Calcium in PDB 9etj: Mouse Cnpase Catalytic Domain with Nanobody 10E
Enzymatic activity of Mouse Cnpase Catalytic Domain with Nanobody 10E
All present enzymatic activity of Mouse Cnpase Catalytic Domain with Nanobody 10E:
3.1.4.37;
Protein crystallography data
The structure of Mouse Cnpase Catalytic Domain with Nanobody 10E, PDB code: 9etj
was solved by
S.Markusson,
A.Raasakka,
F.Opazo,
P.Kursula,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.95 /
2.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.73,
118.25,
122.45,
90,
90,
90
|
R / Rfree (%)
|
25.2 /
30.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Mouse Cnpase Catalytic Domain with Nanobody 10E
(pdb code 9etj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Mouse Cnpase Catalytic Domain with Nanobody 10E, PDB code: 9etj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 9etj
Go back to
Calcium Binding Sites List in 9etj
Calcium binding site 1 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:88.4
occ:1.00
|
O
|
C:PRO114
|
2.4
|
75.4
|
1.0
|
OD2
|
C:ASP98
|
2.6
|
76.1
|
1.0
|
OD1
|
C:ASP116
|
2.6
|
70.7
|
1.0
|
OD1
|
C:ASP96
|
2.7
|
69.8
|
1.0
|
OD1
|
A:ASP237
|
2.9
|
79.5
|
1.0
|
HE2
|
A:TYR238
|
3.5
|
94.6
|
1.0
|
HB2
|
C:ASP98
|
3.5
|
86.8
|
1.0
|
C
|
C:PRO114
|
3.5
|
74.5
|
1.0
|
CG
|
C:ASP98
|
3.7
|
73.1
|
1.0
|
CG
|
C:ASP116
|
3.7
|
70.6
|
1.0
|
CG
|
C:ASP96
|
3.7
|
69.5
|
1.0
|
HB3
|
C:PRO114
|
3.8
|
89.1
|
1.0
|
CG
|
A:ASP237
|
3.9
|
81.8
|
1.0
|
HA
|
C:PRO114
|
3.9
|
92.0
|
1.0
|
H
|
C:ASP98
|
4.0
|
86.4
|
1.0
|
OD2
|
C:ASP96
|
4.0
|
67.4
|
1.0
|
OD2
|
C:ASP116
|
4.1
|
70.9
|
1.0
|
CB
|
C:ASP98
|
4.1
|
71.5
|
1.0
|
CA
|
C:PRO114
|
4.1
|
75.8
|
1.0
|
HD2
|
A:TYR238
|
4.2
|
95.7
|
1.0
|
OD2
|
A:ASP237
|
4.2
|
82.6
|
1.0
|
HA
|
C:TYR115
|
4.3
|
87.9
|
1.0
|
CE2
|
A:TYR238
|
4.3
|
77.9
|
1.0
|
CB
|
C:PRO114
|
4.3
|
73.3
|
1.0
|
HB2
|
C:PRO114
|
4.5
|
89.1
|
1.0
|
O
|
C:TYR115
|
4.5
|
75.5
|
1.0
|
HE2
|
A:LYS240
|
4.6
|
113.5
|
1.0
|
HH12
|
C:ARG102
|
4.6
|
83.2
|
1.0
|
N
|
C:TYR115
|
4.6
|
72.7
|
1.0
|
C
|
C:TYR115
|
4.6
|
73.8
|
1.0
|
CD2
|
A:TYR238
|
4.7
|
78.8
|
1.0
|
N
|
C:ASP98
|
4.7
|
71.1
|
1.0
|
HD3
|
C:ARG102
|
4.7
