Calcium in PDB 7qp3: Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
Protein crystallography data
The structure of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide, PDB code: 7qp3
was solved by
C.Wilkens,
J.Qiu,
A.S.Meyer,
J.P.Morth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.93 /
1.85
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.08,
67.49,
130.61,
90,
90,
90
|
R / Rfree (%)
|
14.9 /
20
|
Other elements in 7qp3:
The structure of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
(pdb code 7qp3). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Pseudogymnoascus Pannorum M36 Protease Without the Propeptide, PDB code: 7qp3:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 7qp3
Go back to
Calcium Binding Sites List in 7qp3
Calcium binding site 1 out
of 5 in the Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:20.6
occ:1.00
|
OD1
|
A:ASN55
|
2.3
|
24.4
|
1.0
|
O
|
A:SER61
|
2.4
|
21.2
|
1.0
|
OD1
|
A:ASP59
|
2.4
|
23.4
|
1.0
|
OD1
|
A:ASP65
|
2.4
|
23.5
|
1.0
|
OD2
|
A:ASP57
|
2.4
|
23.3
|
1.0
|
OD1
|
A:ASN64
|
2.5
|
23.3
|
1.0
|
OD2
|
A:ASP65
|
2.5
|
28.6
|
1.0
|
OD1
|
A:ASP57
|
2.5
|
24.1
|
1.0
|
CG
|
A:ASP65
|
2.8
|
23.9
|
1.0
|
CG
|
A:ASP57
|
2.8
|
26.8
|
1.0
|
CG
|
A:ASP59
|
3.4
|
27.6
|
1.0
|
CG
|
A:ASN64
|
3.5
|
28.8
|
1.0
|
CG
|
A:ASN55
|
3.5
|
25.9
|
1.0
|
C
|
A:SER61
|
3.5
|
23.8
|
1.0
|
HD22
|
A:ASN64
|
3.5
|
29.1
|
1.0
|
HB3
|
A:SER61
|
3.7
|
35.8
|
1.0
|
OD2
|
A:ASP59
|
3.8
|
26.6
|
1.0
|
HA
|
A:TRP62
|
3.8
|
27.6
|
1.0
|
H
|
A:SER61
|
3.8
|
33.2
|
1.0
|
HA
|
A:ASN55
|
3.9
|
25.1
|
1.0
|
H
|
A:ASP59
|
3.9
|
26.1
|
1.0
|
ND2
|
A:ASN64
|
3.9
|
24.3
|
1.0
|
HD21
|
A:ASN55
|
4.1
|
27.0
|
1.0
|
H
|
A:ASN64
|
4.1
|
25.6
|
1.0
|
ND2
|
A:ASN55
|
4.2
|
22.5
|
1.0
|
CB
|
A:ASP65
|
4.3
|
20.8
|
1.0
|
O
|
A:HOH678
|
4.3
|
21.1
|
1.0
|
CA
|
A:SER61
|
4.3
|
23.5
|
1.0
|
N
|
A:SER61
|
4.4
|
27.7
|
1.0
|
CB
|
A:ASP57
|
4.4
|
22.1
|
1.0
|
O
|
A:HOH589
|
4.4
|
22.6
|
1.0
|
O
|
A:HOH557
|
4.4
|
30.1
|
1.0
|
CB
|
A:SER61
|
4.4
|
29.9
|
1.0
|
H
|
A:ASP57
|
4.4
|
26.0
|
1.0
|
N
|
A:TRP62
|
4.5
|
22.0
|
1.0
|
CA
|
A:TRP62
|
4.6
|
23.1
|
1.0
|
HG
|
A:SER61
|
4.6
|
33.8
|
1.0
|
CB
|
A:ASN55
|
4.6
|
18.3
|
1.0
|
N
|
A:ASP59
|
4.6
|
21.8
|
1.0
|
C
|
A:ASN64
|
4.6
|
28.6
