Atomistry » Calcium » PDB 3ti4-3tvc » 3ti4
Atomistry »
  Calcium »
    PDB 3ti4-3tvc »
      3ti4 »

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

Go back to Calcium Binding Sites List in 3ti4
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 Dec 12 04:31:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy