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Calcium in PDB 3nss: The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites

Protein crystallography data

The structure of The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites, PDB code: 3nss was solved by Q.Li, J.X.Qi, W.Zhang, C.J.Vavricka, Y.Shi, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.98 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.537, 137.857, 118.512, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.6

Calcium Binding Sites:

The binding sites of Calcium atom in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites (pdb code 3nss). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites, PDB code: 3nss:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3nss

Go back to Calcium Binding Sites List in 3nss
Calcium binding site 1 out of 5 in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:9.7
occ:1.00
 O A:ASN347 2.5 9.2 1.0
O A:ASP293 2.5 8.4 1.0
OD2 A:ASP324 2.5 8.5 1.0
O A:GLY345 2.5 10.2 1.0
O A:GLY297 2.6 8.5 1.0
O A:HOH476 2.6 11.5 1.0
C A:GLY345 3.5 14.9 1.0
CG A:ASP324 3.6 13.2 1.0
C A:ASN347 3.6 13.4 1.0
C A:GLY297 3.6 12.6 1.0
C A:ASP293 3.7 8.2 1.0
CA A:GLY348 4.0 7.6 1.0
O A:ALA346 4.1 9.3 1.0
O A:HOH41 4.1 6.9 1.0
CA A:GLY345 4.1 13.8 1.0
C A:ALA346 4.2 10.5 1.0
N A:GLY348 4.3 7.3 1.0
CB A:ASP324 4.3 9.4 1.0
CA A:ASN294 4.4 8.1 1.0
N A:GLY297 4.4 9.7 1.0
CA A:SER298 4.4 11.1 1.0
N A:SER298 4.4 10.7 1.0
OD1 A:ASP324 4.5 6.6 1.0
N A:ASN347 4.5 11.6 1.0
N A:ALA346 4.5 11.0 1.0
N A:ASN294 4.5 7.3 1.0
CA A:GLY297 4.6 8.8 1.0
O A:ASN344 4.6 11.4 1.0
CA A:ASN347 4.7 13.1 1.0
CA A:ASP293 4.7 7.3 1.0
CA A:ALA346 4.7 13.2 1.0
C A:ASN294 4.7 11.0 1.0
CB A:ASP293 4.8 6.3 1.0
OD1 A:ASP293 4.9 9.1 1.0
O A:PRO326 4.9 9.9 1.0
N A:ASP293 4.9 7.5 1.0

Calcium binding site 2 out of 5 in 3nss

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Calcium binding site 2 out of 5 in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:16.5
occ:1.00
 OD1 A:ASN381 2.5 10.1 1.0
OD1 A:ASP379 2.5 11.4 1.0
O A:HOH565 2.6 23.2 1.0
O A:ASN389 2.6 14.2 1.0
O A:HOH493 2.6 32.1 1.0
OD1 A:ASP387 2.6 20.6 1.0
OD2 A:ASP379 3.1 15.9 1.0
CG A:ASP379 3.2 12.7 1.0
CG A:ASP387 3.3 18.8 1.0
OD2 A:ASP387 3.3 16.9 1.0
C A:ASN389 3.6 15.8 1.0
CG A:ASN381 3.7 14.5 1.0
N A:ASN389 4.0 12.9 1.0
O A:ASP387 4.1 14.4 1.0
CA A:ASN389 4.2 13.2 1.0
ND2 A:ASN381 4.2 22.7 1.0
CB A:ASN389 4.4 17.1 1.0
C A:ASP387 4.4 16.1 1.0
N A:GLY382 4.5 7.1 1.0
C A:ASN381 4.6 10.8 1.0
CB A:ASP379 4.6 7.8 1.0
N A:ASN381 4.6 6.5 1.0
CB A:ASP387 4.7 16.8 1.0
CA A:GLY382 4.7 8.3 1.0
N A:PHE390 4.7 12.1 1.0
O A:ASN381 4.9 12.3 1.0
C A:ASN388 4.9 18.8 1.0
CB A:ASN381 4.9 10.4 1.0
O A:HOH59 4.9 17.6 1.0
CA A:ASN381 4.9 9.0 1.0
N A:ASN388 5.0 16.6 1.0
CA A:ASP387 5.0 19.5 1.0
CA A:PHE390 5.0 11.2 1.0

Calcium binding site 3 out of 5 in 3nss

Go back to Calcium Binding Sites List in 3nss
Calcium binding site 3 out of 5 in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:21.6
occ:0.50
 O B:HOH903 2.5 59.0 1.0
O B:HOH905 2.6 33.9 0.5
O B:HOH902 2.7 59.7 1.0
O B:HOH488 2.9 28.6 0.5
OD2 B:ASP113 4.4 14.8 1.0
OD2 A:ASP113 4.4 14.2 1.0
OD1 B:ASP113 4.5 11.2 1.0
OD1 A:ASP113 4.6 11.8 1.0
O A:HOH483 4.8 30.6 1.0
O B:HOH606 4.8 35.0 1.0
CG B:ASP113 4.8 11.5 1.0
CG A:ASP113 4.9 10.5 1.0

