Calcium in PDB 3k39: Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
Enzymatic activity of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
All present enzymatic activity of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir:
3.2.1.18;
Protein crystallography data
The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir, PDB code: 3k39
was solved by
A.J.Oakley,
J.L.Mckimm-Breschkin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
55.90 /
2.54
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.964,
124.874,
125.245,
90.03,
92.11,
91.27
|
|
R / Rfree (%)
|
19.8 /
21.4
|
Other elements in 3k39:
The structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
(pdb code 3k39). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir, PDB code: 3k39:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 1 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1000
b:53.4
occ:1.00
|
O
|
A:ASP293
|
2.4
|
20.3
|
1.0
|
|
O
|
A:GLY346
|
2.4
|
28.0
|
1.0
|
|
O
|
A:GLY344
|
2.6
|
32.9
|
1.0
|
|
O
|
A:THR297
|
2.7
|
22.2
|
1.0
|
|
OD2
|
A:ASP324
|
2.9
|
25.4
|
1.0
|
|
C
|
A:GLY344
|
3.6
|
32.5
|
1.0
|
|
C
|
A:ASP293
|
3.6
|
20.3
|
1.0
|
|
C
|
A:GLY346
|
3.6
|
27.5
|
1.0
|
|
CG
|
A:ASP324
|
3.6
|
23.5
|
1.0
|
|
C
|
A:THR297
|
3.7
|
22.0
|
1.0
|
|
CA
|
A:GLY347
|
4.1
|
24.5
|
1.0
|
|
O
|
A:HOH2064
|
4.1
|
40.4
|
1.0
|
|
CA
|
A:GLY344
|
4.2
|
32.7
|
1.0
|
|
CA
|
A:ALA298
|
4.2
|
20.9
|
1.0
|
|
N
|
A:ALA298
|
4.2
|
21.5
|
1.0
|
|
CA
|
A:ASN294
|
4.3
|
21.8
|
1.0
|
|
OD1
|
A:ASP324
|
4.3
|
24.9
|
1.0
|
|
N
|
A:GLY347
|
4.3
|
26.4
|
1.0
|
|
N
|
A:ASN294
|
4.4
|
21.0
|
1.0
|
|
CB
|
A:ASP324
|
4.4
|
22.3
|
1.0
|
|
C
|
A:ASN294
|
4.5
|
22.8
|
1.0
|
|
N
|
A:THR297
|
4.6
|
22.1
|
1.0
|
|
N
|
A:SER345
|
4.6
|
31.8
|
1.0
|
|
N
|
A:GLY346
|
4.6
|
29.6
|
1.0
|
|
C
|
A:SER345
|
4.6
|
30.6
|
1.0
|
|
CA
|
A:ASP293
|
4.6
|
20.1
|
1.0
|
|
N
|
A:SER295
|
4.7
|
23.4
|
1.0
|
|
CA
|
A:THR297
|
4.7
|
21.8
|
1.0
|
|
CA
|
A:GLY346
|
4.7
|
28.2
|
1.0
|
|
CB
|
A:ASP293
|
4.8
|
19.8
|
1.0
|
|
N
|
A:ASP293
