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Calcium in PDB 2hty: N1 Neuraminidase

Protein crystallography data

The structure of N1 Neuraminidase, PDB code: 2hty was solved by R.J.Russell, L.F.Haire, D.J.Stevens, P.J.Collins, Y.P.Lin, G.M.Blackburn, A.J.Hay, S.J.Gamblin, J.J.Skehel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 200.210, 200.770, 211.680, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the N1 Neuraminidase (pdb code 2hty). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the N1 Neuraminidase, PDB code: 2hty:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2hty

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Calcium binding site 1 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca991

b:21.6
occ:1.00
O A:TYR347 2.3 24.1 1.0
OD1 A:ASP324 2.3 22.6 1.0
O A:GLY297 2.5 17.4 1.0
O A:ASP293 2.5 12.8 1.0
C A:TYR347 3.1 23.8 1.0
O A:GLY345 3.2 38.2 1.0
C A:GLY345 3.3 38.4 1.0
N A:TYR347 3.3 29.8 1.0
CG A:ASP324 3.4 22.4 1.0
CA A:GLY345 3.6 38.8 1.0
C A:GLY297 3.6 16.5 1.0
C A:ASP293 3.7 14.4 1.0
N A:GLY348 3.8 21.6 1.0
CA A:GLY348 3.8 19.7 1.0
N A:ALA346 3.9 37.3 1.0
CA A:TYR347 3.9 26.1 1.0
OD2 A:ASP324 4.1 23.4 1.0
CB A:ASP324 4.2 20.1 1.0
C A:ALA346 4.2 33.1 1.0
CA A:ASN294 4.2 15.0 1.0
CA A:ALA346 4.2 34.0 1.0
N A:GLY297 4.2 14.3 1.0
O A:HOH1205 4.3 20.2 1.0
N A:ASN294 4.4 14.6 1.0
CA A:GLY297 4.5 14.2 1.0
N A:SER298 4.5 18.4 1.0
CA A:SER298 4.7 19.2 1.0
C A:ASN294 4.7 15.7 1.0
O A:PRO326 4.8 12.1 1.0
CA A:ASP293 4.9 15.0 1.0
OD2 A:ASP293 4.9 19.8 1.0
O A:HOH1152 4.9 17.0 1.0
O A:ASN294 5.0 15.8 1.0
CB A:TYR347 5.0 27.6 1.0

Calcium binding site 2 out of 8 in 2hty

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Calcium binding site 2 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca992

b:21.8
occ:1.00
O B:TYR347 2.1 26.5 1.0
O B:ASP293 2.3 16.6 1.0
OD1 B:ASP324 2.4 22.6 1.0
O B:GLY297 2.4 23.0 1.0
C B:TYR347 3.2 26.3 1.0
O B:GLY345 3.2 37.8 1.0
CG B:ASP324 3.4 22.5 1.0
C B:GLY345 3.5 38.3 1.0
C B:ASP293 3.6 16.8 1.0
C B:GLY297 3.6 21.2 1.0
N B:TYR347 3.7 32.0 1.0
CA B:GLY345 3.7 38.8 1.0
CA B:GLY348 3.8 21.8 1.0
N B:GLY348 4.0 23.6 1.0
CA B:TYR347 4.1 28.5 1.0
OD2 B:ASP324 4.2 22.9 1.0
CB B:ASP324 4.2 21.9 1.0
CA B:ASN294 4.3 18.4 1.0
N B:GLY297 4.3 19.1 1.0
N B:ALA346 4.3 38.5 1.0
N B:ASN294 4.4 16.9 1.0
CA B:GLY297 4.5 20.8 1.0
N B:SER298 4.5 22.1 1.0
OD2 B:ASP293 4.6 22.3 1.0
CA B:ASP293 4.6 17.3 1.0
CA B:SER298 4.6 22.4 1.0
CB B:ASP293 4.7 18.4 1.0
C B:ALA346 4.7 34.9 1.0
C B:ASN294 4.7 19.4 1.0
O B:PRO326 4.7 16.8 1.0
N B:ASP293 4.8 17.9 1.0
CA B:ALA346 4.8 36.4 1.0
CG B:ASP293 5.0 21.9 1.0

