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Calcium 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
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6yd4

Go back to Calcium Binding Sites List in 6yd4
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:29.4
occ:1.00
 OD2 A:ASP174 2.3 28.5 1.0
O A:HOH830 2.4 34.2 1.0
O A:HOH1090 2.4 33.1 1.0
O A:HOH851 2.4 34.8 1.0
O A:ASP181 2.5 31.7 1.0
OD1 A:ASP179 2.5 34.2 1.0
OD2 A:ASP179 2.6 36.7 1.0
CG A:ASP179 2.9 37.5 1.0
HB3 A:ASP181 3.2 41.9 1.0
HB2 A:ASP174 3.3 34.3 1.0
CG A:ASP174 3.3 30.0 1.0
HB3 A:ASP174 3.5 34.3 1.0
CB A:ASP174 3.6 28.6 1.0
C A:ASP181 3.6 31.2 1.0
HB2 A:ASP177 3.7 40.6 1.0
HH21 A:ARG225 3.8 41.6 1.0
H A:ASP181 3.9 36.6 1.0
CB A:ASP181 4.1 34.9 1.0
HD3 A:ARG225 4.1 34.1 1.0
CA A:ASP181 4.2 29.6 1.0
N A:ASP181 4.4 30.5 1.0
HA A:PRO182 4.4 32.9 1.0
H A:GLN183 4.4 36.5 1.0
CB A:ASP179 4.4 34.6 1.0
OD1 A:ASP174 4.5 28.6 1.0
NH2 A:ARG225 4.5 34.7 1.0
HB3 A:ASP177 4.5 40.6 1.0
O A:HOH1150 4.5 47.6 1.0
CB A:ASP177 4.5 33.9 1.0
CG A:ASP181 4.6 41.4 1.0
OD2 A:ASP177 4.7 44.3 1.0
HH22 A:ARG225 4.7 41.6 1.0
N A:PRO182 4.7 30.7 1.0
HB2 A:ASP179 4.8 41.5 1.0
HB2 A:ASP181 4.8 41.9 1.0
HB3 A:ASP179 4.8 41.5 1.0
O A:GLN183 4.9 29.3 1.0
N A:GLN183 4.9 30.4 1.0
CA A:PRO182 4.9 27.4 1.0

Calcium binding site 2 out of 3 in 6yd4

Go back to Calcium Binding Sites List in 6yd4
Calcium 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 Calcium with other atoms in the Ca 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:Ca602

b:30.3
occ:1.00
 O A:VAL210 2.3 32.8 1.0
O A:VAL205 2.3 33.8 1.0
OD2 A:ASP115 2.4 34.8 1.0
O A:GLY212 2.4 29.5 1.0
OD1 A:ASP162 2.4 35.9 1.0
OD2 A:ASP162 2.6 33.2 1.0
OD1 A:ASN208 2.6 34.8 1.0
CG A:ASP162 2.9 38.3 1.0
C A:VAL210 3.5 38.1 1.0
CG A:ASP115 3.5 30.3 1.0
C A:VAL205 3.5 34.8 1.0
HD21 A:ASN208 3.5 43.8 1.0
H A:VAL210 3.6 40.5 1.0
CG A:ASN208 3.6 37.6 1.0
C A:GLY212 3.6 34.9 1.0
HB A:VAL210 3.6 45.2 1.0
HA A:ALA206 3.6 43.2 1.0
HB3 A:ASP115 3.7 38.0 1.0
ND2 A:ASN208 3.9 36.5 1.0
HG12 A:VAL213 4.0 41.1 1.0
HA A:VAL213 4.0 33.2 1.0
H A:ASN208 4.1 42.2 1.0
CB A:ASP115 4.1 31.7 1.0
N A:GLY212 4.1 29.6 1.0
HB3 A:CYS211 4.2 47.4 1.0
HB A:VAL205 4.2 42.0 1.0
HB1 A:ALA204 4.2 33.9 1.0
N A:VAL210 4.2 33.8 1.0
C A:CYS211 4.2 37.0 1.0
CA A:VAL210 4.2 37.1 1.0
H A:GLY212 4.3 35.5 1.0
CB A:VAL210 4.3 37.7 1.0
CA A:ALA206 4.4 36.0 1.0
HG12 A:VAL210 4.4 44.9 1.0
N A:ALA206 4.4 32.9 1.0
CA A:GLY212 4.4 30.9 1.0
CB A:ASP162 4.4 34.1 1.0
CA A:VAL205 4.5 33.3 1.0
OD1 A:ASP115 4.5 36.0 1.0
N A:VAL205 4.5 32.7 1.0
H A:VAL205 4.5 39.3 1.0
N A:CYS211 4.5 31.9 1.0
O A:CYS211 4.5 32.2 1.0
HA2 A:GLY212 4.5 37.0 1.0
HB2 A:ASP115 4.6 38.0 1.0
N A:VAL213 4.6 31.6 1.0
H A:ASN207 4.7 40.8 1.0
HA A:ASP162 4.7 38.4 1.0
O A:HOH884 4.7 27.9 1.0
HG13 A:VAL213 4.7 41.1 1.0
HG12 A:VAL205 4.7 41.0 1.0
CG1 A:VAL213 4.7 34.2 1.0
CA A:VAL213 4.7 27.7 1.0
CA A:CYS211 4.8 37.7 1.0
C A:ALA206 4.8 38.7 1.0
HB2 A:ASP162 4.8 40.9 1.0
HD22 A:ASN208 4.8 43.8 1.0
CB A:VAL205 4.8 35.0 1.0
HB3 A:ASP162 4.8 40.9 1.0
HD2 A:PRO116 4.8 49.9 1.0
N A:ASN208 4.8 35.2 1.0
N A:ASN207 4.9 34.0 1.0
CG1 A:VAL210 4.9 37.4 1.0
CB A:CYS211 4.9 39.5 1.0
CB A:ASN208 4.9 44.6 1.0
C A:ALA204 4.9 31.8 1.0