|
81.4
|
1.0
|
HD11
|
A:LEU167
|
4.7
|
88.2
|
1.0
|
HA
|
C:ASP96
|
4.7
|
82.4
|
1.0
|
CA
|
C:TYR115
|
4.7
|
72.4
|
1.0
|
HE3
|
A:LYS240
|
4.8
|
113.5
|
1.0
|
HD13
|
A:LEU167
|
4.8
|
88.2
|
1.0
|
H
|
C:ASN97
|
4.8
|
84.5
|
1.0
|
HB3
|
C:ASP98
|
4.8
|
86.8
|
1.0
|
OD1
|
C:ASP98
|
4.8
|
75.8
|
1.0
|
HD2
|
C:ARG102
|
4.9
|
81.4
|
1.0
|
N
|
C:ASP116
|
5.0
|
73.0
|
1.0
|
CB
|
C:ASP96
|
5.0
|
67.0
|
1.0
|
|
Calcium binding site 2 out
of 7 in 9etj
Go back to
Calcium Binding Sites List in 9etj
Calcium binding site 2 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca202
b:73.8
occ:1.00
|
OD1
|
C:ASN97
|
2.3
|
68.9
|
1.0
|
O
|
C:ASN97
|
2.5
|
68.8
|
1.0
|
O
|
C:ASP31
|
2.6
|
74.4
|
1.0
|
CG
|
C:ASN97
|
3.5
|
70.3
|
1.0
|
C
|
C:ASN97
|
3.5
|
66.3
|
1.0
|
HA
|
C:ASN97
|
3.6
|
85.3
|
1.0
|
O
|
C:LEU99
|
3.8
|
68.7
|
1.0
|
C
|
C:ASP31
|
3.8
|
78.1
|
1.0
|
HA
|
C:ASP31
|
4.0
|
94.8
|
1.0
|
CA
|
C:ASN97
|
4.1
|
70.1
|
1.0
|
OD2
|
C:ASP101
|
4.1
|
68.2
|
1.0
|
HG3
|
C:PRO53
|
4.2
|
93.6
|
1.0
|
HB3
|
C:ASP31
|
4.3
|
92.2
|
1.0
|
CB
|
C:ASN97
|
4.4
|
69.8
|
1.0
|
HA
|
C:PHE32
|
4.4
|
93.9
|
1.0
|
HA
|
C:ASP98
|
4.4
|
81.2
|
1.0
|
CA
|
C:ASP31
|
4.4
|
78.1
|
1.0
|
ND2
|
C:ASN97
|
4.5
|
69.7
|
1.0
|
HD22
|
C:ASN97
|
4.5
|
84.7
|
1.0
|
N
|
C:ASP98
|
4.7
|
71.1
|
1.0
|
HG2
|
C:PRO53
|
4.7
|
93.6
|
1.0
|
H
|
C:LEU99
|
4.8
|
92.1
|
1.0
|
HB3
|
C:ASN97
|
4.8
|
84.9
|
1.0
|
CB
|
C:ASP31
|
4.9
|
75.9
|
1.0
|
C
|
C:LEU99
|
4.9
|
66.1
|
1.0
|
N
|
C:PHE32
|
4.9
|
77.7
|
1.0
|
CG
|
C:PRO53
|
4.9
|
77.1
|
1.0
|
HD2
|
C:PRO100
|
5.0
|
83.4
|
1.0
|
CA
|
C:ASP98
|
5.0
|
66.7
|
1.0
|
|
Calcium binding site 3 out
of 7 in 9etj
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Calcium Binding Sites List in 9etj
Calcium binding site 3 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:80.3
occ:1.00
|
O
|
D:PRO114
|
2.5
|
78.1
|
1.0
|
OD1
|
B:ASP237
|
2.6
|
86.2
|
1.0
|
OD2
|
D:ASP98
|
2.7
|
76.3
|
1.0
|
OD1
|
D:ASP116
|
2.8
|
72.9
|
1.0
|
HE2
|
B:TYR238
|
3.3
|
98.7
|
1.0
|
OD1
|
D:ASP96
|
3.3
|
70.3
|
1.0
|
HZ3
|
B:LYS240
|
3.4
|
120.7
|
1.0
|
CG
|
B:ASP237
|
3.5
|
87.0
|
1.0
|
C
|
D:PRO114
|
3.6
|
76.1
|
1.0
|
HA
|
D:PRO114
|
3.7
|
93.0
