Calcium in PDB 1w1x: Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
Enzymatic activity of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
All present enzymatic activity of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.:
3.2.1.18;
Protein crystallography data
The structure of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K., PDB code: 1w1x
was solved by
E.Rudino-Pinera,
P.Tunnah,
S.J.Crennell,
R.G.Webster,
W.G.Laver,
E.F.Garman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.71 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.993,
73.464,
107.413,
90.00,
90.38,
90.00
|
R / Rfree (%)
|
16.4 /
20.7
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
(pdb code 1w1x). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K., PDB code: 1w1x:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1w1x
Go back to
Calcium Binding Sites List in 1w1x
Calcium binding site 1 out
of 4 in the Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1479
b:7.0
occ:1.00
|
OD2
|
A:ASP331
|
2.4
|
17.3
|
1.0
|
O
|
A:GLY304
|
2.5
|
21.0
|
1.0
|
O
|
A:ASP300
|
2.5
|
17.1
|
1.0
|
O
|
A:PRO354
|
2.6
|
17.7
|
1.0
|
O
|
A:HOH2259
|
3.2
|
21.6
|
1.0
|
CG
|
A:ASP331
|
3.4
|
17.4
|
1.0
|
C
|
A:GLY304
|
3.5
|
20.8
|
1.0
|
C
|
A:ASP300
|
3.7
|
16.4
|
1.0
|
C
|
A:PRO354
|
3.7
|
17.9
|
1.0
|
O
|
A:HOH2230
|
3.9
|
22.7
|
1.0
|
CA
|
A:GLY355
|
4.0
|
14.5
|
1.0
|
CB
|
A:ASP331
|
4.0
|
16.9
|
1.0
|
N
|
A:ALA305
|
4.2
|
18.5
|
1.0
|
OD1
|
A:ASP331
|
4.3
|
20.5
|
1.0
|
N
|
A:GLY355
|
4.3
|
16.4
|
1.0
|
CA
|
A:ALA305
|
4.3
|
17.7
|
1.0
|
CA
|
A:ASN301
|
4.4
|
17.3
|
1.0
|
N
|
A:ASN301
|
4.5
|
16.7
|
1.0
|
CA
|
A:GLY304
|
4.5
|
21.2
|
1.0
|
O
|
A:HOH2211
|
4.5
|
29.2
|
1.0
|
N
|
A:GLY304
|
4.5
|
21.2
|
1.0
|
N
|
A:ASP300
|
4.6
|
16.3
|
1.0
|
O
|
A:HOH2254
|
4.7
|
35.8
|
1.0
|
CA
|
A:ASP300
|
4.7
|
15.9
|
1.0
|
C
|
A:ASN301
|
4.7
|
19.3
|
1.0
|
CA
|
A:PRO354
|
4.8
|
18.2
|
1.0
|
CB
|
A:ASP300
|
4.9
|
16.6
|
1.0
|
C
|
A:LYS303
|
5.0
|
22.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1w1x
Go back to
Calcium Binding Sites List in 1w1x
Calcium binding site 2 out
of 4 in the Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2479
b:14.9
occ:1.00
|
O
|
B:ASP1300
|
2.4
|
17.8
|
1.0
|
O
|
B:GLY1304
|
2.5
|
19.7
|
1.0
|
OD2
|
B:ASP1331
|
2.7
|
18.8
|
1.0
|
O
|
B:PRO1354
|
2.7
|
20.9
|
1.0
|
O
|
B:HOH2261
|
3.0
|
20.3
|
1.0
|
C
|
B:GLY1304
|
3.5
|
19.9
|
1.0
|
CG
|
B:ASP1331
|
3.5
|
22.1
|
1.0
|
O
|
B:HOH2233
|
3.5
|
13.1
|
1.0
|
C
|
B:ASP1300
|
3.6
|
17.5
|
1.0
|
C
|
B:PRO1354
|
3.9
|
17.9
|
1.0
|
CB
|
B:ASP1331
|
4.1
|
20.1
|
1.0
|
O
|
B:HOH2211
|
4.1
|
29.7
|
1.0
|
N
|
B:ALA1305
|
4.1
|
19.5
|
1.0
|
CA
|
B:ALA1305
|
4.2
|
20.6
|
1.0
|
CA
|
B:GLY1355
|
4.2
|
15.2
|
1.0
|
OD1
|
B:ASP1331
|
4.3
|
21.1
|
1.0
|
CA
|
B:ASN1301
|
4.4
|
16.7
|
1.0
|
N
|
B:ASN1301
|
4.4
|
18.5
|
1.0
|
CA
|
B:GLY1304
|
4.5
|
18.1
|
1.0
|
CA
|
B:ASP1300
|
4.5
|
16.4
|
1.0
|
N
|
B:GLY1304
|
4.5
|
18.2
|
1.0
|
N
|
B:ASP1300
|
4.6
|
15.8
|
1.0
|
N
|
B:GLY1355
|
4.6
|
16.4
|
1.0
|
CB
|