Calcium binding site 4 out of 5 in 3nss

Go back to Calcium Binding Sites List in 3nss
Calcium binding site 4 out of 5 in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:8.2
occ:1.00
 O B:ASN347 2.5 7.2 1.0
O B:ASP293 2.5 6.2 1.0
OD2 B:ASP324 2.5 7.8 1.0
O B:GLY297 2.6 8.1 1.0
O B:GLY345 2.6 7.7 1.0
O B:HOH3 2.6 10.8 1.0
C B:GLY345 3.6 11.4 1.0
CG B:ASP324 3.6 9.3 1.0
C B:ASN347 3.6 9.2 1.0
C B:GLY297 3.6 9.1 1.0
C B:ASP293 3.7 7.4 1.0
CA B:GLY348 4.0 4.4 1.0
O B:ALA346 4.1 8.2 1.0
O B:HOH22 4.1 5.8 1.0
C B:ALA346 4.2 10.1 1.0
CA B:GLY345 4.2 10.7 1.0
N B:GLY348 4.3 6.4 1.0
CB B:ASP324 4.3 8.6 1.0
N B:GLY297 4.3 6.7 1.0
CA B:ASN294 4.4 8.2 1.0
N B:SER298 4.4 9.8 1.0
CA B:SER298 4.4 9.5 1.0
OD1 B:ASP324 4.4 5.8 1.0
N B:ASN347 4.5 11.0 1.0
N B:ASN294 4.5 8.0 1.0
CA B:GLY297 4.5 8.5 1.0
N B:ALA346 4.5 12.0 1.0
O B:ASN344 4.6 10.6 1.0
CA B:ASP293 4.7 6.3 1.0
CA B:ASN347 4.7 12.4 1.0
CA B:ALA346 4.7 12.4 1.0
CB B:ASP293 4.8 5.3 1.0
C B:ASN294 4.8 8.8 1.0
N B:ASP293 4.8 6.2 1.0
OD1 B:ASP293 4.9 8.6 1.0
O B:PRO326 4.9 7.7 1.0

Calcium binding site 5 out of 5 in 3nss

Go back to Calcium Binding Sites List in 3nss
Calcium binding site 5 out of 5 in the The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:14.1
occ:1.00
 OD1 B:ASP379 2.5 6.8 1.0
OD1 B:ASN381 2.5 9.0 1.0
O B:ASN389 2.6 13.1 1.0
OD1 B:ASP387 2.6 17.6 1.0
O B:HOH56 2.8 28.1 1.0
O B:HOH575 2.9 22.9 1.0
OD2 B:ASP379 3.0 10.7 1.0
CG B:ASP379 3.1 7.1 1.0
CG B:ASP387 3.3 18.3 1.0
OD2 B:ASP387 3.4 18.8 1.0
CG B:ASN381 3.6 17.5 1.0
C B:ASN389 3.7 13.8 1.0
O B:ASP387 4.0 11.8 1.0
N B:ASN389 4.1 12.8 1.0
ND2 B:ASN381 4.2 20.3 1.0
CA B:ASN389 4.3 12.9 1.0
N B:GLY382 4.4 7.1 1.0
C B:ASP387 4.5 12.5 1.0
CB B:ASN389 4.5 18.1 1.0
CB B:ASP379 4.5 5.6 1.0
C B:ASN381 4.5 10.3 1.0
N B:ASN381 4.6 7.1 1.0
CA B:GLY382 4.6 6.6 1.0
CB B:ASP387 4.7 16.4 1.0
O B:HOH532 4.7 37.0 1.0
N B:PHE390 4.8 11.3 1.0
CB B:ASN381 4.8 8.3 1.0
O B:ASN381 4.9 10.0 1.0
O B:HOH475 4.9 12.3 1.0
CA B:ASN381 4.9 8.3 1.0
C B:ASN388 4.9 19.8 1.0
CA B:ASP387 5.0 15.8 1.0
O B:HOH867 5.0 41.4 1.0

Reference:

Q.Li, J.X.Qi, W.Zhang, C.J.Vavricka, Y.Shi, J.H.Wei, E.G.Feng, J.S.Shen, J.L.Chen, D.Liu, J.H.He, J.H.Yan, H.Liu, H.L.Jiang, M.K.Teng, X.B.Li, G.F.Gao. The 2009 Pandemic H1N1 Neuraminidase N1 Lacks the 150-Cavity in Its Active Site Nat.Struct.Mol.Biol. V. 17 1266 2010.
ISSN: ISSN 1545-9993
PubMed: 20852645
DOI: 10.1038/NSMB.1909
Page generated: Sat Jul 13 15:08:15 2024

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