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Calcium in PDB 3ti3: Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir

Protein crystallography data

The structure of Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir, PDB code: 3ti3 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) 34.60 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.260, 137.089, 118.482, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir (pdb code 3ti3). 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, PDB code: 3ti3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3ti3

Go back to Calcium Binding Sites List in 3ti3
Calcium binding site 1 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:7.7
occ:1.00
 O A:ASN347 2.4 8.1 1.0
O A:ASP293 2.5 6.9 1.0
OD2 A:ASP324 2.5 4.3 1.0
O A:HOH4 2.5 10.1 1.0
O A:GLY345 2.5 7.4 1.0
O A:GLY297 2.6 7.8 1.0
C A:GLY345 3.5 12.0 1.0
CG A:ASP324 3.5 10.0 1.0
C A:ASN347 3.6 8.6 1.0
C A:GLY297 3.6 10.1 1.0
C A:ASP293 3.7 9.2 1.0
O A:ALA346 4.0 9.6 1.0
CA A:GLY348 4.0 7.5 1.0
O A:HOH57 4.1 7.7 1.0
C A:ALA346 4.2 9.1 1.0
CA A:GLY345 4.2 12.7 1.0
N A:GLY348 4.3 4.7 1.0
CB A:ASP324 4.3 9.7 1.0
N A:GLY297 4.3 8.8 1.0
CA A:ASN294 4.3 7.7 1.0
CA A:SER298 4.4 7.7 1.0
OD1 A:ASP324 4.4 7.4 1.0
N A:SER298 4.4 8.8 1.0
N A:ASN294 4.5 6.1 1.0
N A:ASN347 4.5 8.2 1.0
N A:ALA346 4.5 7.5 1.0
CA A:GLY297 4.5 7.8 1.0
O A:ASN344 4.6 11.8 1.0
CA A:ASN347 4.7 7.4 1.0
C A:ASN294 4.7 6.3 1.0
CA A:ASP293 4.7 5.6 1.0
CA A:ALA346 4.7 6.8 1.0
CB A:ASP293 4.8 5.7 1.0
OD1 A:ASP293 4.8 7.1 1.0
N A:ASP293 4.9 5.0 1.0
O A:PRO326 4.9 9.3 1.0

Calcium binding site 2 out of 5 in 3ti3

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:13.0
occ:1.00
 OD1 A:ASN381 2.4 12.6 1.0
OD1 A:ASP379 2.5 9.4 1.0
OD1 A:ASP387 2.5 16.5 1.0
O A:HOH689 2.5 24.1 1.0
O A:HOH42 2.5 15.0 1.0
O A:ASN389 2.6 12.7 1.0
OD2 A:ASP379 2.9 10.6 1.0
CG A:ASP379 3.0 8.9 1.0
CG A:ASP387 3.4 21.7 1.0
CG A:ASN381 3.6 13.1 1.0
OD2 A:ASP387 3.6 15.4 1.0
C A:ASN389 3.6 16.8 1.0
N A:ASN389 4.0 12.3 1.0
O A:ASP387 4.0 9.4 1.0
ND2 A:ASN381 4.1 22.4 1.0
CA A:ASN389 4.2 12.5 1.0
CB A:ASN389 4.4 24.3 1.0
CB A:ASP379 4.5 6.8 1.0
C A:ASP387 4.5 15.5 1.0
N A:GLY382 4.5 10.4 1.0
C A:ASN381 4.6 13.4 1.0
CA A:GLY382 4.6 7.7 1.0
N A:ASN381 4.6 10.4 1.0
N A:PHE390 4.7 14.1 1.0
CB A:ASP387 4.7 16.6 1.0
CB A:ASN381 4.8 13.3 1.0
O A:ASN381 4.9 12.6 1.0
CA A:ASN381 4.9 9.3 1.0
C A:ASN388 4.9 17.9 1.0
CA A:PHE390 4.9 13.8 1.0
O A:HOH546 5.0 20.5 1.0
OG A:SER319 5.0 8.5 1.0
CA A:ASP387 5.0 12.6 1.0