|
4.8
|
19.5
|
1.0
|
|
CA
|
A:SER345
|
4.8
|
31.2
|
1.0
|
|
O
|
A:PRO326
|
4.8
|
23.0
|
1.0
|
|
CB
|
A:ALA298
|
4.9
|
20.3
|
1.0
|
|
OD1
|
A:ASP293
|
4.9
|
19.2
|
1.0
|
|
O
|
A:LYS343
|
5.0
|
34.1
|
1.0
|
|
O
|
A:ASN294
|
5.0
|
22.8
|
1.0
|
|
O
|
A:SER345
|
5.0
|
31.0
|
1.0
|
|
Calcium binding site 2 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 2 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1000
b:53.1
occ:1.00
|
O
|
B:GLY346
|
2.2
|
28.2
|
1.0
|
|
O
|
B:GLY344
|
2.5
|
32.8
|
1.0
|
|
O
|
B:ASP293
|
2.5
|
20.5
|
1.0
|
|
O
|
B:THR297
|
3.0
|
21.9
|
1.0
|
|
OD2
|
B:ASP324
|
3.0
|
25.4
|
1.0
|
|
C
|
B:GLY344
|
3.5
|
32.4
|
1.0
|
|
C
|
B:GLY346
|
3.5
|
27.5
|
1.0
|
|
CG
|
B:ASP324
|
3.7
|
23.4
|
1.0
|
|
C
|
B:ASP293
|
3.7
|
20.4
|
1.0
|
|
C
|
B:THR297
|
3.8
|
21.8
|
1.0
|
|
CA
|
B:GLY347
|
4.0
|
24.4
|
1.0
|
|
CA
|
B:GLY344
|
4.1
|
32.5
|
1.0
|
|
N
|
B:GLY347
|
4.2
|
26.1
|
1.0
|
|
CA
|
B:ASN294
|
4.3
|
21.9
|
1.0
|
|
CA
|
B:ALA298
|
4.3
|
20.8
|
1.0
|
|
N
|
B:GLY346
|
4.3
|
29.6
|
1.0
|
|
OD1
|
B:ASP324
|
4.4
|
24.6
|
1.0
|
|
C
|
B:SER345
|
4.4
|
30.4
|
1.0
|
|
N
|
B:ALA298
|
4.4
|
21.5
|
1.0
|
|
O
|
B:HOH2064
|
4.4
|
40.3
|
1.0
|
|
N
|
B:SER345
|
4.4
|
31.9
|
1.0
|
|
CB
|
B:ASP324
|
4.5
|
22.4
|
1.0
|
|
N
|
B:ASN294
|
4.5
|
21.0
|
1.0
|
|
C
|
B:ASN294
|
4.5
|
22.7
|
1.0
|
|
CA
|
B:GLY346
|
4.5
|
28.2
|
1.0
|
|
CA
|
B:SER345
|
4.6
|
31.3
|
1.0
|
|
N
|
B:THR297
|
4.7
|
22.1
|
1.0
|
|
O
|
B:SER345
|
4.7
|
31.1
|
1.0
|
|
O
|
B:PRO326
|
4.8
|
23.1
|
1.0
|
|
N
|
B:SER295
|
4.8
|
23.3
|
1.0
|
|
O
|
B:LYS343
|
4.8
|
34.0
|
1.0
|
|
CA
|
B:ASP293
|
4.8
|
19.9
|
1.0
|
|
CA
|
B:THR297
|
4.8
|
21.8
|
1.0
|
|
O
|
B:ASN294
|
4.9
|
22.8
|
1.0
|
|
OD1
|
B:ASP293
|
4.9
|
19.1
|
1.0
|
|
CB
|
B:ASP293
|
5.0
|
19.6
|
1.0
|
|
CB
|
B:ALA298
|
5.0
|
20.3
|
1.0
|
|
Calcium binding site 3 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 3 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1000
b:53.3
occ:1.00
|
O
|
C:GLY346
|
2.4
|
28.1
|
1.0
|
|
O
|
C:ASP293
|
2.4
|
20.3
|
