Calcium in PDB 1r64: The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Enzymatic activity of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
All present enzymatic activity of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor:
3.4.21.61;
Protein crystallography data
The structure of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor, PDB code: 1r64
was solved by
T.Holyoak,
C.A.Kettner,
G.A.Petsko,
R.S.Fuller,
D.Ringe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.541,
113.541,
364.971,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.7 /
23.4
|
Other elements in 1r64:
The structure of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
(pdb code 1r64). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor, PDB code: 1r64:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1r64
Go back to
Calcium Binding Sites List in 1r64
Calcium binding site 1 out
of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca700
b:18.7
occ:1.00
|
OE1
|
A:GLU350
|
2.3
|
15.5
|
1.0
|
OD2
|
A:ASP320
|
2.4
|
16.9
|
1.0
|
OD2
|
A:ASP277
|
2.4
|
21.1
|
1.0
|
O
|
A:HOH1128
|
2.4
|
10.6
|
1.0
|
O
|
A:HOH1129
|
2.4
|
10.7
|
1.0
|
OE2
|
A:GLU350
|
2.5
|
17.2
|
1.0
|
O
|
A:HOH1130
|
2.6
|
21.5
|
1.0
|
CD
|
A:GLU350
|
2.7
|
15.7
|
1.0
|
CG
|
A:ASP320
|
3.2
|
17.5
|
1.0
|
CG
|
A:ASP277
|
3.4
|
20.9
|
1.0
|
OD1
|
A:ASP320
|
3.8
|
17.5
|
1.0
|
NH2
|
C:BOR5
|
3.8
|
17.1
|
1.0
|
CB
|
A:ASP277
|
4.1
|
18.6
|
1.0
|
CA
|
A:ASP277
|
4.2
|
18.4
|
1.0
|
CB
|
A:ASP320
|
4.2
|
18.6
|
1.0
|
CG
|
A:GLU350
|
4.2
|
14.9
|
1.0
|
OD1
|
A:ASP277
|
4.2
|
21.4
|
1.0
|
CA
|
A:GLY313
|
4.4
|
18.5
|
1.0
|
O
|
A:SER312
|
4.4
|
19.4
|
1.0
|
CZ
|
C:BOR5
|
4.5
|
17.8
|
1.0
|
O
|
A:ASN321
|
4.6
|
16.2
|
1.0
|
OD1
|
A:ASP325
|
4.7
|
17.8
|
1.0
|
CB
|
A:ASP325
|
4.7
|
17.3
|
1.0
|
O
|
A:HOH958
|
4.7
|
14.5
|
1.0
|
O
|
A:HOH986
|
4.7
|
22.0
|
1.0
|
O
|
A:PRO275
|
4.8
|
19.5
|
1.0
|
O
|
A:ALA276
|
4.8
|
17.5
|
1.0
|
C
|
A:ASN321
|
4.9
|
18.4
|
1.0
|
CB
|
A:GLU350
|
4.9
|
14.3
|
1.0
|
N
|
A:ASP277
|
5.0
|
17.8
|
1.0
|
CA
|
A:CYS322
|
5.0
|
18.4
|
1.0
|
NE
|
C:BOR5
|
5.0
|
19.3
|
1.0
|
N
|
A:GLY315
|
5.0
|
17.2
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1r64
Go back to
Calcium Binding Sites List in 1r64
Calcium binding site 2 out
of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:24.6
occ:1.00
|
O
|
A:LYS224
|
2.3
|
24.6
|
1.0
|
O
|
A:PHE229
|
2.3
|
30.5
|
1.0
|
OD1
|
A:ASP135
