Calcium in PDB 6yd3: X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba
Enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba
All present enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-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 Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba, PDB code: 6yd3
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)
|
43.06 /
2.00
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.561,
131.561,
155.3,
90,
90,
120
|
R / Rfree (%)
|
16 /
18.5
|
Other elements in 6yd3:
The structure of X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba
(pdb code 6yd3). 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 Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba, PDB code: 6yd3:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 6yd3
Go back to
Calcium Binding Sites List in 6yd3
Calcium binding site 1 out
of 3 in the X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-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 Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:31.9
occ:1.00
|
OD2
|
A:ASP174
|
2.3
|
26.3
|
1.0
|
O
|
A:HOH896
|
2.4
|
29.1
|
1.0
|
O
|
A:ASP181
|
2.4
|
30.5
|
1.0
|
O
|
A:HOH788
|
2.4
|
30.5
|
1.0
|
OD2
|
A:ASP179
|
2.5
|
38.9
|
1.0
|
OD1
|
A:ASP179
|
2.5
|
36.4
|
1.0
|
O
|
A:HOH1060
|
2.6
|
39.4
|
1.0
|
CG
|
A:ASP179
|
2.9
|
33.6
|
1.0
|
HB2
|
A:ASP174
|
3.2
|
40.3
|
1.0
|
HB3
|
A:ASP181
|
3.3
|
40.5
|
1.0
|
CG
|
A:ASP174
|
3.3
|
33.3
|
1.0
|
HB3
|
A:ASP174
|
3.4
|
40.3
|
1.0
|
CB
|
A:ASP174
|
3.5
|
33.5
|
1.0
|
C
|
A:ASP181
|
3.6
|
28.3
|
1.0
|
HH21
|
A:ARG225
|
3.8
|
41.2
|
1.0
|
HB2
|
A:ASP177
|
3.8
|
45.3
|
1.0
|
H
|
A:ASP181
|
3.8
|
37.9
|
1.0
|
CB
|
A:ASP181
|
4.1
|
33.7
|
1.0
|
HD3
|
A:ARG225
|
4.1
|
41.8
|
1.0
|
CA
|
A:ASP181
|
4.2
|
28.9
|
1.0
|
N
|
A:ASP181
|
4.4
|
31.5
|
1.0
|
HA
|
A:PRO182
|
4.4
|
36.9
|
1.0
|
NH2
|
A:ARG225
|
4.4
|
34.3
|
1.0
|
CB
|
A:ASP179
|
4.4
|
30.7
|
1.0
|
H
|
A:GLN183
|
4.4
|
40.0
|
1.0
|
OD1
|
A:ASP174
|
4.5
|
30.8
|
1.0
|
HH22
|
A:ARG225
|
4.6
|
41.2
|
1.0
|
O
|
A:HOH1106
|
4.6
|
45.0
|
1.0
|
CG
|
A:ASP181
|
4.6
|
42.7
|
1.0
|
CB
|
A:ASP177
|
4.6
|
37.7
|
1.0
|
HB3
|
A:ASP177
|
4.6
|
45.3
|
1.0
|
N
|
A:PRO182
|
4.7
|
31.4
|
1.0
|
OD2
|
A:ASP177
|
4.7
|
47.7
|
1.0
|
HB3
|
A:ASP179
|
4.8
|
36.9
|
1.0
|
HB2
|
A:ASP179
|
4.8
|
36.9
|
1.0
|
O
|
A:GLN183
|
4.8
|
27.9
|
1.0
|
HB2
|
A:ASP181
|
4.8
|
40.5
|
1.0
|
N
|
A:GLN183
|
4.8
|
33.2
|
1.0
|
CA
|
A:PRO182
|
4.9
|
30.7