1.0
|
|
O
|
C:GLY344
|
2.8
|
32.6
|
1.0
|
|
O
|
C:THR297
|
2.8
|
22.0
|
1.0
|
|
OD2
|
C:ASP324
|
2.9
|
25.3
|
1.0
|
|
C
|
C:GLY346
|
3.6
|
27.5
|
1.0
|
|
CG
|
C:ASP324
|
3.6
|
23.5
|
1.0
|
|
C
|
C:ASP293
|
3.6
|
20.3
|
1.0
|
|
C
|
C:GLY344
|
3.7
|
32.4
|
1.0
|
|
C
|
C:THR297
|
3.8
|
21.9
|
1.0
|
|
CA
|
C:GLY347
|
4.0
|
24.4
|
1.0
|
|
O
|
C:HOH2064
|
4.1
|
40.2
|
1.0
|
|
OD1
|
C:ASP324
|
4.2
|
24.7
|
1.0
|
|
CA
|
C:ALA298
|
4.2
|
20.8
|
1.0
|
|
CA
|
C:GLY344
|
4.2
|
32.7
|
1.0
|
|
N
|
C:GLY347
|
4.2
|
26.3
|
1.0
|
|
CA
|
C:ASN294
|
4.3
|
21.6
|
1.0
|
|
CB
|
C:ASP324
|
4.3
|
22.2
|
1.0
|
|
N
|
C:ALA298
|
4.3
|
21.5
|
1.0
|
|
N
|
C:ASN294
|
4.4
|
20.9
|
1.0
|
|
C
|
C:ASN294
|
4.5
|
22.7
|
1.0
|
|
N
|
C:GLY346
|
4.6
|
29.5
|
1.0
|
|
C
|
C:SER345
|
4.6
|
30.5
|
1.0
|
|
N
|
C:SER345
|
4.6
|
31.8
|
1.0
|
|
CA
|
C:ASP293
|
4.6
|
20.1
|
1.0
|
|
N
|
C:THR297
|
4.7
|
22.2
|
1.0
|
|
CA
|
C:GLY346
|
4.7
|
28.2
|
1.0
|
|
N
|
C:SER295
|
4.8
|
23.1
|
1.0
|
|
N
|
C:ASP293
|
4.8
|
19.4
|
1.0
|
|
O
|
C:PRO326
|
4.8
|
23.1
|
1.0
|
|
CB
|
C:ASP293
|
4.8
|
19.6
|
1.0
|
|
CA
|
C:THR297
|
4.8
|
21.8
|
1.0
|
|
CA
|
C:SER345
|
4.9
|
31.2
|
1.0
|
|
CB
|
C:ALA298
|
4.9
|
20.3
|
1.0
|
|
O
|
C:SER345
|
5.0
|
31.2
|
1.0
|
|
OD1
|
C:ASP293
|
5.0
|
19.6
|
1.0
|
|
O
|
C:ASN294
|
5.0
|
22.8
|
1.0
|
|
Calcium binding site 4 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 4 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1000
b:53.0
occ:1.00
|
O
|
D:GLY346
|
2.3
|
28.1
|
1.0
|
|
O
|
D:GLY344
|
2.6
|
32.6
|
1.0
|
|
O
|
D:ASP293
|
2.7
|
20.6
|
1.0
|
|
OD2
|
D:ASP324
|
2.9
|
25.3
|
1.0
|
|
O
|
D:THR297
|
2.9
|
21.7
|
1.0
|
|
C
|
D:GLY346
|
3.5
|
27.5
|
1.0
|
|
C
|
D:GLY344
|
3.5
|
32.3
|
1.0
|
|
CG
|
D:ASP324
|
3.6
|
23.3
|
1.0
|
|
C
|
D:THR297
|
3.8
|
21.6
|
1.0
|
|
C
|
D:ASP293
|
3.9
|
20.3
|
1.0
|
|
CA
|
D:GLY347
|
3.9
|
24.3
|
1.0
|
|
CA
|
D:GLY344
|
4.1
|
32.5
|
1.0
|
|
N
|
D:GLY347
|
4.2
|
26.2
|
1.0
|
|
CA
|
D:ALA298
|
4.2
|
20.8
|
1.0
|
|
OD1
|
D:ASP324
|
4.2
|
24.4
|
1.0
|
|
O
|
D:HOH2064
|
4.3
