Atomistry » Calcium » PDB 6y4m-6ydy » 6yd4
Atomistry »
  Calcium »
    PDB 6y4m-6ydy »
      6yd4 »

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

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy