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Calcium in PDB 3ti4: Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate

Protein crystallography data

The structure of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate, PDB code: 3ti4 was solved by C.J.Vavricka, Q.Li, Y.Wu, J.Qi, M.Wang, Y.Liu, F.Gao, J.Liu, E.Feng, J.He, J.Wang, H.Liu, H.Jiang, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.89 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.664, 137.102, 118.571, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate (pdb code 3ti4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate, PDB code: 3ti4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3ti4

Go back to Calcium Binding Sites List in 3ti4
Calcium binding site 1 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:5.8
occ:1.00
 O A:ASP293 2.4 6.5 1.0
OD2 A:ASP324 2.4 5.9 1.0
O A:ASN347 2.4 7.5 1.0
O A:GLY297 2.4 6.2 1.0
O A:GLY345 2.4 8.5 1.0
O A:HOH5 2.5 9.5 1.0
C A:GLY345 3.5 8.2 1.0
CG A:ASP324 3.5 6.3 1.0
C A:ASN347 3.5 7.6 1.0
C A:GLY297 3.5 5.5 1.0
C A:ASP293 3.6 7.0 1.0
CA A:GLY348 4.0 5.7 1.0
O A:HOH37 4.0 7.6 1.0
O A:ALA346 4.1 8.7 1.0
CA A:GLY345 4.1 8.4 1.0
C A:ALA346 4.2 8.0 1.0
CB A:ASP324 4.2 6.1 1.0
N A:GLY348 4.2 6.1 1.0
CA A:ASN294 4.3 7.5 1.0
N A:GLY297 4.3 6.3 1.0
CA A:SER298 4.3 7.4 1.0
N A:SER298 4.3 6.1 1.0
N A:ASN294 4.4 7.0 1.0
OD1 A:ASP324 4.4 7.3 1.0
N A:ASN347 4.4 9.0 1.0
N A:ALA346 4.4 8.2 1.0
CA A:GLY297 4.5 6.4 1.0
CA A:ASN347 4.6 9.7 1.0
CA A:ASP293 4.6 6.1 1.0
CA A:ALA346 4.6 8.0 1.0
O A:ASN344 4.7 9.7 1.0
CB A:ASP293 4.7 7.1 1.0
C A:ASN294 4.7 7.9 1.0
OD1 A:ASP293 4.8 7.8 1.0
N A:ASP293 4.8 5.8 1.0
O A:PRO326 4.9 7.8 1.0

Calcium binding site 2 out of 5 in 3ti4

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Calcium binding site 2 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:11.7
occ:1.00
 OD1 A:ASN381 2.4 12.9 1.0
O A:ASN389 2.5 13.8 1.0
OD1 A:ASP387 2.5 14.5 1.0
OD1 A:ASP379 2.5 10.7 1.0
O A:HOH744 2.5 21.8 1.0
O A:HOH488 2.5 15.1 1.0
OD2 A:ASP379 2.8 10.8 1.0
CG A:ASP379 3.0 9.6 1.0
CG A:ASP387 3.3 14.2 1.0
CG A:ASN381 3.5 13.1 1.0
C A:ASN389 3.5 14.5 1.0
OD2 A:ASP387 3.6 15.7 1.0
O A:ASP387 3.9 9.9 1.0
N A:ASN389 4.0 15.9 1.0
ND2 A:ASN381 4.0 14.2 1.0
O A:HOH844 4.1 33.6 1.0
CA A:ASN389 4.1 15.8 1.0
CB A:ASN389 4.3 17.7 1.0
C A:ASP387 4.4 11.6 1.0
CB A:ASP379 4.4 8.3 1.0
N A:GLY382 4.4 8.4 1.0
C A:ASN381 4.5 10.0 1.0
N A:PHE390 4.6 13.9 1.0
N A:ASN381 4.6 9.5 1.0
CA A:GLY382 4.6 8.3 1.0
CB A:ASP387 4.7 12.7 1.0
CB A:ASN381 4.7 12.7 1.0
O A:ASN381 4.8 11.0 1.0
CA A:PHE390 4.8 12.7 1.0
CA A:ASN381 4.8 10.3 1.0
OG A:SER319 4.8 10.0 1.0
O A:HOH642 4.8 22.6 1.0
C A:ASN388 4.9 18.4 1.0
CA A:ASP387 4.9 11.6 1.0
N A:ASN388 5.0 15.2 1.0

Calcium binding site 3 out of 5 in 3ti4

Go back to Calcium Binding Sites List in 3ti4
Calcium binding site 3 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:14.3
occ:0.50
 O A:HOH651 2.1 30.2 0.5
O A:HOH717 2.4 40.0 1.0
O A:HOH732 2.5 50.3 1.0
O A:HOH1049 4.2 40.3 1.0
O B:HOH574 4.3 35.0 1.0
O A:HOH594 4.3 27.7 1.0
OD2 B:ASP113 4.6 8.8 1.0
OD2 A:ASP113 4.6 8.2 1.0
OD1 A:ASP113 4.6 9.5 1.0
OD1 B:ASP113 4.6 9.0 1.0