|
1.0
|
HB3
|
D:PRO114
|
3.7
|
91.4
|
1.0
|
HD2
|
B:TYR238
|
3.8
|
101.2
|
1.0
|
CG
|
D:ASP98
|
3.8
|
75.3
|
1.0
|
HB2
|
D:ASP98
|
3.8
|
88.4
|
1.0
|
OD2
|
B:ASP237
|
3.8
|
88.3
|
1.0
|
HZ1
|
B:LYS240
|
3.9
|
120.7
|
1.0
|
CG
|
D:ASP116
|
3.9
|
72.0
|
1.0
|
NZ
|
B:LYS240
|
4.0
|
99.6
|
1.0
|
CE2
|
B:TYR238
|
4.0
|
81.3
|
1.0
|
CA
|
D:PRO114
|
4.0
|
76.6
|
1.0
|
HZ2
|
B:LYS240
|
4.2
|
120.7
|
1.0
|
CG
|
D:ASP96
|
4.3
|
70.5
|
1.0
|
CB
|
D:PRO114
|
4.3
|
75.2
|
1.0
|
OD2
|
D:ASP116
|
4.3
|
74.7
|
1.0
|
CD2
|
B:TYR238
|
4.3
|
83.5
|
1.0
|
CB
|
D:ASP98
|
4.4
|
72.8
|
1.0
|
HB2
|
D:PRO114
|
4.4
|
91.4
|
1.0
|
OD2
|
D:ASP96
|
4.5
|
71.5
|
1.0
|
H
|
D:ASP98
|
4.5
|
86.4
|
1.0
|
HA
|
D:TYR115
|
4.5
|
90.3
|
1.0
|
HD11
|
B:LEU167
|
4.6
|
91.4
|
1.0
|
N
|
D:TYR115
|
4.7
|
75.2
|
1.0
|
OD1
|
D:ASP98
|
4.7
|
77.5
|
1.0
|
C
|
D:TYR115
|
4.7
|
78.3
|
1.0
|
O
|
D:TYR115
|
4.8
|
77.2
|
1.0
|
HD12
|
B:LEU167
|
4.8
|
91.4
|
1.0
|
HD3
|
D:ARG102
|
4.8
|
81.8
|
1.0
|
HA
|
B:ASP237
|
4.8
|
103.3
|
1.0
|
CB
|
B:ASP237
|
4.9
|
86.4
|
1.0
|
HB3
|
D:ASP98
|
4.9
|
88.4
|
1.0
|
CA
|
D:TYR115
|
4.9
|
74.3
|
1.0
|
HD13
|
B:LEU167
|
5.0
|
91.4
|
1.0
|
HD3
|
B:LYS240
|
5.0
|
135.8
|
1.0
|
HA
|
D:ASP116
|
5.0
|
89.8
|
1.0
|
|
Calcium binding site 4 out
of 7 in 9etj
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Calcium Binding Sites List in 9etj
Calcium binding site 4 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:88.4
occ:1.00
|
O
|
D:ASN97
|
2.5
|
82.5
|
1.0
|
OD2
|
D:ASP101
|
2.6
|
69.7
|
1.0
|
OD1
|
D:ASN97
|
3.4
|
71.0
|
1.0
|
O
|
D:LEU99
|
3.4
|
71.7
|
1.0
|
HA
|
D:ASP98
|
3.7
|
89.7
|
1.0
|
CG
|
D:ASP101
|
3.7
|
69.0
|
1.0
|
C
|
D:ASN97
|
3.8
|
73.1
|
1.0
|
HD2
|
D:PRO100
|
3.9
|
84.5
|
1.0
|
C
|
D:LEU99
|
4.1
|
65.3
|
1.0
|
OD1
|
D:ASP101
|
4.1
|
70.8
|
1.0
|
H
|
D:ASP101
|
4.2
|
82.4
|
1.0
|
O
|
D:ASP31
|
4.3
|
74.3
|
1.0
|
CA
|
D:ASP98
|
4.4
|
73.8
|
1.0
|
CG
|
D:ASN97
|
4.5
|
71.7
|
1.0
|
N
|
D:LEU99
|
4.5
|
76.2
|
1.0
|
H
|
D:LEU99
|
4.5
|
92.6
|
1.0
|
N
|
D:ASP98
|
4.5
|
71.1
|
1.0
|
C
|
D:ASP98
|
4.5
|
71.3
|
1.0
|
HA
|
D:ASN97
|
4.6
|
86.7
|
1.0
|
CD
|
D:PRO100
|
4.6
|
69.5
|
1.0
|
N
|
D:PRO100
|
4.6
|
86.2
|
