Calcium in PDB 4gdj: A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010
Protein crystallography data
The structure of A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010, PDB code: 4gdj
was solved by
X.Zhu,
I.A.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.85 /
2.00
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.902,
107.902,
345.210,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.9 /
22.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010
(pdb code 4gdj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010, PDB code: 4gdj:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 4gdj
Go back to
Calcium Binding Sites List in 4gdj
Calcium binding site 1 out
of 4 in the A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca507
b:23.5
occ:1.00
|
O
|
A:ASN293
|
2.3
|
23.2
|
1.0
|
|
O
|
A:GLY347
|
2.3
|
23.6
|
1.0
|
|
O
|
A:ASP297
|
2.3
|
23.4
|
1.0
|
|
OD2
|
A:ASP324
|
2.4
|
21.6
|
1.0
|
|
O
|
A:GLY345
|
2.4
|
27.2
|
1.0
|
|
O
|
A:HOH601
|
2.4
|
22.3
|
1.0
|
|
HA
|
A:ALA298
|
3.4
|
30.4
|
1.0
|
|
C
|
A:GLY345
|
3.4
|
33.0
|
1.0
|
|
C
|
A:ASP297
|
3.5
|
24.0
|
1.0
|
|
C
|
A:ASN293
|
3.5
|
25.7
|
1.0
|
|
C
|
A:GLY347
|
3.5
|
24.6
|
1.0
|
|
CG
|
A:ASP324
|
3.5
|
31.7
|
1.0
|
|
HA3
|
A:GLY348
|
3.6
|
28.5
|
1.0
|
|
HA
|
A:LEU294
|
3.6
|
32.9
|
1.0
|
|
HA2
|
A:GLY345
|
3.6
|
36.1
|
1.0
|
|
H
|
A:ASP297
|
3.7
|
34.6
|
1.0
|
|
HA2
|
A:GLY348
|
3.9
|
28.5
|
1.0
|
|
O
|
A:HOH623
|
4.0
|
18.5
|
1.0
|
|
HB3
|
A:ASP324
|
4.0
|
27.4
|
1.0
|
|
CA
|
A:GLY345
|
4.1
|
30.1
|
1.0
|
|
CA
|
A:GLY348
|
4.1
|
23.8
|
1.0
|
|
HB3
|
A:ASN293
|
4.1
|
26.2
|
1.0
|
|
N
|
A:ALA298
|
4.2
|
24.0
|
1.0
|
|
CA
|
A:ALA298
|
4.2
|
25.4
|
1.0
|
|
CB
|
A:ASP324
|
4.3
|
22.9
|
1.0
|
|
H
|
A:ASN293
|
4.3
|
27.8
|
1.0
|
|
N
|
A:GLY348
|
4.3
|
25.8
|
1.0
|
|
C
|
A:GLU346
|
4.3
|
26.1
|
1.0
|
|
CA
|
A:LEU294
|
4.3
|
27.5
|
1.0
|
|
N
|
A:LEU294
|
4.3
|
22.0
|
1.0
|
|
N
|
A:GLY347
|
4.3
|
23.3
|
1.0
|
|
OD1
|
A:ASP324
|
4.4
|
23.6
|
1.0
|
|
HB2
|
A:ASP324
|
4.4
|
27.4
|
1.0
|
|
N
|
A:ASP297
|
4.4
|
28.9
|
1.0
|
|
CA
|
A:ASN293
|
4.5
|
19.9
|
1.0
|
