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Calcium in PDB 1w21: Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 43 Hours at 291 K.

Enzymatic activity of Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 43 Hours at 291 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 43 Hours at 291 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 43 Hours at 291 K., PDB code: 1w21 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) 30.43 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.478, 73.995, 106.465, 90.00, 90.50, 90.00
R / Rfree (%) 15 / 19.5

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 43 Hours at 291 K. (pdb code 1w21). 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 43 Hours at 291 K., PDB code: 1w21:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1w21

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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 43 Hours at 291 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 43 Hours at 291 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1488

b:8.8
occ:1.00
 O A:ASP300 2.4 17.4 1.0
O A:PRO354 2.5 19.7 1.0
OD2 A:ASP331 2.5 20.7 1.0
O A:GLY304 2.6 20.4 1.0
O A:HOH2277 2.9 24.3 1.0
CG A:ASP331 3.4 22.7 1.0
C A:ASP300 3.6 16.9 1.0
C A:PRO354 3.6 18.4 1.0
C A:GLY304 3.6 21.5 1.0
CA A:GLY355 3.9 15.9 1.0
O A:HOH2248 3.9 14.2 1.0
CB A:ASP331 4.1 20.9 1.0
OD1 A:ASP331 4.1 21.5 1.0
N A:GLY355 4.2 17.0 1.0
CA A:ASN301 4.2 17.1 1.0
O A:HOH2230 4.3 33.5 1.0
N A:ASN301 4.3 16.6 1.0
CA A:ALA305 4.4 17.4 1.0
N A:ALA305 4.4 19.9 1.0
N A:GLY304 4.5 24.0 1.0
CA A:GLY304 4.6 22.9 1.0
CA A:ASP300 4.6 17.2 1.0
N A:ASP300 4.7 18.7 1.0
C A:ASN301 4.7 18.0 1.0
CA A:PRO354 4.7 17.3 1.0
CB A:ASP300 4.8 16.8 1.0
C A:LYS303 4.9 23.9 1.0
OD2 A:ASP300 5.0 17.3 1.0

Calcium binding site 2 out of 4 in 1w21

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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 43 Hours at 291 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 43 Hours at 291 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2487

b:5.2
occ:1.00
 O B:ASP1300 2.4 14.8 1.0
O B:GLY1304 2.5 16.1 1.0
OD2 B:ASP1331 2.5 18.5 1.0
O B:PRO1354 2.6 17.9 1.0
O B:HOH2283 2.7 19.7 1.0
CG B:ASP1331 3.4 20.9 1.0
C B:ASP1300 3.6 15.4 1.0
C B:GLY1304 3.6 16.7 1.0
C B:PRO1354 3.7 18.1 1.0
O B:HOH2251 3.8 12.1 1.0
CA B:GLY1355 4.0 16.8 1.0
CB B:ASP1331 4.1 14.9 1.0
O B:HOH2273 4.1 22.0 1.0
OD1 B:ASP1331 4.2 17.6 1.0
CA B:ASN1301 4.3 14.5 1.0
N B:GLY1355 4.3 17.9 1.0
N B:ASN1301 4.4 13.8 1.0
CA B:ALA1305 4.4 16.0 1.0
N B:ALA1305 4.4 16.0 1.0
N B:GLY1304 4.5 17.0 1.0
N B:ASP1300 4.6 15.2 1.0
CA B:ASP1300 4.6 14.7 1.0
CA B:GLY1304 4.6 16.8 1.0
CB B:ASP1300 4.7 13.4 1.0
C B:ASN1301 4.7 15.1 1.0
CA B:PRO1354 4.8 17.4 1.0
C B:LYS1303 4.8 16.6 1.0
O B:LYS1303 4.8 16.0 1.0
O B:HOH2107 4.9 41.9 1.0

Calcium binding site 3 out of 4 in 1w21

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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 43 Hours at 291 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 43 Hours at 291 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3491

b:2.1
occ:1.00
 O C:ASP2300 2.4 19.0 1.0
OD2 C:ASP2331 2.4 22.9 1.0
O C:GLY2304 2.4 17.5 1.0
O C:PRO2354 2.5 15.0 1.0
CG C:ASP2331 3.4 21.5 1.0
C C:GLY2304 3.5 18.4 1.0
C C:ASP2300 3.6 16.3 1.0
C C:PRO2354 3.6 17.4 1.0
O C:HOH3260 4.0 13.6 1.0
CA C:GLY2355 4.1 15.0 1.0
CB C:ASP2331 4.1 18.3 1.0
OD1 C:ASP2331 4.2 23.4 1.0
CA C:ASN2301 4.2 16.8 1.0
N C:ALA2305 4.3 18.2 1.0
N C:GLY2355 4.3 15.2 1.0
CA C:ALA2305 4.4 17.7 1.0
N C:GLY2304 4.4 19.7 1.0
N C:ASN2301 4.4 14.8 1.0
CA C:GLY2304 4.5 19.6 1.0
O C:HOH3280 4.5 44.0 1.0
C C:ASN2301 4.6 18.3 1.0
CA C:ASP2300 4.6 15.7 1.0
N C:ASP2300 4.6 15.3 1.0
CA C:PRO2354 4.7 17.1 1.0
CB C:ASP2300 4.7 15.1 1.0
C C:LYS2303 4.7 21.1 1.0
OD2 C:ASP2300 4.8 17.7 1.0
O C:ASN2301 4.9 18.9 1.0
O C:LYS2303 4.9 22.1 1.0
CG C:ASP2300 5.0 17.6 1.0

Calcium binding site 4 out of 4 in 1w21

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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 43 Hours at 291 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 43 Hours at 291 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4481

b:4.9
occ:1.00
 O D:ASP3300 2.5 13.0 1.0
O D:PRO3354 2.5 16.1 1.0
O D:GLY3304 2.5 18.6 1.0
OD2 D:ASP3331 2.6 22.0 1.0
CG D:ASP3331 3.4 18.1 1.0
C D:PRO3354 3.6 16.6 1.0
C D:GLY3304 3.6 19.9 1.0
C D:ASP3300 3.6 14.6 1.0
O D:HOH2289 4.0 12.7 1.0
CA D:GLY3355 4.0 15.3 1.0
CB D:ASP3331 4.1 16.2 1.0
O D:HOH2308 4.2 32.0 1.0
OD1 D:ASP3331 4.2 17.4 1.0
CA D:ASN3301 4.3 17.0 1.0
N D:GLY3355 4.3 16.1 1.0
N D:ALA3305 4.4 19.2 1.0
CA D:ALA3305 4.4 18.5 1.0
N D:ASN3301 4.4 15.2 1.0
N D:GLY3304 4.5 19.4 1.0
CA D:ASP3300 4.6 14.7 1.0
CA D:GLY3304 4.6 19.1 1.0
N D:ASP3300 4.7 14.9 1.0
CA D:PRO3354 4.7 16.3 1.0
C D:ASN3301 4.7 17.3 1.0
C D:LYS3303 4.7 18.2 1.0
O D:LYS3303 4.7 17.4 1.0
CB D:ASP3300 4.7 13.7 1.0
OD2 D:ASP3300 5.0 15.9 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 06:59:06 2024

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