|
1.0
|
CA
|
A:ASN55
|
4.6
|
20.9
|
1.0
|
CB
|
A:ASP59
|
4.6
|
24.3
|
1.0
|
HB3
|
A:ASP57
|
4.7
|
26.5
|
1.0
|
HB2
|
A:ASP65
|
4.7
|
24.9
|
1.0
|
O
|
A:ASN64
|
4.7
|
24.0
|
1.0
|
HB3
|
A:ASP65
|
4.7
|
24.9
|
1.0
|
O
|
A:ASP59
|
4.7
|
21.5
|
1.0
|
HD21
|
A:ASN64
|
4.8
|
29.1
|
1.0
|
C
|
A:ASP59
|
4.8
|
22.0
|
1.0
|
N
|
A:ASP65
|
4.8
|
23.8
|
1.0
|
CB
|
A:ASN64
|
4.8
|
31.7
|
1.0
|
HB2
|
A:ASP57
|
4.8
|
26.5
|
1.0
|
HB2
|
A:ASN55
|
4.9
|
22.0
|
1.0
|
OG
|
A:SER61
|
4.9
|
28.2
|
1.0
|
N
|
A:ASN64
|
4.9
|
21.4
|
1.0
|
CA
|
A:ASP59
|
4.9
|
25.3
|
1.0
|
HA
|
A:ASP65
|
4.9
|
32.4
|
1.0
|
CA
|
A:ASP65
|
4.9
|
27.0
|
1.0
|
HB3
|
A:ASP59
|
4.9
|
29.2
|
1.0
|
|
Calcium binding site 2 out
of 5 in 7qp3
Go back to
Calcium Binding Sites List in 7qp3
Calcium binding site 2 out
of 5 in the Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca405
b:17.2
occ:1.00
|
OD1
|
A:ASP155
|
2.3
|
23.1
|
1.0
|
O
|
A:LYS130
|
2.3
|
17.8
|
1.0
|
O
|
A:ASN119
|
2.3
|
16.5
|
1.0
|
OD2
|
A:ASP133
|
2.4
|
17.6
|
1.0
|
O
|
A:HOH593
|
2.4
|
20.1
|
1.0
|
O
|
A:HOH617
|
2.4
|
19.2
|
1.0
|
OD1
|
A:ASP133
|
2.5
|
21.4
|
1.0
|
CG
|
A:ASP133
|
2.8
|
20.8
|
1.0
|
CG
|
A:ASP155
|
3.4
|
24.7
|
1.0
|
HH12
|
A:ARG193
|
3.4
|
23.6
|
1.0
|
HD21
|
A:ASN124
|
3.4
|
25.8
|
1.0
|
C
|
A:ASN119
|
3.5
|
18.4
|
1.0
|
C
|
A:LYS130
|
3.5
|
22.6
|
1.0
|
H
|
A:GLY156
|
3.5
|
23.7
|
1.0
|
H
|
A:GLU121
|
3.6
|
22.2
|
1.0
|
HA
|
A:PHE120
|
3.7
|
21.5
|
1.0
|
HA2
|
A:GLY131
|
3.8
|
23.1
|
1.0
|
H
|
A:LYS130
|
3.8
|
25.2
|
1.0
|
OD2
|
A:ASP155
|
3.8
|
20.3
|
1.0
|
NH1
|
A:ARG193
|
3.9
|
19.7
|
1.0
|
HH11
|
A:ARG193
|
4.0
|
23.6
|
1.0
|
N
|
A:ASN119
|
4.2
|
16.7
|
1.0
|
HA2
|
A:GLY118
|
4.2
|
23.8
|
1.0
|
HA
|
A:ASP155
|
4.2
|
22.1
|
1.0
|
C
|
A:GLY118
|
4.2
|
18.1
|
1.0
|
ND2
|
A:ASN124
|
4.3
|
21.6
|
1.0
|
N
|
A:PHE120
|
4.3
|
18.8
|
1.0
|
HB2
|
A:LYS130
|
4.3
|
28.4
|
1.0
|
OD1
|
A:ASN119
|
4.3
|
16.4
|
1.0
|
N
|
A:GLY156
|
4.3
|
19.8
|
1.0
|
H
|
A:ASN119
|
4.3
|
20.0
|
1.0
|
CB
|
A:ASP133
|
4.3
|
18.5
|
1.0
|
N
|
A:GLU121
|
4.4
|
18.5
|
1.0
|
CA
|
A:PHE120
|
4.4
|
18.0
|
1.0
|
N
|
A:LYS130
|
4.4
|
21.0
|
1.0
|
N
|
A:GLY131
|
4.4
|
19.7
|
1.0
|
CA
|
A:GLY131
|
4.5
|
19.3
|
1.0
|
CA
|
A:ASN119
|
4.5
|
17.1
|
1.0
|
O
|
A:GLY118
|
4.5
|
19.5
|
1.0
|
CA
|
A:LYS130
