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Calcium in PDB 1w20: Structure of Neuraminidase From English Duck Subtype N6 Complexed with 30 Mm Sialic Acid (Nana, NEU5AC), Crystal Soaked For 3 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 3 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 3 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 3 Hours at 291 K, PDB code: 1w20 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) 105.41 / 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 3 Hours at 291 K (pdb code 1w20). 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 291 K, PDB code: 1w20:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1w20

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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 3 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 3 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:HOH2278 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:HOH2249 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:HOH2231 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 1w20

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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 3 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 3 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:HOH2284 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:HOH2252 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:HOH2274 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 1w20

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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 3 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 3 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:HOH3261 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:HOH3281 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 1w20

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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 3 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 3 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:HOH2290 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:HOH2309 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 06:58:41 2024

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