|
2.3
|
24.6
|
1.0
|
O
|
A:GLY231
|
2.4
|
24.0
|
1.0
|
OD1
|
A:ASP184
|
2.4
|
23.8
|
1.0
|
OD1
|
A:ASN227
|
2.5
|
30.0
|
1.0
|
OD2
|
A:ASP184
|
2.7
|
25.3
|
1.0
|
CG
|
A:ASP184
|
2.9
|
24.0
|
1.0
|
CG
|
A:ASP135
|
3.4
|
25.5
|
1.0
|
C
|
A:LYS224
|
3.5
|
24.9
|
1.0
|
C
|
A:PHE229
|
3.5
|
31.0
|
1.0
|
CG
|
A:ASN227
|
3.6
|
28.6
|
1.0
|
C
|
A:GLY231
|
3.6
|
24.6
|
1.0
|
ND2
|
A:ASN227
|
4.0
|
30.4
|
1.0
|
CB
|
A:ASP135
|
4.1
|
25.9
|
1.0
|
N
|
A:PHE229
|
4.2
|
32.1
|
1.0
|
N
|
A:GLY231
|
4.2
|
27.7
|
1.0
|
CA
|
A:PHE229
|
4.2
|
30.8
|
1.0
|
C
|
A:CYS230
|
4.2
|
28.8
|
1.0
|
CB
|
A:PHE229
|
4.3
|
30.3
|
1.0
|
OD2
|
A:ASP135
|
4.3
|
25.0
|
1.0
|
CA
|
A:GLY231
|
4.4
|
25.9
|
1.0
|
CA
|
A:LYS224
|
4.4
|
24.5
|
1.0
|
O
|
A:CYS230
|
4.4
|
28.1
|
1.0
|
N
|
A:LYS225
|
4.4
|
25.6
|
1.0
|
CB
|
A:ASP184
|
4.4
|
22.9
|
1.0
|
CA
|
A:LYS225
|
4.4
|
26.9
|
1.0
|
N
|
A:LYS224
|
4.5
|
24.8
|
1.0
|
N
|
A:CYS230
|
4.5
|
30.0
|
1.0
|
CB
|
A:LYS224
|
4.6
|
25.3
|
1.0
|
N
|
A:VAL232
|
4.7
|
23.1
|
1.0
|
N
|
A:ASN227
|
4.7
|
30.8
|
1.0
|
CA
|
A:CYS230
|
4.8
|
29.6
|
1.0
|
CB
|
A:ASN227
|
4.9
|
29.8
|
1.0
|
CA
|
A:VAL232
|
4.9
|
22.8
|
1.0
|
C
|
A:LYS225
|
4.9
|
28.9
|
1.0
|
C
|
A:ALA223
|
4.9
|
24.7
|
1.0
|
CG2
|
A:VAL232
|
4.9
|
25.5
|
1.0
|
N
|
A:GLY226
|
4.9
|
30.4
|
1.0
|
CD2
|
A:PHE229
|
5.0
|
29.1
|
1.0
|
O
|
A:HOH978
|
5.0
|
23.1
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1r64
Go back to
Calcium Binding Sites List in 1r64
Calcium binding site 3 out
of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:23.1
occ:1.00
|
O
|
A:HOH959
|
2.6
|
16.3
|
1.0
|
O
|
A:SER333
|
2.6
|
16.8
|
1.0
|
O
|
A:SER330
|
2.7
|
17.9
|
1.0
|
O
|
A:THR328
|
2.7
|
17.1
|
1.0
|
OG
|
A:SER333
|
2.9
|
19.0
|
1.0
|
OG1
|
A:THR335
|
2.9
|
18.1
|
1.0
|
C
|
A:SER333
|
3.4
|
17.1
|
1.0
|
C
|
A:THR328
|
3.7
|
16.8
|
1.0
|
O
|
A:HOH913
|
3.7
|
9.3
|
1.0
|
N
|
A:THR335
|
3.7
|
15.1
|
1.0
|
CE
|
A:MET555
|
3.8
|
11.4
|
1.0
|
C
|
A:SER330
|
3.9
|
19.4
|
1.0
|
CB
|
A:THR335
|
3.9
|
16.6
|
1.0
|
CB
|
A:SER333
|
4.0
|
17.6
|
1.0
|
N
|
A:SER330
|
4.0
|
17.7
|
1.0
|
CA
|
A:SER333
|
4.1
|
15.9
|
1.0
|
N
|
A:ILE334
|
4.1
|
15.8
|
1.0
|
O
|
A:ALA354
|
4.3
|
19.2
|
1.0
|
C
|
A:ILE334
|
4.3
|
16.2
|
1.0
|
N
|
A:SER333
|
4.3
|
16.3
|
1.0
|
CA
|
A:ILE334
|
4.3
|
15.8
|
1.0
|
CA
|
A:THR335
|
4.4
|
16.1
|
1.0
|
O
|
A:TYR327
|
4.4
|
16.9
|
1.0
|
CA
|
A:THR328
|
4.4
|
16.6
|
1.0
|
N
|
A:ASN329
|
4.5
|
16.5
|