Calcium binding site 3 out of 8 in 2hty

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Calcium binding site 3 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca993

b:22.1
occ:1.00
O C:TYR347 2.1 23.8 1.0
OD1 C:ASP324 2.3 18.9 1.0
O C:GLY297 2.4 14.0 1.0
O C:ASP293 2.4 10.2 1.0
O C:GLY345 2.8 29.9 1.0
C C:TYR347 3.0 22.8 1.0
N C:TYR347 3.4 28.1 1.0
CG C:ASP324 3.4 17.5 1.0
C C:GLY345 3.5 31.2 1.0
C C:GLY297 3.6 12.8 1.0
C C:ASP293 3.7 11.3 1.0
N C:GLY348 3.8 20.1 1.0
CA C:GLY348 3.8 18.2 1.0
CA C:TYR347 3.9 24.9 1.0
CA C:GLY345 4.0 31.3 1.0
OD2 C:ASP324 4.2 15.0 1.0
N C:GLY297 4.2 12.1 1.0
CA C:ASN294 4.3 10.3 1.0
N C:ALA346 4.3 32.7 1.0
O C:HOH1214 4.3 18.6 1.0
CB C:ASP324 4.3 17.2 1.0
C C:ALA346 4.4 31.1 1.0
N C:ASN294 4.4 10.2 1.0
CA C:GLY297 4.4 12.7 1.0
N C:SER298 4.5 14.0 1.0
CA C:SER298 4.6 14.3 1.0
CA C:ALA346 4.6 31.7 1.0
C C:ASN294 4.6 10.6 1.0
CA C:ASP293 4.8 11.5 1.0
OD2 C:ASP293 4.8 19.1 1.0
CB C:ASP293 4.9 13.7 1.0
O C:PRO326 4.9 14.1 1.0
O C:ASN294 5.0 9.9 1.0
N C:ASP293 5.0 12.7 1.0

Calcium binding site 4 out of 8 in 2hty

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Calcium binding site 4 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca994

b:23.6
occ:1.00
OD1 D:ASP324 2.3 18.2 1.0
O D:TYR347 2.3 24.5 1.0
O D:ASP293 2.4 15.3 1.0
O D:GLY297 2.5 15.8 1.0
O D:GLY345 2.7 29.3 1.0
C D:TYR347 3.2 22.8 1.0
C D:GLY345 3.2 31.2 1.0
CG D:ASP324 3.4 17.8 1.0
N D:TYR347 3.5 27.0 1.0
C D:GLY297 3.6 15.1 1.0
CA D:GLY345 3.6 32.5 1.0
C D:ASP293 3.6 16.2 1.0
N D:GLY348 4.0 19.8 1.0
CA D:GLY348 4.0 18.4 1.0
CA D:TYR347 4.0 24.6 1.0
O D:HOH1174 4.1 9.4 1.0
CB D:ASP324 4.1 15.5 1.0
N D:ALA346 4.2 31.4 1.0
N D:GLY297 4.2 14.4 1.0
OD2 D:ASP324 4.3 20.0 1.0
CA D:ASN294 4.4 16.2 1.0
N D:ASN294 4.4 16.8 1.0
N D:SER298 4.4 16.8 1.0
CA D:GLY297 4.5 13.7 1.0
C D:ALA346 4.5 29.2 1.0
CA D:SER298 4.5 16.7 1.0
CA D:ALA346 4.7 30.2 1.0
CA D:ASP293 4.7 16.2 1.0
O D:PRO326 4.7 15.2 1.0
C D:ASN294 4.8 15.4 1.0
OD2 D:ASP293 4.8 16.8 1.0
CB D:ASP293 4.8 16.2 1.0
N D:ASP293 4.9 15.8 1.0
N D:GLY345 5.0 32.4 1.0

