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Calcium 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:

Sodium (Na) 3 atoms
Chlorine (Cl) 1 atom

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-Arg-Tle-Canavanine-Amba (pdb code 6yd7). 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-Arg-Tle-Canavanine-Amba, PDB code: 6yd7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6yd7

Go back to Calcium Binding Sites List in 6yd7
Calcium 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 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-Arg-Tle-Canavanine-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:27.8
occ:1.00
 OD2 A:ASP174 2.3 26.1 1.0
O A:HOH840 2.4 29.9 1.0
O A:HOH821 2.4 32.4 1.0
O A:ASP181 2.4 30.8 1.0
OD2 A:ASP179 2.5 33.5 1.0
O A:HOH1090 2.5 31.5 1.0
OD1 A:ASP179 2.5 35.6 1.0
CG A:ASP179 2.9 35.6 1.0
HB3 A:ASP181 3.2 41.1 1.0
CG A:ASP174 3.3 30.1 1.0
HB2 A:ASP174 3.3 36.0 1.0
HB3 A:ASP174 3.5 36.0 1.0
CB A:ASP174 3.6 30.0 1.0
C A:ASP181 3.6 26.6 1.0
HB2 A:ASP177 3.7 40.5 1.0
HH21 A:ARG225 3.8 40.1 1.0
H A:ASP181 3.8 36.1 1.0
CB A:ASP181 4.0 34.2 1.0
HD3 A:ARG225 4.1 31.8 1.0
CA A:ASP181 4.2 28.4 1.0
N A:ASP181 4.4 30.1 1.0
CB A:ASP179 4.4 34.5 1.0
NH2 A:ARG225 4.4 33.4 1.0
OD1 A:ASP174 4.4 25.3 1.0
H A:GLN183 4.4 35.1 1.0
HA A:PRO182 4.4 36.2 1.0
HB3 A:ASP177 4.5 40.5 1.0
O A:HOH1137 4.5 46.0 1.0
CB A:ASP177 4.5 33.7 1.0
CG A:ASP181 4.5 39.7 1.0
HH22 A:ARG225 4.6 40.1 1.0
OD2 A:ASP177 4.6 44.2 1.0
N A:PRO182 4.7 28.7 1.0
HB3 A:ASP179 4.8 41.5 1.0
HB2 A:ASP181 4.8 41.1 1.0
HB2 A:ASP179 4.8 41.5 1.0
N A:GLN183 4.9 29.2 1.0
O A:GLN183 4.9 26.7 1.0
CA A:PRO182 4.9 30.1 1.0
OD2 A:ASP181 5.0 35.9 1.0
CD A:ARG225 5.0 26.4 1.0
OD1 A:ASP181 5.0 31.4 1.0

Calcium binding site 2 out of 3 in 6yd7

Go back to Calcium Binding Sites List in 6yd7
Calcium 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 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-Arg-Tle-Canavanine-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:28.7
occ:1.00
 O A:VAL205 2.3 32.9 1.0
O A:VAL210 2.3 32.8 1.0
OD1 A:ASP162 2.4 34.6 1.0
OD2 A:ASP115 2.4 33.3 1.0
O A:GLY212 2.4 30.7 1.0
OD1 A:ASN208 2.6 31.4 1.0
OD2 A:ASP162 2.7 31.0 1.0
CG A:ASP162 2.9 34.2 1.0
C A:VAL205 3.5 30.3 1.0
CG A:ASP115 3.5 32.4 1.0
C A:VAL210 3.5 35.5 1.0
H A:VAL210 3.6 39.7 1.0
C A:GLY212 3.6 33.0 1.0
HA A:ALA206 3.6 38.9 1.0
HD21 A:ASN208 3.6 40.3 1.0
CG A:ASN208 3.6 36.3 1.0
HB3 A:ASP115 3.6 36.3 1.0
HB A:VAL210 3.7 43.3 1.0
HG12 A:VAL213 3.9 40.2 1.0
HA A:VAL213 4.0 32.9 1.0
H A:ASN208 4.0 38.6 1.0
ND2 A:ASN208 4.0 33.6 1.0
CB A:ASP115 4.1 30.2 1.0
N A:GLY212 4.2 29.4 1.0
HB3 A:CYS211 4.2 40.3 1.0
HB A:VAL205 4.2 41.4 1.0
HB1 A:ALA204 4.2 33.4 1.0
N A:VAL210 4.2 33.1 1.0
CA A:VAL210 4.2 37.5 1.0
C A:CYS211 4.3 37.4 1.0
CA A:ALA206 4.3 32.4 1.0
N A:ALA206 4.3 32.0 1.0
H A:GLY212 4.3 35.3 1.0
CB A:VAL210 4.4 36.0 1.0
CA A:GLY212 4.4 26.8 1.0
HG12 A:VAL210 4.4 42.7 1.0
CB A:ASP162 4.4 34.9 1.0
N A:VAL205 4.4 30.0 1.0
CA A:VAL205 4.4 29.5 1.0
OD1 A:ASP115 4.5 34.6 1.0
H A:VAL205 4.5 36.1 1.0
O A:CYS211 4.5 30.4 1.0
HA2 A:GLY212 4.5 32.2 1.0
N A:CYS211 4.5 28.9 1.0
HB2 A:ASP115 4.6 36.3 1.0
H A:ASN207 4.6 37.8 1.0
N A:VAL213 4.6 30.0 1.0
HA A:ASP162 4.6 39.4 1.0
O A:HOH818 4.7 26.6 1.0
CG1 A:VAL213 4.7 33.5 1.0
HG13 A:VAL213 4.7 40.2 1.0
C A:ALA206 4.7 33.6 1.0
CA A:VAL213 4.7 27.4 1.0
HB2 A:ASP162 4.8 41.9 1.0
CA A:CYS211 4.8 39.0 1.0
N A:ASN208 4.8 32.1 1.0
CB A:VAL205 4.8 34.4 1.0
HG12 A:VAL205 4.8 44.7 1.0
N A:ASN207 4.8 31.5 1.0
HB3 A:ASP162 4.9 41.9 1.0
HD22 A:ASN208 4.9 40.3 1.0
HD2 A:PRO116 4.9 49.8 1.0
C A:ALA204 4.9 29.9 1.0
CB A:CYS211 4.9 33.6 1.0
CG1 A:VAL210 4.9 35.6 1.0
CB A:ASN208 4.9 42.0 1.0