|
N
|
A:GLU346
|
4.5
|
23.8
|
1.0
|
|
O
|
A:GLU346
|
4.5
|
27.6
|
1.0
|
|
CA
|
A:GLY347
|
4.6
|
21.6
|
1.0
|
|
HA
|
A:GLU346
|
4.6
|
36.4
|
1.0
|
|
CA
|
A:ASP297
|
4.6
|
24.1
|
1.0
|
|
HD23
|
A:LEU294
|
4.6
|
29.3
|
1.0
|
|
H
|
A:GLY347
|
4.6
|
27.8
|
1.0
|
|
HA3
|
A:GLY345
|
4.6
|
36.1
|
1.0
|
|
N
|
A:ASN293
|
4.6
|
23.3
|
1.0
|
|
O
|
A:LYS344
|
4.6
|
33.4
|
1.0
|
|
HG22
|
A:THR292
|
4.7
|
21.0
|
1.0
|
|
C
|
A:LEU294
|
4.7
|
21.7
|
1.0
|
|
CA
|
A:GLU346
|
4.7
|
30.4
|
1.0
|
|
HG23
|
A:THR292
|
4.7
|
21.0
|
1.0
|
|
CB
|
A:ASN293
|
4.7
|
22.0
|
1.0
|
|
HD2
|
A:PRO326
|
4.8
|
31.6
|
1.0
|
|
O
|
A:PRO326
|
4.8
|
27.4
|
1.0
|
|
HB2
|
A:ALA298
|
4.8
|
29.3
|
1.0
|
|
HB3
|
A:ASP297
|
4.9
|
30.2
|
1.0
|
|
H
|
A:TRP295
|
4.9
|
31.2
|
1.0
|
|
Calcium binding site 2 out
of 4 in 4gdj
Go back to
Calcium Binding Sites List in 4gdj
Calcium binding site 2 out
of 4 in the A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca507
b:23.0
occ:1.00
|
O
|
B:GLY347
|
2.2
|
23.0
|
1.0
|
|
O
|
B:ASN293
|
2.3
|
22.9
|
1.0
|
|
O
|
B:ASP297
|
2.4
|
20.2
|
1.0
|
|
OD2
|
B:ASP324
|
2.4
|
20.3
|
1.0
|
|
O
|
B:HOH716
|
2.4
|
21.6
|
1.0
|
|
O
|
B:GLY345
|
2.5
|
28.9
|
1.0
|
|
HA
|
B:ALA298
|
3.4
|
25.9
|
1.0
|
|
C
|
B:GLY347
|
3.4
|
18.4
|
1.0
|
|
C
|
B:GLY345
|
3.5
|
29.1
|
1.0
|
|
C
|
B:ASP297
|
3.5
|
19.5
|
1.0
|
|
HA3
|
B:GLY348
|
3.5
|
26.9
|
1.0
|
|
CG
|
B:ASP324
|
3.5
|
22.3
|
1.0
|
|
C
|
B:ASN293
|
3.5
|
23.6
|
1.0
|
|
HA2
|
B:GLY345
|
3.6
|
37.5
|
1.0
|
|
HA
|
B:LEU294
|
3.6
|
29.4
|
1.0
|
|
H
|
B:ASP297
|
3.7
|
26.4
|
1.0
|
|
O
|
B:HOH608
|
3.9
|
22.2
|
1.0
|
|
HB3
|
B:ASP324
|
4.0
|
24.1
|
1.0
|
|
HA2
|
B:GLY348
|
4.0
|
26.9
|
1.0
|
|
HB3
|
B:ASN293
|
4.0
|
31.3
|
1.0
|
|
CA
|
B:GLY348
|
4.1
|
22.5
|
1.0
|
|
CA
|
B:GLY345
|
4.1
|
31.3
|
1.0
|
|
CB
|
B:ASP324
|
4.2
|
20.2
|
1.0
|
|
N
|
B:GLY348
|
4.2
|
23.4
|
1.0
|
|
CA
|
B:ALA298
|
4.2
|
21.7
|
1.0
|
|
N
|
B:ALA298
|
4.2
|
21.3
|
1.0
|
|
HB2
|
B:ASP324
|
4.2
|
24.1
|
1.0
|
|
CA
|
B:LEU294
|
4.3
|
24.6
|
1.0
|
|
C
|
B:GLU346
|
4.4
|
26.6
|
1.0
|
|
H
|
B:ASN293
|
4.4
|
23.1
|
1.0
|
|
N
|
B:LEU294
|
4.4
|
21.4