B:ASP1300
|
4.6
|
15.3
|
1.0
|
C
|
B:LYS1303
|
4.7
|
18.6
|
1.0
|
O
|
B:LYS1303
|
4.7
|
15.7
|
1.0
|
C
|
B:ASN1301
|
4.9
|
18.1
|
1.0
|
CA
|
B:PRO1354
|
4.9
|
17.5
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1w1x
Go back to
Calcium Binding Sites List in 1w1x
Calcium binding site 3 out
of 4 in the Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca3479
b:16.4
occ:1.00
|
O
|
C:PRO2354
|
2.5
|
18.0
|
1.0
|
O
|
C:ASP2300
|
2.6
|
21.5
|
1.0
|
O
|
C:GLY2304
|
2.6
|
22.9
|
1.0
|
OD2
|
C:ASP2331
|
2.8
|
21.1
|
1.0
|
O
|
C:HOH3255
|
3.0
|
25.7
|
1.0
|
C
|
C:PRO2354
|
3.6
|
17.8
|
1.0
|
C
|
C:GLY2304
|
3.6
|
22.2
|
1.0
|
CG
|
C:ASP2331
|
3.6
|
21.2
|
1.0
|
C
|
C:ASP2300
|
3.7
|
20.1
|
1.0
|
O
|
C:HOH3223
|
3.9
|
16.3
|
1.0
|
CA
|
C:GLY2355
|
4.1
|
14.1
|
1.0
|
CB
|
C:ASP2331
|
4.3
|
19.8
|
1.0
|
N
|
C:ALA2305
|
4.3
|
23.3
|
1.0
|
N
|
C:GLY2355
|
4.3
|
15.5
|
1.0
|
CA
|
C:ASN2301
|
4.3
|
20.1
|
1.0
|
OD1
|
C:ASP2331
|
4.4
|
23.8
|
1.0
|
CA
|
C:ALA2305
|
4.4
|
22.8
|
1.0
|
N
|
C:ASN2301
|
4.5
|
19.9
|
1.0
|
N
|
C:GLY2304
|
4.5
|
21.8
|
1.0
|
CA
|
C:GLY2304
|
4.6
|
20.8
|
1.0
|
CA
|
C:PRO2354
|
4.6
|
19.7
|
1.0
|
C
|
C:ASN2301
|
4.6
|
21.5
|
1.0
|
O
|
C:LYS2303
|
4.6
|
22.0
|
1.0
|
C
|
C:LYS2303
|
4.7
|
23.8
|
1.0
|
CA
|
C:ASP2300
|
4.7
|
18.7
|
1.0
|
N
|
C:ASP2300
|
4.8
|
17.4
|
1.0
|
CB
|
C:ASP2300
|
4.8
|
18.6
|
1.0
|
OD2
|
C:ASP2300
|
4.9
|
18.3
|
1.0
|
O
|
C:ASN2301
|
4.9
|
22.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1w1x
Go back to
Calcium Binding Sites List in 1w1x
Calcium binding site 4 out
of 4 in the Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K.
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 Hours at 277 K. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca4479
b:11.8
occ:1.00
|
O
|
D:PRO3354
|
2.4
|
19.8
|
1.0
|
O
|
D:GLY3304
|
2.5
|
20.1
|
1.0
|
OD2
|
D:ASP3331
|
2.6
|
21.2
|
1.0
|
O
|
D:ASP3300
|
2.6
|
18.4
|
1.0
|
O
|
D:HOH2288
|
3.0
|
27.4
|
1.0
|
CG
|
D:ASP3331
|
3.4
|
21.3
|
1.0
|
C
|
D:PRO3354
|
3.6
|
18.6
|
1.0
|
C
|
D:GLY3304
|
3.6
|
21.1
|
1.0
|
C
|
D:ASP3300
|
3.8
|
17.9
|
1.0
|
O
|
D:HOH2233
|
3.8
|
34.4
|
1.0
|
O
|
D:HOH2255
|
3.9
|
12.3
|
1.0
|
CA
|
D:GLY3355
|
3.9
|
16.1
|
1.0
|
CB
|
D:ASP3331
|
4.1
|
18.9
|
1.0
|
N
|
D:GLY3355
|
4.2
|
17.8
|
1.0
|
OD1
|
D:ASP3331
|
4.2
|
20.5
|
1.0
|
N
|
D:ALA3305
|
4.3
|
21.4
|
1.0
|
CA
|
D:ALA3305
|
4.3
|
21.0
|
1.0
|
CA
|
D:ASN3301
|
4.4
|
20.5
|
1.0
|
N
|
D:ASN3301
|
4.6
|
18.9
|
1.0
|
CA
|
D:GLY3304
|
4.7
|
20.6
|
1.0
|
N
|
D:GLY3304
|
4.7
|
20.9
|
1.0
|
CA
|
D:PRO3354
|
4.7
|
19.6
|
1.0
|
O
|
D:LYS3303
|
4.7
|
20.7
|
1.0
|
CA
|
D:ASP3300
|
4.8
|
15.6
|
1.0
|
C
|
D:LYS3303
|
4.8
|
20.6
|
1.0
|
N
|
D:ASP3300
|
4.8
|
16.7
|
1.0
|
C
|
D:ASN3301
|
4.9
|
20.8
|
1.0
|
CB
|
D:ASP3300
|
5.0
|
15.6
|
1.0
|
|
Reference:
E.Rudino-Pinera,
P.Tunnah,
S.J.Crennell,
R.G.Webster,
W.G.Laver,
E.F.Garman.
The Crystal Structure of Type A Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate NEU5AC Binding Sites To Be Published.
Page generated: Fri Jul 12 06:58:15 2024
|