1.0
|
CA
|
D:ASN97
|
4.8
|
71.3
|
1.0
|
HB2
|
D:ASP101
|
4.9
|
81.8
|
1.0
|
HD3
|
D:PRO100
|
4.9
|
84.5
|
1.0
|
HG2
|
D:PRO53
|
4.9
|
96.3
|
1.0
|
CB
|
D:ASP101
|
4.9
|
67.2
|
1.0
|
CA
|
D:LEU99
|
5.0
|
69.8
|
1.0
|
N
|
D:ASP101
|
5.0
|
67.8
|
1.0
|
|
Calcium binding site 5 out
of 7 in 9etj
Go back to
Calcium Binding Sites List in 9etj
Calcium binding site 5 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca201
b:76.9
occ:1.00
|
O
|
F:ASN97
|
2.4
|
77.8
|
1.0
|
OD1
|
F:ASN97
|
2.6
|
77.6
|
1.0
|
OD1
|
F:ASP101
|
3.3
|
86.0
|
1.0
|
O
|
F:ASP31
|
3.5
|
78.3
|
1.0
|
O
|
F:LEU99
|
3.6
|
77.2
|
1.0
|
C
|
F:ASN97
|
3.6
|
76.8
|
1.0
|
CG
|
F:ASN97
|
3.8
|
80.7
|
1.0
|
HA
|
F:ASN97
|
4.0
|
94.4
|
1.0
|
HA
|
F:ASP98
|
4.2
|
91.0
|
1.0
|
CA
|
F:ASN97
|
4.3
|
77.7
|
1.0
|
CG
|
F:ASP101
|
4.4
|
85.1
|
1.0
|
C
|
F:LEU99
|
4.6
|
74.4
|
1.0
|
HD2
|
F:PRO100
|
4.6
|
94.5
|
1.0
|
C
|
F:ASP31
|
4.6
|
80.6
|
1.0
|
N
|
F:ASP98
|
4.6
|
76.4
|
1.0
|
CB
|
F:ASN97
|
4.6
|
79.9
|
1.0
|
HG3
|
F:PRO53
|
4.6
|
93.4
|
1.0
|
HG2
|
F:PRO53
|
4.7
|
93.4
|
1.0
|
HD22
|
F:ASN97
|
4.7
|
102.2
|
1.0
|
ND2
|
F:ASN97
|
4.7
|
84.2
|
1.0
|
OD2
|
F:ASP101
|
4.7
|
82.5
|
1.0
|
H
|
F:LEU99
|
4.7
|
86.0
|
1.0
|
HA
|
F:ASP31
|
4.7
|
100.0
|
1.0
|
CA
|
F:ASP98
|
4.8
|
74.9
|
1.0
|
HB3
|
F:ASP31
|
4.8
|
98.3
|
1.0
|
N
|
F:LEU99
|
4.8
|
70.7
|
1.0
|
|
Calcium binding site 6 out
of 7 in 9etj
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Calcium Binding Sites List in 9etj
Calcium binding site 6 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca201
b:156.4
occ:1.00
|
OD1
|
H:ASN97
|
2.3
|
89.8
|
1.0
|
O
|
H:ASN97
|
2.7
|
84.6
|
1.0
|
O
|
H:ASP31
|
3.1
|
83.5
|
1.0
|
CG
|
H:ASN97
|
3.6
|
88.1
|
1.0
|
O
|
H:LEU99
|
3.8
|
77.1
|
1.0
|
C
|
H:ASN97
|
3.8
|
82.2
|
1.0
|
OD1
|
H:ASP101
|
3.9
|
71.5
|
1.0
|
HA
|
H:ASN97
|
3.9
|
100.5
|
1.0
|
HB3
|
H:ASP31
|
4.2
|
103.2
|
1.0
|
HA
|
H:ASP31
|
4.2
|
102.1
|
1.0
|
C
|
H:ASP31
|
4.2
|
82.9
|
1.0
|
CA
|
H:ASN97
|
4.3
|
82.8
|
1.0
|
HD21
|
H:ASN97
|
4.4
|
106.7
|
1.0
|
HA
|
H:ASP98
|
4.4
|
92.8
|
1.0
|
ND2
|
H:ASN97
|
4.5
|
88.0
|
1.0
|
CB
|
H:ASN97
|
4.5
|
85.8
|
1.0
|
CA
|
H:ASP31
|
4.7
|
84.1
|
1.0
|
HG3