Calcium binding site 5 out of 8 in 2hty

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Calcium binding site 5 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca995

b:28.3
occ:1.00
O E:TYR347 2.3 33.4 1.0
OD1 E:ASP324 2.4 24.3 1.0
O E:GLY297 2.4 28.2 1.0
O E:ASP293 2.5 23.8 1.0
O E:GLY345 2.8 39.8 1.0
C E:GLY345 3.2 41.1 1.0
C E:TYR347 3.3 33.3 1.0
CA E:GLY345 3.3 42.4 1.0
CG E:ASP324 3.5 22.8 1.0
C E:GLY297 3.5 27.6 1.0
C E:ASP293 3.7 24.7 1.0
N E:TYR347 3.7 37.3 1.0
CA E:GLY348 4.1 29.3 1.0
N E:GLY348 4.1 30.8 1.0
N E:ALA346 4.1 41.2 1.0
N E:GLY297 4.1 27.6 1.0
CA E:TYR347 4.2 35.7 1.0
CB E:ASP324 4.2 21.3 1.0
OD2 E:ASP324 4.3 24.2 1.0
N E:SER298 4.3 28.3 1.0
CA E:GLY297 4.4 26.6 1.0
CA E:ASN294 4.4 27.8 1.0
CA E:SER298 4.5 27.0 1.0
N E:ASN294 4.5 25.8 1.0
C E:ALA346 4.6 39.2 1.0
CA E:ASP293 4.7 24.8 1.0
CA E:ALA346 4.7 39.6 1.0
CB E:ASP293 4.8 25.4 1.0
O E:PRO326 4.8 21.4 1.0
N E:GLY345 4.8 42.9 1.0
C E:ASN294 4.8 28.8 1.0
N E:ASP293 4.8 25.6 1.0

Calcium binding site 6 out of 8 in 2hty

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Calcium binding site 6 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca996

b:46.0
occ:1.00
O F:TYR347 2.2 38.6 1.0
OD1 F:ASP324 2.4 35.9 1.0
O F:GLY297 2.5 36.4 1.0
O F:ASP293 2.5 31.8 1.0
O F:GLY345 2.9 48.0 1.0
C F:TYR347 3.2 38.4 1.0
C F:GLY345 3.3 48.4 1.0
CG F:ASP324 3.4 38.0 1.0
C F:GLY297 3.5 37.0 1.0
N F:TYR347 3.6 43.7 1.0
CA F:GLY345 3.6 49.1 1.0
C F:ASP293 3.7 31.2 1.0
N F:GLY348 4.0 36.1 1.0
CA F:GLY348 4.0 33.8 1.0
CA F:TYR347 4.0 40.0 1.0
N F:GLY297 4.1 36.7 1.0
N F:ALA346 4.2 48.4 1.0
CB F:ASP324 4.2 37.1 1.0
OD2 F:ASP324 4.3 38.7 1.0
N F:SER298 4.3 37.6 1.0
CA F:GLY297 4.3 37.0 1.0
CA F:SER298 4.4 38.2 1.0
C F:ALA346 4.4 47.0 1.0
CA F:ASN294 4.5 31.9 1.0
N F:ASN294 4.6 31.2 1.0
O F:PRO326 4.6 34.7 1.0
CA F:ALA346 4.7 47.5 1.0
CA F:ASP293 4.7 30.5 1.0
CB F:ASP293 4.8 31.0 1.0
C F:ASN294 4.8 32.5 1.0
N F:ASP293 4.9 30.0 1.0

