Calcium in PDB 8oyh: X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol
Enzymatic activity of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol
All present enzymatic activity of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol:
3.4.21.75;
Protein crystallography data
The structure of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol, PDB code: 8oyh
was solved by
S.O.Dahms,
H.Brandstetter,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.53 /
1.80
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.245,
131.245,
154.618,
90,
90,
120
|
R / Rfree (%)
|
17.4 /
18.8
|
Other elements in 8oyh:
The structure of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol
(pdb code 8oyh). 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 (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol, PDB code: 8oyh:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 8oyh
Go back to
Calcium Binding Sites List in 8oyh
Calcium binding site 1 out
of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol
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 (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:36.8
occ:1.00
|
OD2
|
A:ASP174
|
2.3
|
34.7
|
1.0
|
O
|
A:HOH818
|
2.3
|
39.0
|
1.0
|
O
|
A:HOH740
|
2.4
|
38.6
|
1.0
|
O
|
A:HOH996
|
2.4
|
40.0
|
1.0
|
O
|
A:ASP181
|
2.4
|
37.6
|
1.0
|
OD2
|
A:ASP179
|
2.5
|
44.0
|
1.0
|
OD1
|
A:ASP179
|
2.5
|
42.9
|
1.0
|
CG
|
A:ASP179
|
2.8
|
43.7
|
1.0
|
HB3
|
A:ASP181
|
3.2
|
50.6
|
1.0
|
HB2
|
A:ASP174
|
3.2
|
45.9
|
1.0
|
CG
|
A:ASP174
|
3.3
|
37.1
|
1.0
|
HB3
|
A:ASP174
|
3.5
|
45.9
|
1.0
|
CB
|
A:ASP174
|
3.5
|
38.2
|
1.0
|
C
|
A:ASP181
|
3.6
|
37.4
|
1.0
|
HB2
|
A:ASP177
|
3.7
|
51.6
|
1.0
|
HH11
|
A:ARG225
|
3.8
|
46.1
|
1.0
|
H
|
A:ASP181
|
3.9
|
49.4
|
1.0
|
CB
|
A:ASP181
|
4.0
|
42.1
|
1.0
|
HD3
|
A:ARG225
|
4.2
|
40.8
|
1.0
|
CA
|
A:ASP181
|
4.2
|
38.8
|
1.0
|
H
|
A:GLN183
|
4.4
|
43.3
|
1.0
|
N
|
A:ASP181
|
4.4
|
41.1
|
1.0
|
CB
|
A:ASP179
|
4.4
|
43.6
|
1.0
|
HA
|
A:PRO182
|
4.4
|
42.8
|
1.0
|
OD1
|
A:ASP174
|
4.4
|
36.4
|
1.0
|
O
|
A:HOH1029
|
4.5
|
46.3
|
1.0
|
NH1
|
A:ARG225
|
4.5
|
38.3
|
1.0
|
CB
|
A:ASP177
|
4.6
|
42.9
|
1.0
|
CG
|
A:ASP181
|
4.6
|
44.4
|
1.0
|
HB3
|
A:ASP177
|
4.6
|
51.6
|
1.0
|
HH12
|
A:ARG225
|
4.7
|
46.1
|
1.0
|
OD2
|
A:ASP177
|
4.7
|
47.5
|
1.0
|
N
|
A:PRO182
|
4.7
|
36.4
|
1.0
|
HB2
|
A:ASP179
|
4.7
|
52.3
|
1.0
|
HB3
|
A:ASP179
|
4.7
|
52.3
|
1.0
|
HB2
|
A:ASP181
|
4.8
|
50.6
|
1.0
|
N
|
A:GLN183
|
4.8
|
36.0
|
1.0
|
O
|
A:GLN183
|
4.8
|
36.1
|
1.0
|
CA
|
A:PRO182
|
4.9
|
35.6
|
1.0
|
HB3
|
A:GLN183
|
5.0
|
48.8
|
1.0
|
OD1
|
A:ASP181
|
5.0
|
43.1
|
1.0
|
|
Calcium binding site 2 out