Calcium binding site 4 out of 5 in 3ti4

Go back to Calcium Binding Sites List in 3ti4
Calcium binding site 4 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:5.3
occ:1.00
 O B:ASN347 2.3 7.0 1.0
O B:ASP293 2.4 6.6 1.0
OD2 B:ASP324 2.4 5.1 1.0
O B:GLY297 2.4 6.5 1.0
O B:GLY345 2.4 7.3 1.0
O B:HOH8 2.5 7.6 1.0
C B:GLY345 3.5 8.0 1.0
CG B:ASP324 3.5 5.4 1.0
C B:GLY297 3.5 5.8 1.0
C B:ASN347 3.5 6.8 1.0
C B:ASP293 3.6 6.5 1.0
CA B:GLY348 4.0 4.8 1.0
O B:HOH50 4.1 6.2 1.0
O B:ALA346 4.1 7.6 1.0
C B:ALA346 4.1 8.2 1.0
CA B:GLY345 4.2 8.4 1.0
CB B:ASP324 4.2 5.8 1.0
N B:GLY348 4.3 5.9 1.0
N B:GLY297 4.3 6.4 1.0
CA B:ASN294 4.3 6.4 1.0
N B:SER298 4.3 5.8 1.0
CA B:SER298 4.3 6.6 1.0
N B:ASN347 4.4 7.6 1.0
OD1 B:ASP324 4.4 5.7 1.0
N B:ASN294 4.4 6.7 1.0
CA B:GLY297 4.4 7.3 1.0
N B:ALA346 4.5 7.8 1.0
CA B:ASN347 4.6 8.7 1.0
CA B:ASP293 4.6 6.0 1.0
CA B:ALA346 4.7 8.0 1.0
CB B:ASP293 4.7 5.8 1.0
C B:ASN294 4.7 7.0 1.0
O B:ASN344 4.7 8.9 1.0
N B:ASP293 4.8 5.3 1.0
OD1 B:ASP293 4.8 6.5 1.0
O B:PRO326 4.9 7.6 1.0
CG B:ASP293 5.0 6.8 1.0

Calcium binding site 5 out of 5 in 3ti4

Go back to Calcium Binding Sites List in 3ti4
Calcium binding site 5 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir Octanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:9.8
occ:1.00
 OD1 B:ASN381 2.4 11.3 1.0
OD1 B:ASP379 2.4 8.1 1.0
OD1 B:ASP387 2.5 14.1 1.0
O B:HOH610 2.5 17.5 1.0
O B:HOH24 2.5 11.7 1.0
O B:ASN389 2.5 13.2 1.0
OD2 B:ASP379 2.8 9.1 1.0
CG B:ASP379 2.9 7.9 1.0
CG B:ASP387 3.3 14.7 1.0
C B:ASN389 3.6 12.7 1.0
CG B:ASN381 3.6 11.3 1.0
OD2 B:ASP387 3.6 15.8 1.0
O B:ASP387 4.0 9.6 1.0
N B:ASN389 4.0 14.3 1.0
O B:HOH829 4.1 29.9 1.0
ND2 B:ASN381 4.1 13.6 1.0
CA B:ASN389 4.2 14.2 1.0
CB B:ASP379 4.4 7.1 1.0
CB B:ASN389 4.4 16.7 1.0
N B:GLY382 4.4 7.8 1.0
C B:ASP387 4.4 10.7 1.0
C B:ASN381 4.5 8.9 1.0
N B:ASN381 4.6 8.7 1.0
CA B:GLY382 4.6 7.5 1.0
N B:PHE390 4.6 11.7 1.0
CB B:ASP387 4.7 12.8 1.0
CB B:ASN381 4.8 10.3 1.0
OG B:SER319 4.8 9.3 1.0
CA B:ASN381 4.8 9.1 1.0
CA B:PHE390 4.8 10.7 1.0
O B:HOH628 4.9 18.9 1.0
O B:ASN381 4.9 9.3 1.0
CA B:ASP387 5.0 10.9 1.0
C B:ASN388 5.0 16.1 1.0
CA B:ASP379 5.0 6.8 1.0

Reference:

C.J.Vavricka, Q.Li, Y.Wu, J.Qi, M.Wang, Y.Liu, F.Gao, J.Liu, E.Feng, J.He, J.Wang, H.Liu, H.Jiang, G.F.Gao. Structural and Functional Analysis of Laninamivir and Its Octanoate Prodrug Reveals Group Specific Mechanisms For Influenza Na Inhibition Plos Pathog. V. 7 02249 2011.
ISSN: ISSN 1553-7366
PubMed: 22028647
DOI: 10.1371/JOURNAL.PPAT.1002249
Page generated: Sat Jul 13 19:45:29 2024

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