|
40.2
|
1.0
|
|
N
|
D:ALA298
|
4.3
|
21.7
|
1.0
|
|
CB
|
D:ASP324
|
4.3
|
22.3
|
1.0
|
|
N
|
D:GLY346
|
4.4
|
29.4
|
1.0
|
|
CA
|
D:ASN294
|
4.4
|
21.8
|
1.0
|
|
N
|
D:SER345
|
4.5
|
31.9
|
1.0
|
|
C
|
D:SER345
|
4.5
|
30.4
|
1.0
|
|
CA
|
D:GLY346
|
4.6
|
28.2
|
1.0
|
|
O
|
D:PRO326
|
4.6
|
23.3
|
1.0
|
|
N
|
D:ASN294
|
4.6
|
20.9
|
1.0
|
|
C
|
D:ASN294
|
4.6
|
22.7
|
1.0
|
|
N
|
D:THR297
|
4.7
|
22.1
|
1.0
|
|
CA
|
D:SER345
|
4.8
|
31.1
|
1.0
|
|
O
|
D:LYS343
|
4.8
|
34.0
|
1.0
|
|
N
|
D:SER295
|
4.8
|
23.1
|
1.0
|
|
O
|
D:SER345
|
4.9
|
31.1
|
1.0
|
|
CA
|
D:THR297
|
4.9
|
21.8
|
1.0
|
|
CB
|
D:ALA298
|
4.9
|
20.1
|
1.0
|
|
CA
|
D:ASP293
|
4.9
|
19.9
|
1.0
|
|
Calcium binding site 5 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 5 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1000
b:53.6
occ:1.00
|
O
|
E:GLY346
|
2.4
|
28.0
|
1.0
|
|
O
|
E:GLY344
|
2.6
|
32.7
|
1.0
|
|
O
|
E:ASP293
|
2.6
|
20.5
|
1.0
|
|
O
|
E:THR297
|
2.7
|
22.0
|
1.0
|
|
OD2
|
E:ASP324
|
2.8
|
25.8
|
1.0
|
|
C
|
E:GLY346
|
3.6
|
27.6
|
1.0
|
|
C
|
E:GLY344
|
3.6
|
32.3
|
1.0
|
|
CG
|
E:ASP324
|
3.6
|
23.3
|
1.0
|
|
C
|
E:THR297
|
3.6
|
21.9
|
1.0
|
|
C
|
E:ASP293
|
3.8
|
20.4
|
1.0
|
|
CA
|
E:GLY347
|
4.0
|
24.5
|
1.0
|
|
CA
|
E:GLY344
|
4.1
|
32.6
|
1.0
|
|
CA
|
E:ALA298
|
4.1
|
20.9
|
1.0
|
|
O
|
E:HOH2064
|
4.2
|
40.2
|
1.0
|
|
N
|
E:ALA298
|
4.2
|
21.7
|
1.0
|
|
N
|
E:GLY347
|
4.2
|
26.3
|
1.0
|
|
OD1
|
E:ASP324
|
4.2
|
24.3
|
1.0
|
|
CB
|
E:ASP324
|
4.3
|
22.4
|
1.0
|
|
CA
|
E:ASN294
|
4.5
|
21.8
|
1.0
|
|
C
|
E:SER345
|
4.5
|
30.5
|
1.0
|
|
N
|
E:SER345
|
4.6
|
31.8
|
1.0
|
|
O
|
E:PRO326
|
4.6
|
23.2
|
1.0
|
|
N
|
E:GLY346
|
4.6
|
29.6
|
1.0
|
|
N
|
E:ASN294
|
4.6
|
21.0
|
1.0
|
|
N
|
E:THR297
|
4.6
|
22.0
|
1.0
|
|
O
|
E:SER345
|
4.7
|
30.9
|
1.0
|
|
C
|
E:ASN294
|
4.7
|
22.7
|
1.0
|
|
CA
|
E:GLY346
|
4.7
|
28.4
|
1.0
|
|
CA
|
E:THR297
|
4.7
|
21.9
|
1.0
|
|
O
|
E:LYS343
|
4.8
|
34.0
|
1.0
|
|
CA
|
E:SER345
|
4.8
|
31.3
|
1.0
|
|
CA
|
E:ASP293
|
4.8
|
20.0
|
1.0
|
|
CB
|
E:ALA298
