Calcium in PDB 6yd2: X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba
Enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba
All present enzymatic activity of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-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-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba, PDB code: 6yd2
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)
|
43.05 /
1.80
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.506,
131.506,
155.243,
90,
90,
120
|
R / Rfree (%)
|
15.8 /
17.7
|
Other elements in 6yd2:
The structure of X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-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-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba
(pdb code 6yd2). 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-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba, PDB code: 6yd2:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 6yd2
Go back to
Calcium Binding Sites List in 6yd2
Calcium binding site 1 out
of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-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-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:31.4
occ:1.00
|
OD2
|
A:ASP174
|
2.3
|
28.2
|
1.0
|
O
|
A:HOH865
|
2.4
|
31.3
|
1.0
|
O
|
A:ASP181
|
2.4
|
30.9
|
1.0
|
O
|
A:HOH891
|
2.4
|
34.1
|
1.0
|
OD2
|
A:ASP179
|
2.5
|
39.6
|
1.0
|
O
|
A:HOH1064
|
2.5
|
33.4
|
1.0
|
OD1
|
A:ASP179
|
2.6
|
41.4
|
1.0
|
CG
|
A:ASP179
|
2.9
|
34.7
|
1.0
|
HB3
|
A:ASP181
|
3.2
|
47.2
|
1.0
|
HB2
|
A:ASP174
|
3.3
|
41.5
|
1.0
|
CG
|
A:ASP174
|
3.3
|
31.8
|
1.0
|
HB3
|
A:ASP174
|
3.5
|
41.5
|
1.0
|
CB
|
A:ASP174
|
3.6
|
34.5
|
1.0
|
C
|
A:ASP181
|
3.6
|
29.0
|
1.0
|
HB2
|
A:ASP177
|
3.7
|
46.4
|
1.0
|
HH21
|
A:ARG225
|
3.8
|
42.6
|
1.0
|
H
|
A:ASP181
|
3.8
|
39.0
|
1.0
|
CB
|
A:ASP181
|
4.0
|
39.3
|
1.0
|
HD3
|
A:ARG225
|
4.1
|
33.0
|
1.0
|
CA
|
A:ASP181
|
4.2
|
30.2
|
1.0
|
N
|
A:ASP181
|
4.4
|
32.5
|
1.0
|
HA
|
A:PRO182
|
4.4
|
39.1
|
1.0
|
NH2
|
A:ARG225
|
4.4
|
35.5
|
1.0
|
H
|
A:GLN183
|
4.4
|
40.7
|
1.0
|
CB
|
A:ASP179
|
4.4
|
34.6
|
1.0
|
OD1
|
A:ASP174
|
4.4
|
28.9
|
1.0
|
O
|
A:HOH1126
|
4.5
|
44.4
|
1.0
|
HB3
|
A:ASP177
|
4.5
|
46.4
|
1.0
|
CB
|
A:ASP177
|
4.5
|
38.7
|
1.0
|
CG
|
A:ASP181
|
4.5
|
44.3
|
1.0
|
HH22
|
A:ARG225
|
4.6
|
42.6
|
1.0
|
N
|
A:PRO182
|
4.7
|
31.8
|
1.0
|
OD2
|
A:ASP177
|
4.7
|
48.9
|
1.0
|
HB3
|
A:ASP179
|
4.8
|
41.5
|
1.0
|
HB2
|
A:ASP181
|
4.8
|
47.2
|
1.0
|
HB2
|
A:ASP179
|
4.8
|
41.5
|
1.0
|
N
|
