 1.0
C A:SER544 3.1 25.5 1.0
HB3 A:PRO508 3.5 30.3 1.0
HB2 A:PRO508 3.5 30.3 1.0
HB3 A:SER544 3.6 30.6 1.0
HG A:SER544 3.6 37.8 1.0
CA A:GLY545 3.9 24.8 1.0
N A:GLY545 3.9 26.0 1.0
CB A:PRO508 3.9 25.2 1.0
CA A:SER544 4.1 23.3 1.0
CB A:SER544 4.1 25.5 1.0
HA2 A:GLY545 4.1 29.8 1.0
OG A:SER544 4.2 31.5 1.0
H A:SER544 4.5 28.4 1.0
N A:SER544 4.5 23.7 1.0
HG2 A:PRO508 4.5 26.8 1.0
O A:ASP542 4.6 25.1 1.0
HB3 A:ASP542 4.6 29.1 1.0
H A:GLY545 4.7 31.2 1.0
CG A:PRO508 4.8 22.4 1.0
HG3 A:MET509 4.9 31.9 0.5
HA A:SER544 4.9 28.0 1.0
OD1 A:ASP542 5.0 23.5 1.0
O A:HOH714 5.0 33.8 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

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