|
4.9
|
20.2
|
1.0
|
|
CB
|
E:ASP293
|
4.9
|
19.5
|
1.0
|
|
N
|
E:SER295
|
4.9
|
23.3
|
1.0
|
|
N
|
E:ASP293
|
5.0
|
19.4
|
1.0
|
|
Calcium binding site 6 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 6 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca1000
b:53.7
occ:1.00
|
O
|
F:GLY346
|
2.2
|
28.2
|
1.0
|
|
O
|
F:GLY344
|
2.5
|
32.9
|
1.0
|
|
O
|
F:ASP293
|
2.5
|
20.2
|
1.0
|
|
O
|
F:THR297
|
2.8
|
22.0
|
1.0
|
|
OD2
|
F:ASP324
|
3.0
|
25.2
|
1.0
|
|
C
|
F:GLY346
|
3.4
|
27.7
|
1.0
|
|
C
|
F:GLY344
|
3.5
|
32.5
|
1.0
|
|
C
|
F:THR297
|
3.7
|
22.2
|
1.0
|
|
CG
|
F:ASP324
|
3.7
|
23.5
|
1.0
|
|
C
|
F:ASP293
|
3.8
|
20.4
|
1.0
|
|
CA
|
F:GLY347
|
4.0
|
24.3
|
1.0
|
|
CA
|
F:GLY344
|
4.1
|
32.7
|
1.0
|
|
N
|
F:GLY347
|
4.2
|
26.2
|
1.0
|
|
CA
|
F:ALA298
|
4.3
|
20.9
|
1.0
|
|
N
|
F:ALA298
|
4.3
|
21.7
|
1.0
|
|
CA
|
F:ASN294
|
4.4
|
21.9
|
1.0
|
|
N
|
F:GLY346
|
4.4
|
29.6
|
1.0
|
|
C
|
F:SER345
|
4.4
|
30.7
|
1.0
|
|
OD1
|
F:ASP324
|
4.4
|
24.7
|
1.0
|
|
N
|
F:SER345
|
4.4
|
31.9
|
1.0
|
|
CB
|
F:ASP324
|
4.4
|
22.3
|
1.0
|
|
O
|
F:HOH2064
|
4.5
|
40.5
|
1.0
|
|
N
|
F:ASN294
|
4.5
|
21.1
|
1.0
|
|
CA
|
F:GLY346
|
4.5
|
28.3
|
1.0
|
|
C
|
F:ASN294
|
4.6
|
22.9
|
1.0
|
|
CA
|
F:SER345
|
4.7
|
31.3
|
1.0
|
|
N
|
F:THR297
|
4.7
|
22.4
|
1.0
|
|
O
|
F:PRO326
|
4.7
|
23.6
|
1.0
|
|
O
|
F:SER345
|
4.7
|
31.0
|
1.0
|
|
CA
|
F:THR297
|
4.8
|
22.0
|
1.0
|
|
O
|
F:LYS343
|
4.8
|
34.2
|
1.0
|
|
CA
|
F:ASP293
|
4.8
|
20.0
|
1.0
|
|
N
|
F:SER295
|
4.8
|
23.4
|
1.0
|
|
CB
|
F:ALA298
|
5.0
|
20.2
|
1.0
|
|
OD1
|
F:ASP293
|
5.0
|
19.8
|
1.0
|
|
Calcium binding site 7 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 7 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca1000
b:53.4
occ:1.00
|
O
|
G:GLY346
|
2.4
|
28.0
|
1.0
|
|
O
|
G:ASP293
|
2.6
|
20.1
|
1.0
|
|
O
|
G:THR297
|
2.7
|
21.9
|
1.0
|
|
O
|
G:GLY344
|
2.7
|
32.6
|
1.0
|
|
OD2
|
G:ASP324
|
2.8
|
25.7
|
1.0
|
|
CG
|
G:ASP324
|
3.5
|
23.5
|
1.0
|
|
C
|
G:GLY346
|
3.5
|
27.5
|
1.0
|
|
C
|
G:GLY344
|
3.6
|
32.4
|