|
4.5
|
19.8
|
1.0
|
OD1
|
A:ASN124
|
4.6
|
18.2
|
1.0
|
HB3
|
A:ASP133
|
4.6
|
22.2
|
1.0
|
O
|
A:GLU121
|
4.6
|
16.9
|
1.0
|
CB
|
A:ASP155
|
4.7
|
22.6
|
1.0
|
HA2
|
A:GLY156
|
4.7
|
27.7
|
1.0
|
HB2
|
A:ASP133
|
4.7
|
22.2
|
1.0
|
CA
|
A:GLY118
|
4.8
|
19.9
|
1.0
|
CA
|
A:ASP155
|
4.8
|
18.4
|
1.0
|
O
|
A:GLY131
|
4.8
|
18.5
|
1.0
|
HD22
|
A:ASN124
|
4.9
|
25.8
|
1.0
|
CG
|
A:ASN124
|
4.9
|
23.4
|
1.0
|
C
|
A:GLY131
|
4.9
|
22.0
|
1.0
|
C
|
A:PHE120
|
4.9
|
15.9
|
1.0
|
CB
|
A:LYS130
|
4.9
|
23.7
|
1.0
|
H
|
A:ASP133
|
4.9
|
23.6
|
1.0
|
O
|
A:GLU115
|
5.0
|
18.8
|
1.0
|
CZ
|
A:ARG193
|
5.0
|
19.4
|
1.0
|
|
Calcium binding site 3 out
of 5 in 7qp3
Go back to
Calcium Binding Sites List in 7qp3
Calcium binding site 3 out
of 5 in the Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:47.0
occ:1.00
|
O
|
A:HOH508
|
1.9
|
31.2
|
1.0
|
O
|
A:HOH560
|
2.0
|
28.7
|
1.0
|
O
|
A:HOH506
|
2.1
|
17.9
|
1.0
|
OE1
|
A:GLU121
|
2.1
|
22.4
|
1.0
|
OE2
|
A:GLU115
|
2.2
|
26.5
|
1.0
|
CD
|
A:GLU121
|
2.8
|
23.4
|
1.0
|
OE2
|
A:GLU121
|
2.8
|
18.3
|
1.0
|
CD
|
A:GLU115
|
3.2
|
25.1
|
1.0
|
HG3
|
A:GLU115
|
3.3
|
28.2
|
1.0
|
HG2
|
A:GLU115
|
3.3
|
28.2
|
1.0
|
CG
|
A:GLU115
|
3.5
|
23.5
|
1.0
|
O
|
A:HOH727
|
3.6
|
29.6
|
1.0
|
O
|
A:HOH750
|
3.6
|
33.9
|
1.0
|
HA
|
A:ASN124
|
3.6
|
32.7
|
1.0
|
OE1
|
A:GLU31
|
3.7
|
23.5
|
1.0
|
HD22
|
A:ASN48
|
3.7
|
25.9
|
1.0
|
HD21
|
A:ASN48
|
3.8
|
25.9
|
1.0
|
HE2
|
A:HIS109
|
3.8
|
26.9
|
1.0
|
OE2
|
A:GLU31
|
3.8
|
29.2
|
1.0
|
O
|
A:HOH584
|
3.9
|
19.4
|
1.0
|
O
|
A:ASN123
|
4.0
|
17.4
|
1.0
|
ND2
|
A:ASN48
|
4.1
|
21.6
|
1.0
|
CD
|
A:GLU31
|
4.2
|
30.5
|
1.0
|
CG
|
A:GLU121
|
4.2
|
21.2
|
1.0
|
O
|
A:ALA29
|
4.2
|
23.3
|
1.0
|
HD2
|
A:HIS109
|
4.3
|
21.9
|
1.0
|
OE1
|
A:GLU115
|
4.3
|
25.7
|
1.0
|
HE2
|
A:HIS105
|
4.4
|
24.7
|
1.0
|
NE2
|
A:HIS109
|
4.4
|
22.4
|
1.0
|
HD21
|
A:ASN119
|
4.4
|
23.6
|
1.0
|
O
|
A:ASN124
|
4.5
|
18.2
|
1.0
|
CA
|
A:ASN124
|
4.5
|
27.3
|
1.0
|
HB3
|
A:GLU121
|
4.5
|
20.6
|
1.0
|
HB2
|
A:GLU121
|
4.6
|
20.6
|
1.0
|
HG2
|
A:GLU121
|
4.6
|
25.4
|
1.0
|
CD2
|
A:HIS109
|
4.6
|
18.3
|
1.0
|
C
|
A:ASN124
|
4.7
|
21.1
|
1.0
|
HB3
|
A:ASN125
|
4.7
|
24.9
|
1.0
|
CB
|
A:GLU121
|
4.7
|
17.2
|
1.0
|
HG3
|
A:GLU121
|
4.8
|
25.4
|
1.0
|
HB2
|
A:ASN125