|
1.0
|
|
N
|
B:ASP297
|
4.4
|
22.1
|
1.0
|
|
OD1
|
B:ASP324
|
4.4
|
19.5
|
1.0
|
|
N
|
B:GLY347
|
4.4
|
24.9
|
1.0
|
|
HD23
|
B:LEU294
|
4.5
|
27.0
|
1.0
|
|
O
|
B:GLU346
|
4.5
|
30.1
|
1.0
|
|
N
|
B:GLU346
|
4.5
|
27.2
|
1.0
|
|
CA
|
B:ASN293
|
4.5
|
26.3
|
1.0
|
|
HG22
|
B:THR292
|
4.5
|
24.2
|
1.0
|
|
CA
|
B:GLY347
|
4.6
|
22.4
|
1.0
|
|
CA
|
B:ASP297
|
4.6
|
20.8
|
1.0
|
|
HA3
|
B:GLY345
|
4.6
|
37.5
|
1.0
|
|
HA
|
B:GLU346
|
4.6
|
31.3
|
1.0
|
|
O
|
B:LYS344
|
4.7
|
32.8
|
1.0
|
|
N
|
B:ASN293
|
4.7
|
19.4
|
1.0
|
|
CB
|
B:ASN293
|
4.7
|
26.2
|
1.0
|
|
C
|
B:LEU294
|
4.7
|
22.4
|
1.0
|
|
HG23
|
B:THR292
|
4.7
|
24.2
|
1.0
|
|
CA
|
B:GLU346
|
4.8
|
26.2
|
1.0
|
|
H
|
B:GLY347
|
4.8
|
29.8
|
1.0
|
|
H
|
B:TRP295
|
4.8
|
33.9
|
1.0
|
|
O
|
B:PRO326
|
4.8
|
21.4
|
1.0
|
|
HD2
|
B:PRO326
|
4.9
|
37.5
|
1.0
|
|
HB2
|
B:ALA298
|
4.9
|
24.6
|
1.0
|
|
HB3
|
B:ASP297
|
4.9
|
29.1
|
1.0
|
|
N
|
B:TRP295
|
5.0
|
28.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 4gdj
Go back to
Calcium Binding Sites List in 4gdj
Calcium binding site 3 out
of 4 in the A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca506
b:25.4
occ:1.00
|
O
|
C:HOH601
|
2.3
|
21.4
|
1.0
|
|
O
|
C:GLY347
|
2.3
|
22.6
|
1.0
|
|
O
|
C:ASN293
|
2.3
|
27.6
|
1.0
|
|
O
|
C:GLY345
|
2.4
|
31.1
|
1.0
|
|
O
|
C:ASP297
|
2.4
|
28.4
|
1.0
|
|
OD2
|
C:ASP324
|
2.4
|
23.5
|
1.0
|
|
HA
|
C:ALA298
|
3.3
|
31.6
|
1.0
|
|
C
|
C:GLY345
|
3.4
|
28.1
|
1.0
|
|
CG
|
C:ASP324
|
3.5
|
27.7
|
1.0
|
|
C
|
C:GLY347
|
3.5
|
25.8
|
1.0
|
|
C
|
C:ASP297
|
3.5
|
29.1
|
1.0
|
|
HA
|
C:LEU294
|
3.5
|
29.0
|
1.0
|
|
C
|
C:ASN293
|
3.5
|
25.7
|
1.0
|
|
HA2
|
C:GLY345
|
3.6
|
38.7
|
1.0
|
|
HA3
|
C:GLY348
|
3.6
|
26.9
|
1.0
|
|
H
|
C:ASP297
|
3.7
|
35.7
|
1.0
|
|
HA2
|
C:GLY348
|
3.9
|
26.9
|
1.0
|
|
HB3
|
C:ASP324
|
4.0
|
26.5
|
1.0
|
|
O
|
C:HOH607
|
4.0
|
22.5
|
1.0
|
|
CA
|
C:GLY345
|
4.1
|
32.3
|
1.0
|
|
CA
|
C:GLY348
|
4.1
|
22.5
|
1.0
|
|
HB3
|
C:ASN293
|
4.1
|
29.9
|
1.0
|
|
CB
|
C:ASP324
|
4.2
|
22.2
|
1.0
|
|
CA
|
C:ALA298
|
4.2
|
26.4
|
1.0
|
|
HB2
|
C:ASP324
|
4.2
|
26.5
|
1.0
|
|
N
|