|
1.0
|
HB3
|
A:GLN183
|
4.9
|
42.7
|
1.0
|
CD
|
A:ARG225
|
5.0
|
34.8
|
1.0
|
OD2
|
A:ASP181
|
5.0
|
43.1
|
1.0
|
|
Calcium binding site 2 out
of 3 in 6yd3
Go back to
Calcium Binding Sites List in 6yd3
Calcium binding site 2 out
of 3 in the X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-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 Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:31.5
occ:1.00
|
O
|
A:VAL210
|
2.2
|
27.9
|
1.0
|
OD2
|
A:ASP115
|
2.3
|
31.4
|
1.0
|
O
|
A:VAL205
|
2.3
|
35.3
|
1.0
|
O
|
A:GLY212
|
2.4
|
35.6
|
1.0
|
OD1
|
A:ASP162
|
2.4
|
33.1
|
1.0
|
OD2
|
A:ASP162
|
2.5
|
31.2
|
1.0
|
OD1
|
A:ASN208
|
2.6
|
31.6
|
1.0
|
CG
|
A:ASP162
|
2.8
|
40.5
|
1.0
|
CG
|
A:ASP115
|
3.4
|
31.9
|
1.0
|
C
|
A:VAL210
|
3.4
|
36.9
|
1.0
|
C
|
A:VAL205
|
3.5
|
33.5
|
1.0
|
C
|
A:GLY212
|
3.6
|
40.0
|
1.0
|
HD21
|
A:ASN208
|
3.6
|
41.4
|
1.0
|
H
|
A:VAL210
|
3.6
|
43.5
|
1.0
|
HB
|
A:VAL210
|
3.6
|
45.7
|
1.0
|
CG
|
A:ASN208
|
3.6
|
38.1
|
1.0
|
HB3
|
A:ASP115
|
3.6
|
42.4
|
1.0
|
HA
|
A:ALA206
|
3.7
|
48.0
|
1.0
|
HG12
|
A:VAL213
|
3.9
|
47.2
|
1.0
|
ND2
|
A:ASN208
|
4.0
|
34.5
|
1.0
|
HA
|
A:VAL213
|
4.0
|
31.3
|
1.0
|
H
|
A:ASN208
|
4.1
|
41.0
|
1.0
|
CB
|
A:ASP115
|
4.1
|
35.3
|
1.0
|
HB3
|
A:CYS211
|
4.1
|
46.2
|
1.0
|
N
|
A:GLY212
|
4.1
|
33.4
|
1.0
|
HB
|
A:VAL205
|
4.2
|
44.0
|
1.0
|
HB1
|
A:ALA204
|
4.2
|
36.7
|
1.0
|
C
|
A:CYS211
|
4.2
|
36.8
|
1.0
|
CA
|
A:VAL210
|
4.2
|
38.5
|
1.0
|
N
|
A:VAL210
|
4.2
|
36.2
|
1.0
|
CA
|
A:GLY212
|
4.3
|
32.5
|
1.0
|
CB
|
A:ASP162
|
4.3
|
32.4
|
1.0
|
CB
|
A:VAL210
|
4.3
|
38.1
|
1.0
|
H
|
A:GLY212
|
4.3
|
40.2
|
1.0
|
OD1
|
A:ASP115
|
4.4
|
32.2
|
1.0
|
N
|
A:ALA206
|
4.4
|
29.1
|
1.0
|
CA
|
A:ALA206
|
4.4
|
40.0
|
1.0
|
HG12
|
A:VAL210
|
4.4
|
40.6
|
1.0
|
CA
|
A:VAL205
|
4.5
|
27.5
|
1.0
|
N
|
A:CYS211
|
4.5
|
32.1
|
1.0
|
N
|
A:VAL205
|
4.5
|
28.5
|
1.0
|
HA2
|
A:GLY212
|
4.5
|
39.0
|
1.0
|
O
|
A:CYS211
|
4.5
|
29.2
|
1.0
|
HB2
|
A:ASP115
|
4.5
|
42.4
|
1.0
|
H
|
A:VAL205
|
4.6
|
34.3
|
1.0
|
H
|
A:ASN207
|
4.6
|
46.1
|
1.0
|
N
|
A:VAL213
|
4.6
|
34.5
|
1.0
|
HA
|
A:ASP162
|
4.6
|
41.5
|
1.0
|
O
|
A:HOH823
|
4.6
|
31.2
|
1.0
|
HG12
|
A:VAL205
|
4.7
|
44.2
|
1.0
|
CA
|
A:VAL213
|
4.7
|
26.0
|
1.0
|
HB2
|
A:ASP162
|
4.7
|
38.9
|
1.0
|
CA
|
A:CYS211
|
4.7
|
36.9
|
1.0
|
CG1
|
A:VAL213
|
4.7
|
39.3
|
1.0
|
HG13
|
A:VAL213
|
4.8
|
47.2
|
1.0
|
HB3
|
A:ASP162
|
4.8
|
38.9
|
1.0
|
C
|
A:ALA206
|
4.8
|
39.3
|
1.0
|
CB
|
A:VAL205
|
4.8
|