Calcium binding site 7 out of 8 in 2hty

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Calcium binding site 7 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca997

b:29.2
occ:1.00
OD1 G:ASP324 2.2 16.7 1.0
O G:HOH1147 2.2 39.1 1.0
O G:TYR347 2.3 22.9 1.0
O G:GLY297 2.4 15.4 1.0
O G:ASP293 2.6 22.8 1.0
C G:TYR347 3.2 23.1 1.0
CG G:ASP324 3.2 16.9 1.0
C G:GLY297 3.4 15.2 1.0
C G:GLY345 3.5 33.9 1.0
N G:TYR347 3.6 28.9 1.0
O G:GLY345 3.6 36.0 1.0
CA G:GLY345 3.6 33.8 1.0
C G:ASP293 3.8 21.6 1.0
CA G:GLY348 3.9 20.4 1.0
N G:GLY348 3.9 21.7 1.0
OD2 G:ASP324 4.0 16.8 1.0
N G:ALA346 4.0 35.3 1.0
CB G:ASP324 4.1 17.7 1.0
CA G:TYR347 4.1 25.4 1.0
N G:GLY297 4.2 14.7 1.0
O G:HOH1186 4.3 14.1 1.0
CA G:GLY297 4.3 14.3 1.0
N G:SER298 4.3 14.6 1.0
CA G:SER298 4.5 15.8 1.0
CA G:ASN294 4.5 19.9 1.0
C G:ALA346 4.6 32.3 1.0
O G:PRO326 4.6 17.5 1.0
N G:ASN294 4.6 20.0 1.0
CA G:ALA346 4.7 34.0 1.0
CA G:ASP293 4.8 21.9 1.0
C G:ASN294 4.9 19.0 1.0
CB G:ASP293 4.9 21.6 1.0
N G:ASP293 4.9 21.5 1.0
N G:GLY345 5.0 33.4 1.0

Calcium binding site 8 out of 8 in 2hty

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Calcium binding site 8 out of 8 in the N1 Neuraminidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of N1 Neuraminidase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca998

b:40.2
occ:1.00
O H:TYR347 2.2 46.8 1.0
OD1 H:ASP324 2.3 39.3 1.0
O H:GLY297 2.5 40.5 1.0
O H:ASP293 2.6 39.0 1.0
O H:GLY345 2.8 52.5 1.0
C H:GLY345 3.1 53.4 1.0
C H:TYR347 3.2 45.9 1.0
CA H:GLY345 3.4 54.8 1.0
C H:GLY297 3.4 38.0 1.0
CG H:ASP324 3.5 38.2 1.0
N H:TYR347 3.6 50.0 1.0
C H:ASP293 3.9 39.2 1.0
CA H:GLY348 4.0 41.3 1.0
N H:ALA346 4.0 53.0 1.0
N H:GLY348 4.1 43.4 1.0
N H:GLY297 4.1 37.2 1.0
CA H:TYR347 4.2 47.7 1.0
CB H:ASP324 4.2 37.2 1.0
N H:SER298 4.2 36.8 1.0
OD2 H:ASP324 4.3 38.7 1.0
CA H:GLY297 4.3 37.2 1.0
CA H:SER298 4.4 35.3 1.0
O H:PRO326 4.4 39.4 1.0
CA H:ASN294 4.4 41.1 1.0
C H:ALA346 4.5 52.3 1.0
CA H:ALA346 4.6 52.8 1.0
N H:ASN294 4.6 39.8 1.0
C H:ASN294 4.8 40.8 1.0
N H:GLY345 4.8 56.3 1.0
CA H:ASP293 4.9 38.8 1.0

Reference:

R.J.Russell, L.F.Haire, D.J.Stevens, P.J.Collins, Y.P.Lin, G.M.Blackburn, A.J.Hay, S.J.Gamblin, J.J.Skehel. The Structure of H5N1 Avian Influenza Neuraminidase Suggests New Opportunities For Drug Design. Nature V. 443 45 2006.
ISSN: ISSN 0028-0836
PubMed: 16915235
DOI: 10.1038/NATURE05114
Page generated: Fri Jul 12 12:50:26 2024

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