C:GLY348
|
4.2
|
24.9
|
1.0
|
|
N
|
C:ALA298
|
4.2
|
28.9
|
1.0
|
|
CA
|
C:LEU294
|
4.3
|
24.3
|
1.0
|
|
C
|
C:GLU346
|
4.3
|
26.8
|
1.0
|
|
OD1
|
C:ASP324
|
4.3
|
23.4
|
1.0
|
|
N
|
C:GLY347
|
4.4
|
31.2
|
1.0
|
|
N
|
C:LEU294
|
4.4
|
27.2
|
1.0
|
|
H
|
C:ASN293
|
4.4
|
28.8
|
1.0
|
|
N
|
C:ASP297
|
4.4
|
29.9
|
1.0
|
|
N
|
C:GLU346
|
4.4
|
26.2
|
1.0
|
|
HD23
|
C:LEU294
|
4.5
|
30.1
|
1.0
|
|
HA
|
C:GLU346
|
4.6
|
37.8
|
1.0
|
|
O
|
C:LYS344
|
4.6
|
31.0
|
1.0
|
|
CA
|
C:ASN293
|
4.6
|
25.3
|
1.0
|
|
CA
|
C:GLY347
|
4.6
|
26.1
|
1.0
|
|
HA3
|
C:GLY345
|
4.6
|
38.7
|
1.0
|
|
H
|
C:GLY347
|
4.6
|
37.4
|
1.0
|
|
O
|
C:GLU346
|
4.6
|
33.5
|
1.0
|
|
HG22
|
C:THR292
|
4.6
|
27.8
|
1.0
|
|
CA
|
C:ASP297
|
4.6
|
24.7
|
1.0
|
|
C
|
C:LEU294
|
4.7
|
30.7
|
1.0
|
|
CA
|
C:GLU346
|
4.7
|
31.6
|
1.0
|
|
HG23
|
C:THR292
|
4.7
|
27.8
|
1.0
|
|
N
|
C:ASN293
|
4.7
|
24.1
|
1.0
|
|
CB
|
C:ASN293
|
4.8
|
25.1
|
1.0
|
|
HB2
|
C:ALA298
|
4.8
|
29.4
|
1.0
|
|
O
|
C:PRO326
|
4.8
|
29.9
|
1.0
|
|
HB3
|
C:ASP297
|
4.9
|
34.1
|
1.0
|
|
H
|
C:TRP295
|
4.9
|
32.8
|
1.0
|
|
HD2
|
C:PRO326
|
5.0
|
38.2
|
1.0
|
|
N
|
C:TRP295
|
5.0
|
27.5
|
1.0
|
|
Calcium binding site 4 out
of 4 in 4gdj
Go back to
Calcium Binding Sites List in 4gdj
Calcium binding site 4 out
of 4 in the A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010
 Mono view
 Stereo pair view
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|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of A Subtype N10 Neuraminidase-Like Protein of A/Little Yellow-Shouldered Bat/Guatemala/060/2010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca506
b:24.9
occ:1.00
|
OD2
|
D:ASP324
|
2.3
|
24.6
|
1.0
|
|
O
|
D:GLY345
|
2.3
|
30.6
|
1.0
|
|
O
|
D:ASP297
|
2.3
|
21.6
|
1.0
|
|
O
|
D:GLY347
|
2.4
|
24.0
|
1.0
|
|
O
|
D:ASN293
|
2.4
|
25.5
|
1.0
|
|
O
|
D:HOH601
|
2.4
|
22.3
|
1.0
|
|
HA
|
D:ALA298
|
3.4
|
32.5
|
1.0
|
|
CG
|
D:ASP324
|
3.4
|
22.3
|
1.0
|
|
C
|
D:GLY345
|
3.4
|
28.7
|
1.0
|
|
C
|
D:ASP297
|
3.5
|
28.1
|
1.0
|
|
HA3
|
D:GLY348
|
3.5
|
29.1
|
1.0
|
|
C
|
D:GLY347
|
3.6
|
27.6
|
1.0
|
|
C
|
D:ASN293