36.6
|
1.0
|
HD2
|
A:PRO116
|
4.8
|
54.9
|
1.0
|
HD22
|
A:ASN208
|
4.8
|
41.4
|
1.0
|
N
|
A:ASN208
|
4.8
|
34.1
|
1.0
|
N
|
A:ASN207
|
4.9
|
38.4
|
1.0
|
CB
|
A:CYS211
|
4.9
|
38.5
|
1.0
|
C
|
A:ALA204
|
4.9
|
27.6
|
1.0
|
CG1
|
A:VAL210
|
4.9
|
33.8
|
1.0
|
CB
|
A:ASN208
|
5.0
|
44.4
|
1.0
|
|
Calcium binding site 3 out
of 3 in 6yd3
Go back to
Calcium Binding Sites List in 6yd3
Calcium binding site 3 out
of 3 in the X-Ray Structure of Furin in Complex with the Canavanine Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-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 Derived Inhibitor 4-Guanidinomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:24.5
occ:1.00
|
OD2
|
A:ASP301
|
2.3
|
21.1
|
1.0
|
O
|
A:HOH811
|
2.3
|
18.8
|
1.0
|
OD1
|
A:ASP258
|
2.4
|
28.2
|
1.0
|
OE1
|
A:GLU331
|
2.4
|
23.3
|
1.0
|
OE2
|
A:GLU331
|
2.4
|
22.7
|
1.0
|
O
|
A:HOH893
|
2.5
|
20.8
|
1.0
|
O
|
A:HOH760
|
2.5
|
20.8
|
1.0
|
CD
|
A:GLU331
|
2.7
|
24.1
|
1.0
|
CG
|
A:ASP301
|
3.3
|
25.9
|
1.0
|
HA
|
A:ASP258
|
3.3
|
27.3
|
1.0
|
CG
|
A:ASP258
|
3.5
|
31.2
|
1.0
|
HB3
|
A:ASP301
|
3.7
|
27.3
|
1.0
|
HA3
|
A:GLY294
|
3.8
|
26.9
|
1.0
|
HB2
|
A:ASP306
|
3.8
|
26.3
|
1.0
|
HA
|
A:CYS303
|
3.9
|
26.3
|
1.0
|
OD1
|
A:ASP301
|
4.1
|
21.6
|
1.0
|
CB
|
A:ASP301
|
4.1
|
22.7
|
1.0
|
HB3
|
A:ASP258
|
4.1
|
30.9
|
1.0
|
CA
|
A:ASP258
|
4.2
|
22.7
|
1.0
|
HA3
|
A:GLY296
|
4.2
|
28.1
|
1.0
|
CB
|
A:ASP258
|
4.2
|
25.8
|
1.0
|
CG
|
A:GLU331
|
4.2
|
23.9
|
1.0
|
N35
|
A:00S615
|
4.2
|
21.6
|
1.0
|
H
|
A:GLY296
|
4.2
|
30.3
|
1.0
|
O
|
A:HOH908
|
4.3
|
27.8
|
1.0
|
OD2
|
A:ASP258
|
4.4
|
26.9
|
1.0
|
O
|
A:SER302
|
4.5
|
20.3
|
1.0
|
O
|
A:SER293
|
4.5
|
23.8
|
1.0
|
HB2
|
A:ASP301
|
4.5
|
27.3
|
1.0
|
OD2
|
A:ASP306
|
4.5
|
22.4
|
1.0
|
HG2
|
A:GLU331
|
4.5
|
28.7
|
1.0
|
HB3
|
A:CYS303
|
4.6
|
22.8
|
1.0
|
O
|
A:GLU257
|
4.6
|
21.8
|
1.0
|
O
|
A:HOH920
|
4.6
|
26.6
|
1.0
|
HG3
|
A:GLU331
|
4.6
|
28.7
|
1.0
|
CB
|
A:ASP306
|
4.7
|
21.9
|
1.0
|
CA
|
A:GLY294
|
4.7
|
22.4
|
1.0
|
H
|
A:ASN295
|
4.7
|
23.7
|
1.0
|
O
|
A:PRO256
|
4.7
|
22.7
|
1.0
|
CA
|
A:CYS303
|
4.8
|
21.9
|
1.0
|
HA2
|
A:GLY294
|
4.8
|
26.9
|
1.0
|
HB3
|
A:ASP306
|
4.8
|
26.3
|
1.0
|
N
|
A:GLY296
|
4.8
|
25.2
|
1.0
|
C27
|
A:00S615
|
4.8
|
24.5
|
1.0
|
N
|
A:ASP258
|
4.8
|
26.9
|
1.0
|
C
|
A:SER302
|
4.9
|
26.7
|
1.0
|
CA
|
A:GLY296
|
4.9
|
23.4
|
1.0
|
HB3
|
A:GLU331
|
5.0
|
28.5
|
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: Sat Apr 17 14:00:52 2021
|