1.0
|
|
C
|
G:THR297
|
3.7
|
21.9
|
1.0
|
|
C
|
G:ASP293
|
3.8
|
20.4
|
1.0
|
|
CA
|
G:GLY347
|
4.0
|
24.6
|
1.0
|
|
CA
|
G:ALA298
|
4.1
|
20.8
|
1.0
|
|
CA
|
G:GLY344
|
4.2
|
32.7
|
1.0
|
|
OD1
|
G:ASP324
|
4.2
|
24.8
|
1.0
|
|
N
|
G:GLY347
|
4.2
|
26.3
|
1.0
|
|
O
|
G:HOH2064
|
4.2
|
40.1
|
1.0
|
|
N
|
G:ALA298
|
4.2
|
21.6
|
1.0
|
|
CB
|
G:ASP324
|
4.3
|
22.3
|
1.0
|
|
O
|
G:PRO326
|
4.5
|
22.8
|
1.0
|
|
CA
|
G:ASN294
|
4.5
|
21.9
|
1.0
|
|
N
|
G:SER345
|
4.6
|
31.9
|
1.0
|
|
C
|
G:SER345
|
4.6
|
30.4
|
1.0
|
|
N
|
G:GLY346
|
4.6
|
29.5
|
1.0
|
|
N
|
G:ASN294
|
4.6
|
21.1
|
1.0
|
|
CA
|
G:GLY346
|
4.7
|
28.4
|
1.0
|
|
N
|
G:THR297
|
4.7
|
22.2
|
1.0
|
|
C
|
G:ASN294
|
4.8
|
22.6
|
1.0
|
|
O
|
G:LYS343
|
4.8
|
34.0
|
1.0
|
|
CB
|
G:ALA298
|
4.8
|
20.1
|
1.0
|
|
O
|
G:SER345
|
4.8
|
30.7
|
1.0
|
|
CA
|
G:THR297
|
4.8
|
21.9
|
1.0
|
|
CA
|
G:ASP293
|
4.8
|
20.0
|
1.0
|
|
CA
|
G:SER345
|
4.9
|
31.4
|
1.0
|
|
N
|
G:ASP293
|
4.9
|
19.4
|
1.0
|
|
CB
|
G:ASP293
|
5.0
|
19.7
|
1.0
|
|
N
|
G:SER295
|
5.0
|
23.3
|
1.0
|
|
Calcium binding site 8 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 8 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca1000
b:53.7
occ:1.00
|
O
|
H:GLY346
|
2.2
|
28.0
|
1.0
|
|
O
|
H:ASP293
|
2.5
|
20.4
|
1.0
|
|
O
|
H:GLY344
|
2.6
|
32.7
|
1.0
|
|
O
|
H:THR297
|
2.7
|
22.1
|
1.0
|
|
OD2
|
H:ASP324
|
3.0
|
25.4
|
1.0
|
|
C
|
H:GLY346
|
3.4
|
27.8
|
1.0
|
|
C
|
H:GLY344
|
3.5
|
32.5
|
1.0
|
|
C
|
H:THR297
|
3.7
|
22.0
|
1.0
|
|
CG
|
H:ASP324
|
3.7
|
23.4
|
1.0
|
|
C
|
H:ASP293
|
3.8
|
20.4
|
1.0
|
|
CA
|
H:GLY347
|
4.0
|
24.3
|
1.0
|
|
CA
|
H:GLY344
|
4.1
|
32.8
|
1.0
|
|
N
|
H:GLY347
|
4.2
|
26.4
|
1.0
|
|
CA
|
H:ALA298
|
4.2
|
20.9
|
1.0
|
|
O
|
H:HOH2064
|
4.3
|
40.4
|
1.0
|
|
N
|
H:ALA298
|
4.3
|
21.8
|
1.0
|
|
OD1
|
H:ASP324
|
4.4
|
24.5
|
1.0
|
|
CA
|
H:ASN294
|
4.4
|
21.8
|
1.0
|
|
CB
|
H:ASP324
|
4.4
|
22.6
|
1.0
|
|
C
|
H:SER345
|
4.4
|
30.6
|
1.0
|
|
N
|
H:SER345
|
4.5
|
31.9
|
1.0
|
|
N
|
H:GLY346
|
4.5
|
29.5
|
1.0
|
|
N
|
H:ASN294
|
4.6