|
3.6
|
25.3
|
1.0
|
|
HA
|
D:LEU294
|
3.6
|
34.0
|
1.0
|
|
HA2
|
D:GLY345
|
3.6
|
34.5
|
1.0
|
|
H
|
D:ASP297
|
3.7
|
31.4
|
1.0
|
|
O
|
D:HOH618
|
3.9
|
23.5
|
1.0
|
|
HB3
|
D:ASP324
|
4.0
|
23.5
|
1.0
|
|
HA2
|
D:GLY348
|
4.0
|
29.1
|
1.0
|
|
CA
|
D:GLY348
|
4.1
|
24.4
|
1.0
|
|
HB3
|
D:ASN293
|
4.1
|
24.3
|
1.0
|
|
CA
|
D:GLY345
|
4.1
|
28.8
|
1.0
|
|
CB
|
D:ASP324
|
4.2
|
19.7
|
1.0
|
|
CA
|
D:ALA298
|
4.2
|
27.1
|
1.0
|
|
N
|
D:ALA298
|
4.2
|
24.6
|
1.0
|
|
HB2
|
D:ASP324
|
4.3
|
23.5
|
1.0
|
|
N
|
D:GLY348
|
4.3
|
23.5
|
1.0
|
|
OD1
|
D:ASP324
|
4.3
|
20.5
|
1.0
|
|
C
|
D:GLU346
|
4.3
|
23.0
|
1.0
|
|
CA
|
D:LEU294
|
4.3
|
28.5
|
1.0
|
|
H
|
D:ASN293
|
4.4
|
26.6
|
1.0
|
|
N
|
D:LEU294
|
4.4
|
25.3
|
1.0
|
|
N
|
D:ASP297
|
4.4
|
26.3
|
1.0
|
|
N
|
D:GLY347
|
4.4
|
26.5
|
1.0
|
|
N
|
D:GLU346
|
4.4
|
26.4
|
1.0
|
|
O
|
D:GLU346
|
4.5
|
30.1
|
1.0
|
|
HA
|
D:GLU346
|
4.5
|
34.0
|
1.0
|
|
CA
|
D:ASN293
|
4.6
|
23.5
|
1.0
|
|
HD23
|
D:LEU294
|
4.6
|
42.0
|
1.0
|
|
CA
|
D:ASP297
|
4.6
|
25.7
|
1.0
|
|
HD2
|
D:PRO326
|
4.6
|
28.2
|
1.0
|
|
HA3
|
D:GLY345
|
4.6
|
34.5
|
1.0
|
|
CA
|
D:GLY347
|
4.6
|
26.8
|
1.0
|
|
O
|
D:LYS344
|
4.6
|
35.6
|
1.0
|
|
HG22
|
D:THR292
|
4.6
|
31.4
|
1.0
|
|
N
|
D:ASN293
|
4.7
|
22.2
|
1.0
|
|
HG23
|
D:THR292
|
4.7
|
31.4
|
1.0
|
|
CA
|
D:GLU346
|
4.7
|
28.4
|
1.0
|
|
C
|
D:LEU294
|
4.7
|
29.2
|
1.0
|
|
H
|
D:GLY347
|
4.7
|
31.7
|
1.0
|
|
CB
|
D:ASN293
|
4.8
|
20.4
|
1.0
|
|
HB3
|
D:ASP297
|
4.8
|
29.8
|
1.0
|
|
HB2
|
D:ALA298
|
4.8
|
31.9
|
1.0
|
|
O
|
D:PRO326
|
4.8
|
23.1
|
1.0
|
|
H
|
D:TRP295
|
4.9
|
34.3
|
1.0
|
|
N
|
D:TRP295
|
5.0
|
28.7
|
1.0
|
|
Reference:
X.Zhu,
H.Yang,
Z.Guo,
W.Yu,
P.J.Carney,
Y.Li,
L.M.Chen,
J.C.Paulson,
R.O.Donis,
S.Tong,
J.Stevens,
I.A.Wilson.
Crystal Structures of Two Subtype N10 Neuraminidase-Like Proteins From Bat Influenza A Viruses Reveal A Diverged Putative Active Site. Proc.Natl.Acad.Sci.Usa V. 109 18903 2012.
ISSN: ISSN 0027-8424
PubMed: 23012478
DOI: 10.1073/PNAS.1212579109
Page generated: Sat Dec 12 04:47:42 2020
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