of 3 in 8oyh
Go back to
Calcium Binding Sites List in 8oyh
Calcium binding site 2 out
of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol
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 (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:36.6
occ:1.00
|
O
|
A:VAL205
|
2.3
|
39.3
|
1.0
|
OD2
|
A:ASP115
|
2.3
|
41.4
|
1.0
|
O
|
A:VAL210
|
2.3
|
42.4
|
1.0
|
O
|
A:GLY212
|
2.3
|
38.9
|
1.0
|
OD1
|
A:ASP162
|
2.4
|
40.6
|
1.0
|
OD1
|
A:ASN208
|
2.6
|
41.8
|
1.0
|
OD2
|
A:ASP162
|
2.7
|
42.9
|
1.0
|
CG
|
A:ASP162
|
2.9
|
42.0
|
1.0
|
CG
|
A:ASP115
|
3.4
|
42.1
|
1.0
|
C
|
A:VAL205
|
3.4
|
40.4
|
1.0
|
C
|
A:VAL210
|
3.5
|
41.1
|
1.0
|
C
|
A:GLY212
|
3.5
|
38.9
|
1.0
|
H
|
A:VAL210
|
3.5
|
49.8
|
1.0
|
HD21
|
A:ASN208
|
3.5
|
52.6
|
1.0
|
HA
|
A:ALA206
|
3.6
|
49.1
|
1.0
|
CG
|
A:ASN208
|
3.6
|
44.7
|
1.0
|
HB3
|
A:ASP115
|
3.6
|
49.4
|
1.0
|
HB
|
A:VAL210
|
3.7
|
53.7
|
1.0
|
HG12
|
A:VAL213
|
3.8
|
47.8
|
1.0
|
ND2
|
A:ASN208
|
3.9
|
43.8
|
1.0
|
HA
|
A:VAL213
|
4.0
|
43.3
|
1.0
|
H
|
A:ASN208
|
4.0
|
52.6
|
1.0
|
CB
|
A:ASP115
|
4.0
|
41.1
|
1.0
|
N
|
A:GLY212
|
4.1
|
39.6
|
1.0
|
HB2
|
A:CYS211
|
4.1
|
50.5
|
0.2
|
HB3
|
A:CYS211
|
4.2
|
50.3
|
0.8
|
HB1
|
A:ALA204
|
4.2
|
44.4
|
1.0
|
N
|
A:VAL210
|
4.2
|
41.4
|
1.0
|
C
|
A:CYS211
|
4.2
|
41.4
|
0.2
|
HB
|
A:VAL205
|
4.2
|
52.3
|
1.0
|
H
|
A:GLY212
|
4.2
|
47.6
|
0.8
|
C
|
A:CYS211
|
4.2
|
41.4
|
0.8
|
H
|
A:GLY212
|
4.2
|
47.6
|
0.2
|
CA
|
A:VAL210
|
4.3
|
43.5
|
1.0
|
CA
|
A:GLY212
|
4.3
|
37.3
|
1.0
|
N
|
A:ALA206
|
4.3
|
39.6
|
1.0
|
CA
|
A:ALA206
|
4.3
|
40.8
|
1.0
|
OD1
|
A:ASP115
|
4.3
|
42.8
|
1.0
|
CB
|
A:VAL210
|
4.4
|
44.7
|
1.0
|
CB
|
A:ASP162
|
4.4
|
41.3
|
1.0
|
HG12
|
A:VAL210
|
4.4
|
52.4
|
1.0
|
CA
|
A:VAL205
|
4.4
|
40.2
|
1.0
|
HA2
|
A:GLY212
|
4.5
|
44.8
|
1.0
|
N
|
A:VAL205
|
4.5
|
39.3
|
1.0
|
O
|
A:CYS211
|
4.5
|
40.9
|
0.2
|
HB2
|
A:ASP115
|
4.5
|
49.4
|
1.0
|
O
|
A:CYS211
|
4.5
|
40.7
|
0.8
|
N
|
A:CYS211
|
4.5
|
42.1
|
0.2
|
H
|
A:VAL205
|
4.5
|
47.2
|
1.0
|
N
|
A:CYS211
|
4.5
|
42.1
|
0.8
|
N
|
A:VAL213
|
4.5
|
36.9
|
1.0
|
H
|
A:ASN207
|
4.6
|
52.3
|
1.0
|
HA
|
A:ASP162
|
4.6
|
49.9
|
1.0
|
CG1
|
A:VAL213
|
4.6
|
39.8
|
1.0
|
HG12
|
A:VAL205
|
4.7
|
51.0
|
1.0
|
CA
|
A:VAL213
|
4.7
|
36.0
|
1.0
|
C
|
A:ALA206
|
4.7
|
43.5
|
1.0
|
O
|
A:HOH828
|
4.7
|
35.5
|
1.0
|
HB2
|
A:ASP162
|
4.8
|
49.7
|
1.0
|
HD22
|
A:ASN208
|
4.8
|
52.6
|
1.0
|
CA
|
A:CYS211
|
4.8
|
41.9
|
0.2
|
N
|
A:ASN208
|
4.8
|
43.8
|
1.0
|
HG13
|
A:VAL213
|
4.8
|
47.8
|
1.0
|
CB
|
A:VAL205
|
4.8
|
43.5
|
1.0
|
CA
|
A:CYS211
|
4.8
|
41.9
|
0.8
|
N
|
A:ASN207
|
4.8
|
43.5
|
1.0
|
HD2
|
A:PRO116
|
4.8
|
56.5
|
1.0
|