A:GLN183
|
4.8
|
34.0
|
1.0
|
O
|
A:GLN183
|
4.9
|
29.1
|
1.0
|
CA
|
A:PRO182
|
4.9
|
32.6
|
1.0
|
OD2
|
A:ASP181
|
4.9
|
40.0
|
1.0
|
HB3
|
A:GLN183
|
4.9
|
40.7
|
1.0
|
O
|
A:HOH921
|
5.0
|
48.6
|
1.0
|
|
Calcium binding site 2 out
of 3 in 6yd2
Go back to
Calcium Binding Sites List in 6yd2
Calcium binding site 2 out
of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-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-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:30.1
occ:1.00
|
O
|
A:VAL210
|
2.3
|
30.9
|
1.0
|
O
|
A:VAL205
|
2.3
|
33.9
|
1.0
|
OD2
|
A:ASP115
|
2.3
|
33.7
|
1.0
|
OD1
|
A:ASP162
|
2.4
|
36.6
|
1.0
|
O
|
A:GLY212
|
2.4
|
32.0
|
1.0
|
OD1
|
A:ASN208
|
2.6
|
30.4
|
1.0
|
OD2
|
A:ASP162
|
2.6
|
31.9
|
1.0
|
CG
|
A:ASP162
|
2.8
|
36.8
|
1.0
|
CG
|
A:ASP115
|
3.4
|
32.9
|
1.0
|
C
|
A:VAL205
|
3.5
|
32.4
|
1.0
|
C
|
A:VAL210
|
3.5
|
37.5
|
1.0
|
H
|
A:VAL210
|
3.6
|
41.7
|
1.0
|
HB3
|
A:ASP115
|
3.6
|
37.3
|
1.0
|
HD21
|
A:ASN208
|
3.6
|
39.2
|
1.0
|
CG
|
A:ASN208
|
3.6
|
38.3
|
1.0
|
C
|
A:GLY212
|
3.6
|
32.3
|
1.0
|
HB
|
A:VAL210
|
3.6
|
48.1
|
1.0
|
HA
|
A:ALA206
|
3.7
|
38.8
|
1.0
|
HG12
|
A:VAL213
|
3.9
|
39.6
|
1.0
|
ND2
|
A:ASN208
|
4.0
|
32.7
|
1.0
|
HA
|
A:VAL213
|
4.0
|
34.0
|
1.0
|
H
|
A:ASN208
|
4.0
|
39.3
|
1.0
|
CB
|
A:ASP115
|
4.0
|
31.1
|
1.0
|
HB3
|
A:CYS211
|
4.1
|
45.9
|
1.0
|
N
|
A:GLY212
|
4.2
|
31.2
|
1.0
|
HB
|
A:VAL205
|
4.2
|
44.1
|
1.0
|
HB1
|
A:ALA204
|
4.2
|
35.5
|
1.0
|
N
|
A:VAL210
|
4.2
|
34.8
|
1.0
|
CA
|
A:VAL210
|
4.2
|
38.8
|
1.0
|
C
|
A:CYS211
|
4.2
|
36.1
|
1.0
|
H
|
A:GLY212
|
4.3
|
37.4
|
1.0
|
N
|
A:ALA206
|
4.3
|
31.1
|
1.0
|
CB
|
A:VAL210
|
4.3
|
40.1
|
1.0
|
CA
|
A:ALA206
|
4.4
|
32.3
|
1.0
|
OD1
|
A:ASP115
|
4.4
|
34.9
|
1.0
|
CB
|
A:ASP162
|
4.4
|
31.4
|
1.0
|
CA
|
A:GLY212
|
4.4
|
30.7
|
1.0
|
HG12
|
A:VAL210
|
4.4
|
44.9
|
1.0
|
CA
|
A:VAL205
|
4.4
|
29.5
|
1.0
|
N
|
A:VAL205
|
4.5
|
30.7
|
1.0
|
HB2
|
A:ASP115
|
4.5
|
37.3
|
1.0
|
N
|
A:CYS211
|
4.5
|
32.0
|
1.0
|
H
|
A:VAL205
|
4.5
|
36.8
|
1.0
|
HA2
|
A:GLY212
|
4.5
|
36.8
|
1.0
|
O
|
A:CYS211
|
4.5
|
31.4
|
1.0
|
H
|
A:ASN207
|
4.6
|
45.6
|
1.0
|
N
|
A:VAL213
|
4.6
|
29.5
|
1.0
|
HG12
|
A:VAL205
|
4.6
|
43.5
|
1.0
|
HA
|
A:ASP162
|
4.7
|
40.0
|
1.0
|
CG1
|
A:VAL213
|
4.7
|
33.0
|
1.0
|
CA
|
A:VAL213
|
4.7
|
28.3
|
1.0
|
O
|
A:HOH900
|
4.7
|
30.0
|
1.0
|
C
|
A:ALA206
|
4.7
|
39.2
|
1.0
|
HG13
|
A:VAL213
|
4.7
|
39.6
|
1.0
|
HB2
|
A:ASP162
|
4.7
|
37.6
|
1.0
|
CB
|
A:VAL205
|
4.8
|
36.8
|
1.0
|
CA
|
A:CYS211
|
4.8