|
4.9
|
24.9
|
1.0
|
HE2
|
A:PHE32
|
4.9
|
24.8
|
1.0
|
HE1
|
A:HIS105
|
5.0
|
22.1
|
1.0
|
CB
|
A:GLU115
|
5.0
|
20.5
|
1.0
|
|
Calcium binding site 4 out
of 5 in 7qp3
Go back to
Calcium Binding Sites List in 7qp3
Calcium binding site 4 out
of 5 in the Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca407
b:33.1
occ:1.00
|
O
|
A:GLY197
|
2.2
|
19.1
|
1.0
|
O
|
A:THR195
|
2.3
|
18.1
|
1.0
|
O
|
A:ASN200
|
2.3
|
22.4
|
0.5
|
O
|
A:ASN200
|
2.3
|
22.4
|
0.5
|
O
|
A:ASN192
|
2.4
|
16.9
|
1.0
|
O
|
A:ARG193
|
2.4
|
18.1
|
1.0
|
C
|
A:ARG193
|
3.1
|
20.7
|
1.0
|
C
|
A:GLY197
|
3.1
|
20.2
|
1.0
|
HA
|
A:ARG193
|
3.2
|
26.2
|
1.0
|
C
|
A:THR195
|
3.3
|
20.0
|
1.0
|
H
|
A:GLY197
|
3.3
|
25.8
|
1.0
|
N
|
A:GLY197
|
3.4
|
21.6
|
1.0
|
C
|
A:ASN192
|
3.5
|
17.4
|
1.0
|
C
|
A:ASN200
|
3.5
|
25.1
|
0.5
|
C
|
A:ASN200
|
3.5
|
25.1
|
0.5
|
H
|
A:ASN200
|
3.5
|
27.0
|
0.5
|
CA
|
A:ARG193
|
3.5
|
21.9
|
1.0
|
HA
|
A:PRO198
|
3.6
|
28.2
|
1.0
|
H
|
A:ASN200
|
3.6
|
27.1
|
0.5
|
N
|
A:THR195
|
3.7
|
18.1
|
1.0
|
HA
|
A:THR201
|
3.7
|
33.1
|
1.0
|
H
|
A:THR195
|
3.8
|
21.6
|
1.0
|
C
|
A:GLY196
|
3.8
|
25.4
|
1.0
|
HB2
|
A:ASN200
|
3.8
|
30.5
|
0.5
|
CA
|
A:GLY197
|
3.9
|
19.9
|
1.0
|
HG22
|
A:THR201
|
3.9
|
28.3
|
1.0
|
C
|
A:LEU194
|
3.9
|
17.8
|
1.0
|
N
|
A:PRO198
|
4.0
|
21.1
|
1.0
|
N
|
A:ARG193
|
4.0
|
16.7
|
1.0
|
HB3
|
A:ASN200
|
4.0
|
30.6
|
0.5
|
N
|
A:LEU194
|
4.0
|
17.6
|
1.0
|
CA
|
A:THR195
|
4.1
|
17.3
|
1.0
|
CA
|
A:PRO198
|
4.1
|
23.5
|
1.0
|
N
|
A:GLY196
|
4.1
|
18.8
|
1.0
|
HA3
|
A:GLY196
|
4.2
|
30.2
|
1.0
|
N
|
A:ASN200
|
4.2
|
22.6
|
0.5
|
O
|
A:HOH721
|
4.2
|
18.8
|
1.0
|
N
|
A:ASN200
|
4.2
|
22.6
|
0.5
|
CA
|
A:GLY196
|
4.3
|
25.2
|
1.0
|
CA
|
A:ASN200
|
4.3
|
24.0
|
0.5
|
HG23
|
A:THR201
|
4.3
|
28.3
|
1.0
|
O
|
A:LEU194
|
4.3
|
18.3
|
1.0
|
CA
|
A:ASN200
|
4.3
|
24.0
|
0.5
|
HB
|
A:THR195
|
4.4
|
22.8
|
1.0
|
O
|
A:GLY196
|
4.4
|
21.9
|
1.0
|
HA2
|
A:GLY197
|
4.4
|
23.8
|
1.0
|
N
|
A:THR201
|
4.4
|
23.9
|
1.0
|
CA
|
A:LEU194
|
4.5
|
17.6
|
1.0
|
CA
|
A:THR201
|
4.5
|
27.6
|
1.0
|
C
|
A:PRO198
|
4.5
|
25.8
|
1.0
|
CG2
|
A:THR201
|
4.5
|
23.6
|
1.0
|
CB
|
A:ASN200
|
4.5
|
25.5
|
0.5
|
HA3
|
A:GLY197
|
4.6
|
23.8
|
1.0
|
HB2
|
A:CYS203
|
4.6
|
28.8
|
1.0
|
HA
|
A:ASN192
|
4.6
|
21.7
|