1.0
|
C
|
A:ASN329
|
4.5
|
16.9
|
1.0
|
CA
|
A:ASN329
|
4.5
|
17.5
|
1.0
|
CA
|
A:SER330
|
4.6
|
18.2
|
1.0
|
N
|
A:ILE331
|
4.9
|
18.3
|
1.0
|
CB
|
A:ALA354
|
4.9
|
18.0
|
1.0
|
CA
|
A:ILE331
|
4.9
|
18.3
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1r64
Go back to
Calcium Binding Sites List in 1r64
Calcium binding site 4 out
of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca700
b:17.9
occ:1.00
|
O
|
B:HOH1950
|
2.3
|
14.2
|
1.0
|
OD2
|
B:ASP277
|
2.3
|
22.7
|
1.0
|
O
|
B:HOH2029
|
2.3
|
21.4
|
1.0
|
OE1
|
B:GLU350
|
2.4
|
22.5
|
1.0
|
OD2
|
B:ASP320
|
2.4
|
22.2
|
1.0
|
OE2
|
B:GLU350
|
2.4
|
22.0
|
1.0
|
O
|
B:HOH2003
|
2.4
|
15.7
|
1.0
|
CD
|
B:GLU350
|
2.7
|
20.2
|
1.0
|
CG
|
B:ASP277
|
3.3
|
21.4
|
1.0
|
CG
|
B:ASP320
|
3.3
|
20.7
|
1.0
|
NH2
|
D:BOR5
|
3.7
|
19.9
|
1.0
|
OD1
|
B:ASP320
|
3.9
|
17.8
|
1.0
|
CB
|
B:ASP277
|
4.0
|
19.6
|
1.0
|
CA
|
B:ASP277
|
4.1
|
18.3
|
1.0
|
OD1
|
B:ASP277
|
4.1
|
21.2
|
1.0
|
CG
|
B:GLU350
|
4.2
|
19.8
|
1.0
|
O
|
B:HOH1919
|
4.2
|
19.6
|
1.0
|
O
|
B:SER312
|
4.3
|
19.4
|
1.0
|
CB
|
B:ASP320
|
4.3
|
18.4
|
1.0
|
CA
|
B:GLY313
|
4.4
|
18.7
|
1.0
|
CZ
|
D:BOR5
|
4.5
|
18.8
|
1.0
|
OD1
|
B:ASP325
|
4.6
|
19.2
|
1.0
|
O
|
B:PRO275
|
4.7
|
21.0
|
1.0
|
O
|
B:ASN321
|
4.7
|
19.9
|
1.0
|
CB
|
B:ASP325
|
4.7
|
18.3
|
1.0
|
O
|
B:HOH2001
|
4.8
|
31.4
|
1.0
|
O
|
B:ALA276
|
4.8
|
19.1
|
1.0
|
N
|
B:ASP277
|
4.9
|
18.2
|
1.0
|
NE
|
D:BOR5
|
4.9
|
19.9
|
1.0
|
N
|
B:GLY315
|
4.9
|
16.7
|
1.0
|
CB
|
B:GLU350
|
4.9
|
16.7
|
1.0
|
C
|
B:ASN321
|
5.0
|
19.3
|
1.0
|
CA
|
B:CYS322
|
5.0
|
18.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1r64
Go back to
Calcium Binding Sites List in 1r64
Calcium binding site 5 out
of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca701
b:37.2
occ:1.00
|
OD1
|
B:ASP135
|
2.3
|
32.3
|
1.0
|
O
|
B:LYS224
|
2.3
|
33.9
|
1.0
|
OD1
|
B:ASP184
|
2.3
|
35.0
|
1.0
|
O
|
B:PHE229
|
2.3
|
39.6
|
1.0
|
O
|
B:GLY231
|
2.4
|
36.4
|
1.0
|
OD1
|
B:ASN227
|
2.5
|
31.8
|
1.0
|
OD2
|
B:ASP184
|
2.6
|
36.4
|
1.0
|
CG
|
B:ASP184
|
2.8
|
36.7
|
1.0
|
CG
|
B:ASP135
|
3.4
|
33.9
|
1.0
|
C
|
B:PHE229
|
3.4
|
40.0
|
1.0
|
C
|
B:LYS224
|
3.5
|
34.3
|
1.0
|
CG
|
B:ASN227
|
3.5
|
35.2
|
1.0
|
C
|
B:GLY231
|
3.6
|
36.2
|
1.0
|
ND2
|
B:ASN227
|
3.9
|
33.1
|
1.0
|
N
|
B:GLY231
|
4.1
|
37.2
|
1.0
|
CB
|
B:ASP135
|
4.1
|
35.3
|
1.0
|
N
|
B:PHE229
|
4.1
|
41.0
|
1.0
|
CA
|
B:PHE229
|
4.1
|
40.1
|
1.0
|
CB