|
36.7
|
1.0
|
N
|
A:ASN208
|
4.8
|
32.7
|
1.0
|
HD2
|
A:PRO116
|
4.8
|
50.7
|
1.0
|
HD22
|
A:ASN208
|
4.8
|
39.2
|
1.0
|
HB3
|
A:ASP162
|
4.8
|
37.6
|
1.0
|
N
|
A:ASN207
|
4.8
|
38.0
|
1.0
|
CB
|
A:ASN208
|
4.9
|
40.1
|
1.0
|
CB
|
A:CYS211
|
4.9
|
38.2
|
1.0
|
C
|
A:ALA204
|
4.9
|
30.5
|
1.0
|
CG1
|
A:VAL210
|
4.9
|
37.4
|
1.0
|
|
Calcium binding site 3 out
of 3 in 6yd2
Go back to
Calcium Binding Sites List in 6yd2
Calcium binding site 3 out
of 3 in the X-Ray Structure of Furin in Complex with the Canavanine-Based Inhibitor 4-Aminomethyl-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-Based Inhibitor 4-Aminomethyl-Phenylacetyl-Canavanine-Tle-Arg-Amba within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:23.5
occ:1.00
|
OD2
|
A:ASP301
|
2.3
|
22.1
|
1.0
|
O
|
A:HOH819
|
2.4
|
19.6
|
1.0
|
OD1
|
A:ASP258
|
2.4
|
25.7
|
1.0
|
OE1
|
A:GLU331
|
2.4
|
21.8
|
1.0
|
OE2
|
A:GLU331
|
2.4
|
22.4
|
1.0
|
O
|
A:HOH814
|
2.4
|
23.8
|
1.0
|
O
|
A:HOH936
|
2.5
|
21.9
|
1.0
|
CD
|
A:GLU331
|
2.7
|
23.4
|
1.0
|
CG
|
A:ASP301
|
3.3
|
25.0
|
1.0
|
HA
|
A:ASP258
|
3.4
|
25.9
|
1.0
|
CG
|
A:ASP258
|
3.5
|
30.4
|
1.0
|
HB3
|
A:ASP301
|
3.7
|
25.1
|
1.0
|
HA3
|
A:GLY294
|
3.8
|
24.7
|
1.0
|
HB2
|
A:ASP306
|
3.8
|
27.9
|
1.0
|
HA
|
A:CYS303
|
3.9
|
26.3
|
1.0
|
OD1
|
A:ASP301
|
4.0
|
22.0
|
1.0
|
CB
|
A:ASP301
|
4.1
|
20.9
|
1.0
|
HA3
|
A:GLY296
|
4.2
|
28.4
|
1.0
|
CA
|
A:ASP258
|
4.2
|
21.6
|
1.0
|
CB
|
A:ASP258
|
4.2
|
23.8
|
1.0
|
H
|
A:GLY296
|
4.2
|
30.8
|
1.0
|
HB3
|
A:ASP258
|
4.2
|
28.6
|
1.0
|
O
|
A:HOH926
|
4.2
|
26.2
|
1.0
|
N35
|
A:00S615
|
4.2
|
22.4
|
1.0
|
CG
|
A:GLU331
|
4.2
|
26.0
|
1.0
|
OD2
|
A:ASP258
|
4.4
|
27.9
|
1.0
|
O
|
A:SER302
|
4.4
|
23.1
|
1.0
|
O
|
A:SER293
|
4.5
|
22.0
|
1.0
|
HB2
|
A:ASP301
|
4.5
|
25.1
|
1.0
|
OD2
|
A:ASP306
|
4.5
|
25.2
|
1.0
|
O
|
A:HOH923
|
4.5
|
28.3
|
1.0
|
HG2
|
A:GLU331
|
4.5
|
31.2
|
1.0
|
O
|
A:GLU257
|
4.6
|
23.5
|
1.0
|
HB3
|
A:CYS303
|
4.6
|
28.4
|
1.0
|
CA
|
A:GLY294
|
4.6
|
20.6
|
1.0
|
HG3
|
A:GLU331
|
4.7
|
31.2
|
1.0
|
CB
|
A:ASP306
|
4.7
|
23.3
|
1.0
|
H
|
A:ASN295
|
4.7
|
25.9
|
1.0
|
HA2
|
A:GLY294
|
4.7
|
24.7
|
1.0
|
HB3
|
A:ASP306
|
4.8
|
27.9
|
1.0
|
O
|
A:PRO256
|
4.8
|
23.3
|
1.0
|
N
|
A:GLY296
|
4.8
|
25.6
|
1.0
|
CA
|
A:CYS303
|
4.8
|
21.9
|
1.0
|
C
|
A:SER302
|
4.9
|
23.2
|
1.0
|
N
|
A:ASP258
|
4.9
|
24.9
|
1.0
|
C27
|
A:00S615
|
4.9
|
24.3
|
1.0
|
CA
|
A:GLY296
|
4.9
|
23.6
|
1.0
|
HB3
|
A:GLU331
|
5.0
|
29.5
|
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
|