Calcium binding site 3 out of 3 in 6yd7

Go back to Calcium Binding Sites List in 6yd7
Calcium 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 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-Arg-Tle-Canavanine-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:19.9
occ:1.00
 OD2 A:ASP301 2.4 20.1 1.0
OE1 A:GLU331 2.4 19.2 1.0
OD1 A:ASP258 2.4 20.2 1.0
O A:HOH824 2.4 17.0 1.0
OE2 A:GLU331 2.5 19.2 1.0
O A:HOH833 2.5 19.6 1.0
O A:HOH972 2.5 18.3 1.0
CD A:GLU331 2.7 20.5 1.0
CG A:ASP301 3.3 21.0 1.0
HA A:ASP258 3.4 23.8 1.0
CG A:ASP258 3.5 25.4 1.0
HA3 A:GLY294 3.7 21.1 1.0
HB3 A:ASP301 3.8 23.8 1.0
HB2 A:ASP306 3.8 21.9 1.0
HA A:CYS303 4.0 20.7 1.0
OD1 A:ASP301 4.0 19.8 1.0
HB3 A:ASP258 4.1 26.8 1.0
N35 A:00S615 4.1 17.7 1.0
CB A:ASP258 4.1 22.3 1.0
CB A:ASP301 4.1 19.8 1.0
CA A:ASP258 4.2 19.8 1.0
H A:GLY296 4.2 24.5 1.0
HA3 A:GLY296 4.2 27.1 1.0
O A:HOH916 4.3 20.5 1.0
CG A:GLU331 4.3 20.0 1.0
OD2 A:ASP258 4.4 22.4 1.0
O A:SER302 4.5 18.6 1.0
O A:HOH921 4.5 22.2 1.0
O A:SER293 4.5 20.2 1.0
OD2 A:ASP306 4.6 20.5 1.0
HB2 A:ASP301 4.6 23.8 1.0
HG2 A:GLU331 4.6 24.0 1.0
O A:GLU257 4.6 21.5 1.0
CA A:GLY294 4.6 17.5 1.0
HG3 A:GLU331 4.7 24.0 1.0
CB A:ASP306 4.7 18.2 1.0
H A:ASN295 4.7 23.4 1.0
HB3 A:CYS303 4.7 19.7 1.0
HA2 A:GLY294 4.7 21.1 1.0
HB3 A:ASP306 4.7 21.9 1.0
N A:GLY296 4.8 20.4 1.0
O A:PRO256 4.8 21.2 1.0
C27 A:00S615 4.8 23.4 1.0
CA A:CYS303 4.9 17.2 1.0
N A:ASP258 4.9 22.0 1.0
C A:SER302 4.9 20.2 1.0
CA A:GLY296 5.0 22.5 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: Thu Jul 18 22:23:31 2024

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