1.0
|
H
|
A:LEU194
|
4.6
|
21.1
|
1.0
|
HA
|
A:LEU194
|
4.6
|
21.1
|
1.0
|
CB
|
A:ASN200
|
4.6
|
25.6
|
0.5
|
CA
|
A:ASN192
|
4.7
|
18.1
|
1.0
|
CB
|
A:THR195
|
4.8
|
19.0
|
1.0
|
H
|
A:ARG193
|
4.8
|
20.0
|
1.0
|
HA
|
A:THR195
|
4.9
|
20.7
|
1.0
|
HD3
|
A:ARG193
|
4.9
|
22.2
|
1.0
|
H
|
A:GLY196
|
4.9
|
22.5
|
1.0
|
O
|
A:PRO198
|
4.9
|
21.3
|
1.0
|
CB
|
A:ARG193
|
5.0
|
17.6
|
1.0
|
N
|
A:ALA199
|
5.0
|
24.2
|
1.0
|
O
|
A:SER191
|
5.0
|
19.4
|
1.0
|
|
Calcium binding site 5 out
of 5 in 7qp3
Go back to
Calcium Binding Sites List in 7qp3
Calcium binding site 5 out
of 5 in the Pseudogymnoascus Pannorum M36 Protease Without the Propeptide
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Pseudogymnoascus Pannorum M36 Protease Without the Propeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca408
b:71.5
occ:1.00
|
OD2
|
A:ASP313
|
2.5
|
39.7
|
1.0
|
O
|
A:HOH628
|
2.6
|
33.9
|
1.0
|
HB2
|
A:SER299
|
2.8
|
51.5
|
1.0
|
HB3
|
A:SER299
|
3.1
|
51.5
|
1.0
|
CB
|
A:SER299
|
3.2
|
43.0
|
1.0
|
HB3
|
A:ALA301
|
3.3
|
47.8
|
1.0
|
OG
|
A:SER299
|
3.4
|
48.9
|
1.0
|
O
|
A:HOH520
|
3.4
|
32.3
|
1.0
|
CG
|
A:ASP313
|
3.6
|
31.8
|
1.0
|
HB2
|
A:ALA301
|
3.6
|
47.8
|
1.0
|
HD2
|
A:PHE316
|
3.6
|
27.6
|
1.0
|
HE2
|
A:PHE316
|
3.6
|
36.1
|
1.0
|
HB3
|
A:ASP313
|
3.7
|
27.8
|
1.0
|
CB
|
A:ALA301
|
3.9
|
39.9
|
1.0
|
HG
|
A:SER299
|
4.0
|
58.6
|
1.0
|
CB
|
A:ASP313
|
4.2
|
23.2
|
1.0
|
CD2
|
A:PHE316
|
4.2
|
23.1
|
1.0
|
CE2
|
A:PHE316
|
4.2
|
30.1
|
1.0
|
H
|
A:THR305
|
4.2
|
33.7
|
1.0
|
OG1
|
A:THR312
|
4.2
|
44.7
|
1.0
|
HG1
|
A:THR312
|
4.3
|
53.6
|
1.0
|
HB
|
A:THR305
|
4.3
|
34.5
|
1.0
|
H
|
A:ALA301
|
4.3
|
39.1
|
1.0
|
HA
|
A:PRO304
|
4.3
|
32.5
|
1.0
|
HB1
|
A:ALA301
|
4.4
|
47.8
|
1.0
|
OD1
|
A:ASP313
|
4.5
|
30.5
|
1.0
|
H
|
A:ASP313
|
4.6
|
32.0
|
1.0
|
OG1
|
A:THR305
|
4.7
|
38.1
|
1.0
|
HG1
|
A:THR305
|
4.7
|
45.6
|
1.0
|
CA
|
A:SER299
|
4.7
|
36.5
|
1.0
|
HB2
|
A:ASP313
|
4.7
|
27.8
|
1.0
|
O
|
A:GLN303
|
4.8
|
30.4
|
1.0
|
N
|
A:THR305
|
4.8
|
28.1
|
1.0
|
HA
|
A:SER299
|
4.9
|
43.8
|
1.0
|
CB
|
A:THR305
|
4.9
|
28.8
|
1.0
|
|
Reference:
C.Wilkens,
J.Qiu,
A.S.Meyer,
J.P.Morth.
Phaeosphaeria Nodorum M36 Protease Without the Propeptide To Be Published.
Page generated: Fri Jul 19 03:29:47 2024
|