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Calcium in PDB 3ti8: Crystal Structure of Influenza A Virus Neuraminidase N5 Complexed with Laninamivir

Protein crystallography data

The structure of Crystal Structure of Influenza A Virus Neuraminidase N5 Complexed with Laninamivir, PDB code: 3ti8 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) 39.80 / 1.60
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 112.563, 112.563, 66.809, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 16.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Influenza A Virus Neuraminidase N5 Complexed with Laninamivir (pdb code 3ti8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Influenza A Virus Neuraminidase N5 Complexed with Laninamivir, PDB code: 3ti8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3ti8

Go back to Calcium Binding Sites List in 3ti8
Calcium binding site 1 out of 2 in the Crystal Structure of Influenza A Virus Neuraminidase N5 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 Influenza A Virus Neuraminidase N5 Complexed with Laninamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:11.3
occ:1.00
OD2 A:ASP324 2.4 11.7 1.0
O A:ASP293 2.4 10.6 1.0
O A:GLY297 2.4 12.3 1.0
O A:TYR347B 2.5 11.6 1.0
O A:HOH1 2.5 12.4 1.0
O A:HOH8 2.5 10.7 1.0
CG A:ASP324 3.5 12.0 1.0
C A:GLY297 3.6 13.2 1.0
C A:ASP293 3.6 9.9 1.0
C A:TYR347B 3.6 10.2 1.0
CA A:GLY348 3.9 9.5 1.0
O A:HOH526 4.0 12.7 1.0
N A:GLY348 4.2 9.5 1.0
CA A:MET298 4.2 12.4 1.0
N A:MET298 4.3 12.5 1.0
O A:HOH505 4.3 13.2 1.0
O A:THR346 4.3 13.2 1.0
CA A:ASN294 4.3 10.2 1.0
OD1 A:ASP324 4.4 12.0 1.0
CB A:ASP324 4.4 11.0 1.0
N A:ASN294 4.4 9.6 1.0
CA A:ASP293 4.6 9.7 1.0
OD1 A:ASP293 4.6 12.9 1.0
N A:GLY297 4.6 12.3 1.0
CA A:GLY297 4.6 12.8 1.0
CB A:ASP293 4.6 10.9 1.0
N A:TYR347B 4.7 11.7 1.0
C A:ASN294 4.7 11.0 1.0
N A:ASP293 4.8 10.0 1.0
N A:TRP295 4.8 10.2 1.0
CA A:TYR347B 4.8 10.3 1.0
O A:PRO326 4.9 14.2 1.0

Calcium binding site 2 out of 2 in 3ti8

Go back to Calcium Binding Sites List in 3ti8
Calcium binding site 2 out of 2 in the Crystal Structure of Influenza A Virus Neuraminidase N5 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 Influenza A Virus Neuraminidase N5 Complexed with Laninamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:10.1
occ:1.00
O B:ASP293 2.4 11.5 1.0
OD2 B:ASP324 2.4 11.8 1.0
O B:TYR347B 2.4 10.3 1.0
O B:GLY297 2.4 11.8 1.0
O B:HOH6 2.5 12.5 1.0
O B:HOH52 2.5 10.1 1.0
CG B:ASP324 3.5 10.9 1.0
C B:TYR347B 3.6 9.9 1.0
C B:ASP293 3.6 11.2 1.0
C B:GLY297 3.6 11.7 1.0
CA B:GLY348 3.9 8.0 1.0
O B:HOH78 4.1 11.1 1.0
N B:GLY348 4.2 8.6 1.0
O B:HOH20 4.3 11.2 1.0
CA B:MET298 4.3 10.5 1.0
O B:THR346 4.3 13.2 1.0
CA B:ASN294 4.3 9.8 1.0
N B:MET298 4.3 10.6 1.0
OD1 B:ASP324 4.4 10.8 1.0
CB B:ASP324 4.4 10.1 1.0
N B:ASN294 4.4 10.9 1.0
OD1 B:ASP293 4.5 10.7 1.0
CA B:ASP293 4.6 10.2 1.0
CA B:GLY297 4.6 10.8 1.0
N B:GLY297 4.6 11.1 1.0
CB B:ASP293 4.6 10.8 1.0
N B:TYR347B 4.7 10.3 1.0
C B:ASN294 4.7 9.7 1.0
N B:TRP295 4.8 9.8 1.0
CA B:TYR347B 4.8 9.9 1.0
N B:ASP293 4.8 9.4 1.0
O B:PRO326 4.9 11.5 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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