|
20.6
|
1.0
|
|
C
|
H:ASN294
|
4.6
|
22.8
|
1.0
|
|
CA
|
H:GLY346
|
4.6
|
28.4
|
1.0
|
|
N
|
H:THR297
|
4.6
|
22.2
|
1.0
|
|
O
|
H:PRO326
|
4.7
|
23.3
|
1.0
|
|
O
|
H:SER345
|
4.7
|
31.2
|
1.0
|
|
CA
|
H:SER345
|
4.7
|
31.3
|
1.0
|
|
CA
|
H:THR297
|
4.7
|
21.8
|
1.0
|
|
N
|
H:SER295
|
4.8
|
23.4
|
1.0
|
|
CA
|
H:ASP293
|
4.8
|
19.9
|
1.0
|
|
O
|
H:LYS343
|
4.8
|
33.9
|
1.0
|
|
CB
|
H:ASP293
|
4.9
|
19.6
|
1.0
|
|
N
|
H:ASP293
|
4.9
|
19.3
|
1.0
|
|
OD1
|
H:ASP293
|
5.0
|
19.5
|
1.0
|
|
CB
|
H:ALA298
|
5.0
|
20.2
|
1.0
|
|
O
|
H:ASN294
|
5.0
|
22.9
|
1.0
|
|
Calcium binding site 9 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 9 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca1000
b:53.5
occ:1.00
|
O
|
I:GLY346
|
2.4
|
28.0
|
1.0
|
|
O
|
I:ASP293
|
2.5
|
20.5
|
1.0
|
|
O
|
I:GLY344
|
2.6
|
32.7
|
1.0
|
|
O
|
I:THR297
|
2.7
|
22.2
|
1.0
|
|
OD2
|
I:ASP324
|
3.0
|
25.4
|
1.0
|
|
C
|
I:GLY344
|
3.5
|
32.4
|
1.0
|
|
C
|
I:GLY346
|
3.6
|
27.5
|
1.0
|
|
C
|
I:THR297
|
3.7
|
21.9
|
1.0
|
|
CG
|
I:ASP324
|
3.7
|
23.1
|
1.0
|
|
C
|
I:ASP293
|
3.8
|
20.5
|
1.0
|
|
CA
|
I:GLY344
|
4.1
|
32.4
|
1.0
|
|
CA
|
I:GLY347
|
4.1
|
24.5
|
1.0
|
|
CA
|
I:ALA298
|
4.2
|
20.9
|
1.0
|
|
N
|
I:ALA298
|
4.2
|
21.6
|
1.0
|
|
O
|
I:HOH2064
|
4.3
|
40.3
|
1.0
|
|
N
|
I:GLY347
|
4.3
|
26.2
|
1.0
|
|
OD1
|
I:ASP324
|
4.4
|
24.6
|
1.0
|
|
CA
|
I:ASN294
|
4.4
|
21.9
|
1.0
|
|
CB
|
I:ASP324
|
4.4
|
22.3
|
1.0
|
|
N
|
I:SER345
|
4.5
|
31.9
|
1.0
|
|
C
|
I:SER345
|
4.5
|
30.5
|
1.0
|
|
N
|
I:GLY346
|
4.5
|
29.6
|
1.0
|
|
N
|
I:ASN294
|
4.5
|
20.9
|
1.0
|
|
N
|
I:THR297
|
4.6
|
22.1
|
1.0
|
|
C
|
I:ASN294
|
4.6
|
22.6
|
1.0
|
|
CA
|
I:GLY346
|
4.7
|
28.2
|
1.0
|
|
O
|
I:PRO326
|
4.7
|
23.4
|
1.0
|
|
CA
|
I:THR297
|
4.7
|
21.8
|
1.0
|
|
CA
|
I:SER345
|
4.7
|
31.2
|
1.0
|
|
CA
|
I:ASP293
|
4.8
|
20.2
|
1.0
|
|
O
|
I:LYS343
|
4.8
|
34.1
|
1.0
|
|
N
|
I:SER295
|
4.8
|
23.3
|
1.0
|
|
CB
|
I:ALA298
|
4.8
|
20.3
|
1.0
|
|
O
|
I:SER345
|
4.9
|
30.9
|
1.0
|
|
CB
|
I:ASP293
|
4.9
|
19.8
|
1.0
|
|
N
|
I:ASP293