Calcium binding site 3 out of 5 in 3ti3

Go back to Calcium Binding Sites List in 3ti3
Calcium binding site 3 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:13.1
occ:0.50
 O A:HOH1302 2.4 20.1 0.5
O B:HOH716 2.4 30.2 1.0
O B:HOH1035 2.5 31.9 1.0
OD2 A:ASP113 4.4 10.3 1.0
OD2 B:ASP113 4.4 12.8 1.0
OD1 A:ASP113 4.5 10.5 1.0
O A:HOH561 4.6 29.0 1.0
OD1 B:ASP113 4.6 10.2 1.0
O B:HOH820 4.6 27.9 1.0
O A:HOH1208 4.7 33.8 1.0
CG A:ASP113 4.9 11.7 1.0
CG B:ASP113 4.9 12.9 1.0

Calcium binding site 4 out of 5 in 3ti3

Go back to Calcium Binding Sites List in 3ti3
Calcium binding site 4 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:7.5
occ:1.00
 O B:ASN347 2.4 7.0 1.0
OD2 B:ASP324 2.4 5.2 1.0
O B:ASP293 2.5 7.2 1.0
O B:HOH28 2.5 10.9 1.0
O B:GLY345 2.5 6.5 1.0
O B:GLY297 2.6 6.6 1.0
C B:GLY345 3.5 10.8 1.0
CG B:ASP324 3.5 9.9 1.0
C B:GLY297 3.6 8.4 1.0
C B:ASN347 3.6 7.3 1.0
C B:ASP293 3.7 7.8 1.0
O B:HOH77 4.0 7.2 1.0
O B:ALA346 4.0 9.1 1.0
CA B:GLY348 4.1 6.4 1.0
CA B:GLY345 4.2 10.6 1.0
C B:ALA346 4.2 10.1 1.0
CB B:ASP324 4.3 8.4 1.0
N B:GLY297 4.3 9.2 1.0
N B:GLY348 4.3 5.6 1.0
CA B:ASN294 4.3 7.0 1.0
CA B:SER298 4.4 5.8 1.0
N B:SER298 4.4 8.5 1.0
OD1 B:ASP324 4.4 6.6 1.0
N B:ASN294 4.5 4.6 1.0
N B:ASN347 4.5 8.7 1.0
N B:ALA346 4.5 9.2 1.0
CA B:GLY297 4.5 8.4 1.0
O B:ASN344 4.6 11.9 1.0
CA B:ASP293 4.7 6.8 1.0
CA B:ASN347 4.7 7.9 1.0
C B:ASN294 4.7 7.8 1.0
CA B:ALA346 4.7 9.4 1.0
CB B:ASP293 4.7 5.9 1.0
OD1 B:ASP293 4.8 8.5 1.0
O B:PRO326 4.9 8.6 1.0
N B:ASP293 4.9 4.2 1.0

Calcium binding site 5 out of 5 in 3ti3

Go back to Calcium Binding Sites List in 3ti3
Calcium binding site 5 out of 5 in the Crystal Structure of 2009 Pandemic H1N1 Neuraminidase Complexed with Laninamivir


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:11.4
occ:1.00
 OD1 B:ASP379 2.5 8.5 1.0
O B:HOH649 2.5 22.4 1.0
OD1 B:ASN381 2.5 9.4 1.0
O B:HOH38 2.5 14.3 1.0
OD1 B:ASP387 2.6 18.7 1.0
O B:ASN389 2.7 12.7 1.0
OD2 B:ASP379 2.9 8.2 1.0
CG B:ASP379 3.0 10.2 1.0
CG B:ASP387 3.4 18.9 1.0
OD2 B:ASP387 3.5 13.1 1.0
CG B:ASN381 3.7 17.0 1.0
C B:ASN389 3.7 17.5 1.0
O B:ASP387 4.0 11.7 1.0
N B:ASN389 4.0 11.5 1.0
CA B:ASN389 4.3 15.3 1.0
ND2 B:ASN381 4.3 20.9 1.0
N B:GLY382 4.4 9.9 1.0
C B:ASP387 4.4 13.1 1.0
CB B:ASN389 4.5 19.7 1.0
CB B:ASP379 4.5 8.7 1.0
C B:ASN381 4.5 12.6 1.0
CA B:GLY382 4.6 8.1 1.0
N B:ASN381 4.6 12.0 1.0
CB B:ASP387 4.7 18.5 1.0
N B:PHE390 4.7 13.3 1.0
O B:ASN381 4.8 12.0 1.0
CB B:ASN381 4.9 7.3 1.0
CA B:ASN381 4.9 7.3 1.0
O B:HOH585 4.9 17.0 1.0
OG B:SER319 4.9 10.6 1.0
C B:ASN388 5.0 13.9 1.0
CA B:ASP387 5.0 17.1 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 19:42:56 2024

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