|
H:PRO53
|
4.7
|
97.7
|
1.0
|
C
|
H:LEU99
|
4.8
|
75.4
|
1.0
|
HD2
|
H:PRO100
|
4.8
|
92.8
|
1.0
|
H
|
H:LEU99
|
4.9
|
86.8
|
1.0
|
N
|
H:ASP98
|
4.9
|
81.3
|
1.0
|
CB
|
H:ASP31
|
4.9
|
85.1
|
1.0
|
HG2
|
H:PRO53
|
4.9
|
97.7
|
1.0
|
HA
|
H:PHE32
|
5.0
|
97.7
|
1.0
|
|
Calcium binding site 7 out
of 7 in 9etj
Go back to
Calcium Binding Sites List in 9etj
Calcium binding site 7 out
of 7 in the Mouse Cnpase Catalytic Domain with Nanobody 10E
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Mouse Cnpase Catalytic Domain with Nanobody 10E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca202
b:95.5
occ:1.00
|
OD2
|
H:ASP98
|
2.4
|
83.2
|
1.0
|
OD1
|
H:ASP116
|
2.6
|
78.3
|
1.0
|
O
|
H:PRO114
|
2.8
|
75.6
|
1.0
|
OD1
|
H:ASP96
|
2.8
|
79.3
|
1.0
|
CG
|
H:ASP98
|
3.5
|
81.5
|
1.0
|
OD1
|
G:ASP237
|
3.5
|
78.8
|
1.0
|
CG
|
H:ASP116
|
3.5
|
79.3
|
1.0
|
HB2
|
H:ASP98
|
3.5
|
95.2
|
1.0
|
OD2
|
H:ASP116
|
3.8
|
82.0
|
1.0
|
H
|
H:ASP98
|
3.8
|
98.7
|
1.0
|
C
|
H:PRO114
|
3.8
|
76.7
|
1.0
|
CG
|
H:ASP96
|
3.8
|
77.8
|
1.0
|
HE2
|
G:TYR238
|
3.9
|
98.1
|
1.0
|
CB
|
H:ASP98
|
4.0
|
78.4
|
1.0
|
HB3
|
H:PRO114
|
4.1
|
88.0
|
1.0
|
HA
|
H:PRO114
|
4.3
|
89.8
|
1.0
|
OD2
|
H:ASP96
|
4.3
|
76.1
|
1.0
|
HA
|
H:TYR115
|
4.4
|
95.6
|
1.0
|
OD1
|
H:ASP98
|
4.4
|
82.6
|
1.0
|
CA
|
H:PRO114
|
4.4
|
73.9
|
1.0
|
HD2
|
G:TYR238
|
4.5
|
97.9
|
1.0
|
N
|
H:ASP98
|
4.5
|
81.3
|
1.0
|
CG
|
G:ASP237
|
4.5
|
79.8
|
1.0
|
HB2
|
H:PRO114
|
4.5
|
88.0
|
1.0
|
CB
|
H:PRO114
|
4.6
|
72.4
|
1.0
|
H
|
H:ASN97
|
4.7
|
98.2
|
1.0
|
C
|
H:TYR115
|
4.7
|
80.5
|
1.0
|
CE2
|
G:TYR238
|
4.7
|
80.8
|
1.0
|
HA
|
H:ASP96
|
4.7
|
95.6
|
1.0
|
HB3
|
H:ASP98
|
4.8
|
95.2
|
1.0
|
OD2
|
G:ASP237
|
4.8
|
79.2
|
1.0
|
O
|
H:TYR115
|
4.8
|
81.7
|
1.0
|
N
|
H:TYR115
|
4.8
|
77.0
|
1.0
|
HD3
|
H:ARG102
|
4.8
|
85.1
|
1.0
|
CA
|
H:TYR115
|
4.9
|
78.8
|
1.0
|
HA
|
H:ASP116
|
4.9
|
97.2
|
1.0
|
CB
|
H:ASP116
|
4.9
|
79.9
|
1.0
|
N
|
H:ASP116
|
4.9
|
81.5
|
1.0
|
CA
|
H:ASP98
|
4.9
|
76.4
|
1.0
|
|
Reference:
S.Markusson,
A.Raasakka,
F.Opazo,
P.Kursula.
Mouse Cnpase Catalytic Domain with Nanobody 10E To Be Published.
Page generated: Sun Dec 15 09:47:24 2024
|