HB3
|
A:ASP162
|
4.8
|
49.7
|
1.0
|
C
|
A:ALA204
|
4.9
|
37.9
|
1.0
|
CB
|
A:CYS211
|
4.9
|
42.0
|
0.2
|
CB
|
A:ASN208
|
4.9
|
47.0
|
1.0
|
CG1
|
A:VAL210
|
5.0
|
43.6
|
1.0
|
CB
|
A:CYS211
|
5.0
|
41.9
|
0.8
|
|
Calcium binding site 3 out
of 3 in 8oyh
Go back to
Calcium Binding Sites List in 8oyh
Calcium binding site 3 out
of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol
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 (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:26.9
occ:1.00
|
OD2
|
A:ASP301
|
2.3
|
27.3
|
1.0
|
OD1
|
A:ASP258
|
2.4
|
28.8
|
1.0
|
OE2
|
A:GLU331
|
2.4
|
27.2
|
1.0
|
O
|
A:HOH776
|
2.4
|
26.5
|
1.0
|
O
|
A:HOH786
|
2.4
|
26.3
|
1.0
|
O
|
A:HOH830
|
2.5
|
28.0
|
1.0
|
OE1
|
A:GLU331
|
2.5
|
27.3
|
1.0
|
CD
|
A:GLU331
|
2.7
|
27.6
|
1.0
|
CG
|
A:ASP301
|
3.3
|
29.2
|
1.0
|
HA
|
A:ASP258
|
3.4
|
36.4
|
1.0
|
CG
|
A:ASP258
|
3.5
|
32.7
|
1.0
|
HB3
|
A:ASP301
|
3.7
|
33.9
|
1.0
|
HA3
|
A:GLY294
|
3.8
|
32.3
|
1.0
|
HB2
|
A:ASP306
|
3.8
|
30.6
|
1.0
|
HA
|
A:CYS303
|
3.9
|
32.8
|
1.0
|
OD1
|
A:ASP301
|
4.0
|
29.8
|
1.0
|
CB
|
A:ASP301
|
4.1
|
28.2
|
1.0
|
HBU
|
B:OZ3614
|
4.1
|
34.6
|
1.0
|
HA3
|
A:GLY296
|
4.2
|
34.1
|
1.0
|
H
|
A:GLY296
|
4.2
|
35.0
|
1.0
|
O
|
A:HOH857
|
4.2
|
31.1
|
1.0
|
CG
|
A:GLU331
|
4.3
|
27.7
|
1.0
|
CA
|
A:ASP258
|
4.3
|
30.2
|
1.0
|
HBV
|
B:OZ3614
|
4.3
|
33.2
|
1.0
|
CB
|
A:ASP258
|
4.3
|
29.7
|
1.0
|
OD2
|
A:ASP258
|
4.4
|
29.3
|
1.0
|
HB3
|
A:ASP258
|
4.4
|
35.7
|
1.0
|
O
|
A:SER302
|
4.4
|
28.6
|
1.0
|
NBU
|
B:OZ3614
|
4.4
|
28.8
|
1.0
|
HB2
|
A:ASP301
|
4.5
|
33.9
|
1.0
|
OD2
|
A:ASP306
|
4.5
|
28.2
|
1.0
|
O
|
A:HOH871
|
4.5
|
30.9
|
1.0
|
HG2
|
A:GLU331
|
4.6
|
33.3
|
1.0
|
O
|
A:SER293
|
4.6
|
26.4
|
1.0
|
CB
|
A:ASP306
|
4.6
|
25.5
|
1.0
|
CA
|
A:GLY294
|
4.6
|
26.9
|
1.0
|
HG3
|
A:GLU331
|
4.7
|
33.3
|
1.0
|
HB3
|
A:CYS303
|
4.7
|
29.6
|
1.0
|
HB3
|
A:ASP306
|
4.7
|
30.6
|
1.0
|
O
|
A:GLU257
|
4.7
|
29.6
|
1.0
|
H
|
A:ASN295
|
4.7
|
33.7
|
1.0
|
O
|
A:PRO256
|
4.7
|
28.2
|
1.0
|
HA2
|
A:GLY294
|
4.7
|
32.3
|
1.0
|
CA
|
A:CYS303
|
4.8
|
27.3
|
1.0
|
N
|
A:GLY296
|
4.8
|
29.1
|
1.0
|
C
|
A:SER302
|
4.9
|
27.4
|
1.0
|
CBV
|
B:OZ3614
|
4.9
|
27.6
|
1.0
|
N
|
A:ASP258
|
5.0
|
31.2
|
1.0
|
CA
|
A:GLY296
|
5.0
|
28.3
|
1.0
|
HB3
|
A:GLU331
|
5.0
|
33.4
|
1.0
|
|
Reference:
R.W.Lange,
K.Bloch,
M.R.Heindl,
J.Wollenhaupt,
M.S.Weiss,
H.Brandstetter,
G.Klebe,
F.H.Falcone,
E.Bottcher-Friebertshauser,
S.O.Dahms,
T.Steinmetzer.
Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors. Chemmedchem 00057 2024.
ISSN: ESSN 1860-7187
PubMed: 38385828
DOI: 10.1002/CMDC.202400057
Page generated: Fri Jul 19 11:07:55 2024
|