Calcium binding site 3 out of 3 in 6yd4

Go back to Calcium Binding Sites List in 6yd4
Calcium 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 Calcium with other atoms in the Ca 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:Ca603

b:20.4
occ:1.00
 OD1 A:ASP258 2.4 23.2 1.0
OD2 A:ASP301 2.4 22.8 1.0
OE1 A:GLU331 2.4 20.8 1.0
O A:HOH849 2.4 20.0 1.0
O A:HOH792 2.4 19.4 1.0
OE2 A:GLU331 2.5 20.9 1.0
O A:HOH955 2.5 22.4 1.0
CD A:GLU331 2.8 20.1 1.0
CG A:ASP301 3.3 21.5 1.0
HA A:ASP258 3.4 25.6 1.0
CG A:ASP258 3.5 26.7 1.0
HA3 A:GLY294 3.7 22.6 1.0
HB3 A:ASP301 3.8 23.4 1.0
HB2 A:ASP306 3.9 23.6 1.0
HA A:CYS303 4.0 22.6 1.0
OD1 A:ASP301 4.1 21.8 1.0
CB A:ASP301 4.1 19.5 1.0
N35 A:00S615 4.2 21.9 1.0
HB3 A:ASP258 4.2 27.8 1.0
CB A:ASP258 4.2 23.2 1.0
H A:GLY296 4.2 25.1 1.0
CA A:ASP258 4.2 21.3 1.0
HA3 A:GLY296 4.2 26.9 1.0
CG A:GLU331 4.3 20.2 1.0
O A:HOH887 4.3 22.0 1.0
OD2 A:ASP258 4.3 23.7 1.0
O A:SER302 4.5 20.0 1.0
O A:SER293 4.5 20.8 1.0
O A:HOH928 4.5 23.8 1.0
OD2 A:ASP306 4.6 21.7 1.0
HB2 A:ASP301 4.6 23.4 1.0
HG2 A:GLU331 4.6 24.3 1.0
O A:GLU257 4.6 22.9 1.0
CA A:GLY294 4.6 18.8 1.0
HB3 A:CYS303 4.6 24.0 1.0
H A:ASN295 4.7 23.7 1.0
HG3 A:GLU331 4.7 24.3 1.0
CB A:ASP306 4.7 19.7 1.0
HA2 A:GLY294 4.7 22.6 1.0
O A:PRO256 4.8 23.0 1.0
HB3 A:ASP306 4.8 23.6 1.0
C27 A:00S615 4.8 22.5 1.0
N A:GLY296 4.8 20.9 1.0
CA A:CYS303 4.8 18.8 1.0
C A:SER302 4.9 21.2 1.0
N A:ASP258 5.0 23.9 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 Jul 9 20:20:36 2025

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