|
B:PHE229
|
4.2
|
38.7
|
1.0
|
C
|
B:CYS230
|
4.3
|
37.1
|
1.0
|
CA
|
B:GLY231
|
4.3
|
36.5
|
1.0
|
OD2
|
B:ASP135
|
4.3
|
33.8
|
1.0
|
CB
|
B:ASP184
|
4.3
|
35.5
|
1.0
|
CA
|
B:LYS224
|
4.4
|
33.8
|
1.0
|
N
|
B:LYS225
|
4.4
|
34.3
|
1.0
|
CA
|
B:LYS225
|
4.5
|
35.0
|
1.0
|
N
|
B:CYS230
|
4.5
|
39.2
|
1.0
|
N
|
B:LYS224
|
4.5
|
34.0
|
1.0
|
O
|
B:CYS230
|
4.6
|
36.3
|
1.0
|
CB
|
B:LYS224
|
4.6
|
34.7
|
1.0
|
N
|
B:VAL232
|
4.7
|
35.3
|
1.0
|
O
|
B:HOH2040
|
4.7
|
30.6
|
1.0
|
N
|
B:ASN227
|
4.7
|
37.4
|
1.0
|
CA
|
B:CYS230
|
4.8
|
37.5
|
1.0
|
CB
|
B:ASN227
|
4.9
|
35.5
|
1.0
|
C
|
B:LYS225
|
4.9
|
34.6
|
1.0
|
CD2
|
B:PHE229
|
4.9
|
38.6
|
1.0
|
C
|
B:ALA223
|
4.9
|
34.5
|
1.0
|
CA
|
B:VAL232
|
4.9
|
34.4
|
1.0
|
CG2
|
B:VAL232
|
5.0
|
37.5
|
1.0
|
N
|
B:GLY226
|
5.0
|
34.2
|
1.0
|
CB
|
B:CYS230
|
5.0
|
36.5
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1r64
Go back to
Calcium Binding Sites List in 1r64
Calcium binding site 6 out
of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:20.3
occ:1.00
|
O
|
B:SER330
|
2.6
|
16.6
|
1.0
|
O
|
B:SER333
|
2.6
|
19.0
|
1.0
|
O
|
B:THR328
|
2.8
|
16.7
|
1.0
|
O
|
B:HOH1911
|
2.8
|
15.9
|
1.0
|
OG
|
B:SER333
|
2.9
|
18.7
|
1.0
|
OG1
|
B:THR335
|
2.9
|
19.2
|
1.0
|
C
|
B:SER333
|
3.4
|
19.9
|
1.0
|
C
|
B:THR328
|
3.6
|
16.3
|
1.0
|
O
|
B:HOH1991
|
3.7
|
24.8
|
1.0
|
CE
|
B:MET555
|
3.8
|
14.8
|
1.0
|
C
|
B:SER330
|
3.8
|
17.7
|
1.0
|
N
|
B:THR335
|
3.8
|
23.0
|
1.0
|
CB
|
B:THR335
|
4.0
|
19.6
|
1.0
|
N
|
B:SER330
|
4.0
|
18.5
|
1.0
|
CB
|
B:SER333
|
4.0
|
18.6
|
1.0
|
CA
|
B:SER333
|
4.1
|
19.7
|
1.0
|
N
|
B:ILE334
|
4.2
|
20.8
|
1.0
|
N
|
B:SER333
|
4.2
|
20.0
|
1.0
|
O
|
B:TYR327
|
4.3
|
19.7
|
1.0
|
O
|
B:ALA354
|
4.3
|
22.4
|
1.0
|
C
|
B:ASN329
|
4.4
|
19.1
|
1.0
|
C
|
B:ILE334
|
4.4
|
22.9
|
1.0
|
CA
|
B:THR328
|
4.4
|
16.2
|
1.0
|
CA
|
B:ILE334
|
4.4
|
20.9
|
1.0
|
N
|
B:ASN329
|
4.4
|
15.4
|
1.0
|
CA
|
B:THR335
|
4.4
|
19.9
|
1.0
|
CA
|
B:ASN329
|
4.5
|
17.4
|
1.0
|
CA
|
B:SER330
|
4.5
|
17.7
|
1.0
|
N
|
B:ILE331
|
4.8
|
17.9
|
1.0
|
CA
|
B:ILE331
|
4.9
|
19.0
|
1.0
|
CB
|
B:ALA354
|
4.9
|
20.8
|
1.0
|
|
Reference:
T.Holyoak,
C.A.Kettner,
G.A.Petsko,
R.S.Fuller,
D.Ringe.
Structural Basis For Differences in Substrate Selectivity in KEX2 and Furin Protein Convertases Biochemistry V. 43 2412 2004.
ISSN: ISSN 0006-2960
PubMed: 14992578
DOI: 10.1021/BI035849H
Page generated: Thu Jul 11 22:03:45 2024
|