|
5.0
|
19.4
|
1.0
|
|
OD1
|
I:ASP293
|
5.0
|
19.4
|
1.0
|
|
Calcium binding site 10 out
of 16 in 3k39
Go back to
Calcium Binding Sites List in 3k39
Calcium binding site 10 out
of 16 in the Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex with Peramivir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ca1000
b:53.4
occ:1.00
|
O
|
J:GLY346
|
2.4
|
28.1
|
1.0
|
|
O
|
J:GLY344
|
2.6
|
32.7
|
1.0
|
|
O
|
J:ASP293
|
2.6
|
20.4
|
1.0
|
|
OD2
|
J:ASP324
|
2.8
|
25.4
|
1.0
|
|
O
|
J:THR297
|
2.8
|
21.6
|
1.0
|
|
CG
|
J:ASP324
|
3.5
|
23.4
|
1.0
|
|
C
|
J:GLY344
|
3.5
|
32.5
|
1.0
|
|
C
|
J:GLY346
|
3.6
|
27.5
|
1.0
|
|
C
|
J:THR297
|
3.7
|
21.9
|
1.0
|
|
C
|
J:ASP293
|
3.8
|
20.3
|
1.0
|
|
CA
|
J:GLY347
|
4.1
|
24.4
|
1.0
|
|
CA
|
J:ALA298
|
4.1
|
20.9
|
1.0
|
|
CA
|
J:GLY344
|
4.1
|
32.5
|
1.0
|
|
OD1
|
J:ASP324
|
4.1
|
24.7
|
1.0
|
|
N
|
J:ALA298
|
4.2
|
21.6
|
1.0
|
|
O
|
J:HOH2064
|
4.2
|
40.1
|
1.0
|
|
CB
|
J:ASP324
|
4.3
|
22.4
|
1.0
|
|
N
|
J:GLY347
|
4.3
|
26.3
|
1.0
|
|
CA
|
J:ASN294
|
4.5
|
21.8
|
1.0
|
|
N
|
J:SER345
|
4.5
|
32.0
|
1.0
|
|
C
|
J:SER345
|
4.6
|
30.5
|
1.0
|
|
N
|
J:GLY346
|
4.6
|
29.3
|
1.0
|
|
O
|
J:PRO326
|
4.6
|
23.3
|
1.0
|
|
N
|
J:ASN294
|
4.6
|
21.2
|
1.0
|
|
C
|
J:ASN294
|
4.7
|
22.7
|
1.0
|
|
CA
|
J:GLY346
|
4.7
|
28.2
|
1.0
|
|
CB
|
J:ALA298
|
4.7
|
20.3
|
1.0
|
|
N
|
J:THR297
|
4.7
|
22.3
|
1.0
|
|
CA
|
J:THR297
|
4.8
|
21.9
|
1.0
|
|
CA
|
J:SER345
|
4.8
|
31.2
|
1.0
|
|
O
|
J:SER345
|
4.8
|
31.4
|
1.0
|
|
O
|
J:LYS343
|
4.8
|
34.1
|
1.0
|
|
CA
|
J:ASP293
|
4.9
|
19.9
|
1.0
|
|
N
|
J:SER295
|
4.9
|
23.4
|
1.0
|
|
CB
|
J:ASP293
|
5.0
|
19.7
|
1.0
|
|
N
|
J:ASP293
|
5.0
|
19.5
|
1.0
|
|
Reference:
A.J.Oakley,
S.Barrett,
T.S.Peat,
J.Newman,
V.A.Streltsov,
L.Waddington,
T.Saito,
M.Tashiro,
J.L.Mckimm-Breschkin.
Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses. J.Med.Chem. 2010.
ISSN: ISSN 0022-2623
PubMed: 20695427
DOI: 10.1021/JM100621S
Page generated: Sat Jul 13 11:58:09 2024
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