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Calcium in PDB 4b7q: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis

Protein crystallography data

The structure of H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis, PDB code: 4b7q was solved by J.Liu, E.Van Der Vries, S.G.Vachieri, X.Xiong, P.J.Collins, P.A.Walker, L.F.Haire, A.J.Hay, M.Schutten, A.D.M.E.Osterhaus, S.R.Martin, C.A.B.Boucher, J.J.Skehel, S.J.Gamblin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.494 / 2.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.650, 148.820, 166.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 25.81

Calcium Binding Sites:

The binding sites of Calcium atom in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis (pdb code 4b7q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis, PDB code: 4b7q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4b7q

Go back to Calcium Binding Sites List in 4b7q
Calcium binding site 1 out of 5 in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:42.3
occ:1.00
 O A:GLY342 2.5 46.1 1.0
O A:ASN344 2.5 46.1 1.0
O A:GLY298 2.7 46.8 1.0
OD2 A:ASP324 2.8 37.2 1.0
O A:ASP294 2.9 45.2 1.0
C A:GLY342 3.3 43.2 1.0
CG A:ASP324 3.5 38.0 1.0
C A:GLY298 3.5 35.3 1.0
C A:ASN344 3.6 40.7 1.0
CA A:GLY342 3.8 45.0 1.0
O A:ALA343 3.8 41.7 1.0
O A:ASN341 4.0 44.0 1.0
CA A:SER299 4.0 29.3 1.0
CA A:GLY345 4.0 22.8 1.0
C A:ALA343 4.1 43.2 1.0
N A:SER299 4.1 32.4 1.0
O A:PRO326 4.1 35.6 1.0
C A:ASP294 4.1 43.8 1.0
OD1 A:ASP324 4.1 37.9 1.0
CB A:ASP324 4.2 38.5 1.0
N A:GLY345 4.2 33.4 1.0
N A:ALA343 4.3 40.3 1.0
N A:GLY298 4.4 39.5 1.0
O A:HOH2060 4.4 29.6 1.0
N A:ASN344 4.5 45.5 1.0
CA A:GLY298 4.5 36.8 1.0
CA A:ALA343 4.6 38.7 1.0
CA A:ASN344 4.7 41.4 1.0
CB A:SER299 4.7 36.8 1.0
CA A:ASN295 4.8 35.3 1.0
N A:GLY342 4.8 42.2 1.0
C A:ASN341 4.8 42.6 1.0
N A:ASN295 4.9 33.2 1.0

Calcium binding site 2 out of 5 in 4b7q

Go back to Calcium Binding Sites List in 4b7q
Calcium binding site 2 out of 5 in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:77.6
occ:1.00
 OD1 A:ASP376 2.6 59.4 1.0
OD1 A:ASN378 2.6 44.0 1.0
O A:ASN386 2.9 64.2 1.0
OD2 A:ASP376 3.1 41.6 1.0
CG A:ASP376 3.2 47.2 1.0
O A:ASP384 3.3 51.1 1.0
CG A:ASN378 3.3 49.3 1.0
ND2 A:ASN378 3.4 54.1 1.0
CB A:ASP384 3.5 66.9 1.0
N A:ASN386 3.6 46.6 1.0
OD2 A:ASP384 3.6 93.6 1.0
C A:ASP384 3.7 58.5 1.0
C A:ASN386 3.7 59.3 1.0
CG A:ASP384 3.9 85.7 1.0
CB A:ASN386 3.9 70.1 1.0
CA A:ASN386 3.9 58.9 1.0
CA A:ASP384 4.1 58.4 1.0
N A:ASN385 4.4 62.9 1.0
N A:ASP384 4.5 52.1 1.0
C A:ASN385 4.6 50.1 1.0
N A:GLY379 4.6 42.5 1.0
CB A:ASP376 4.7 44.1 1.0
CB A:ASN378 4.7 44.8 1.0
CA A:GLY379 4.7 37.5 1.0
C A:ASN378 4.8 48.6 1.0
CA A:ASN385 4.8 57.9 1.0
N A:PHE387 4.8 55.3 1.0
O A:GLY382 4.9 60.3 1.0
OD1 A:ASP384 5.0 90.4 1.0
N A:ASN378 5.0 39.1 1.0

Calcium binding site 3 out of 5 in 4b7q

Go back to Calcium Binding Sites List in 4b7q
Calcium binding site 3 out of 5 in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:20.7
occ:1.00
 O B:ASP294 2.3 17.1 1.0
O B:HOH2052 2.3 18.0 1.0
O B:ASN344 2.4 21.1 1.0
O B:GLY342 2.5 33.9 1.0
O B:GLY298 2.5 25.1 1.0
OD2 B:ASP324 2.7 30.4 1.0
C B:GLY342 3.4 29.5 1.0
C B:ASP294 3.5 29.0 1.0
C B:ASN344 3.5 20.7 1.0
C B:GLY298 3.6 32.2 1.0
CG B:ASP324 3.7 30.4 1.0
CA B:GLY342 4.0 25.1 1.0
O B:HOH2051 4.1 15.2 1.0
CA B:GLY345 4.1 35.5 1.0
C B:ALA343 4.2 34.4 1.0
O B:ALA343 4.2 35.3 1.0
CA B:ASN295 4.3 33.4 1.0
CA B:SER299 4.3 26.1 1.0
N B:GLY345 4.3 16.8 1.0
N B:SER299 4.3 30.7 1.0
N B:GLY298 4.3 30.9 1.0
N B:ASN295 4.4 32.8 1.0
N B:ASN344 4.4 17.5 1.0
CB B:ASP324 4.4 21.2 1.0
N B:ALA343 4.4 35.0 1.0
CA B:ASP294 4.5 22.0 1.0
C B:ASN295 4.5 31.8 1.0
OD1 B:ASP294 4.5 36.9 1.0
CB B:ASP294 4.5 17.1 1.0
OD1 B:ASP324 4.6 36.3 1.0
CA B:ASN344 4.6 17.2 1.0
CA B:GLY298 4.6 34.8 1.0
O B:ASN341 4.6 36.1 1.0
O B:ASN295 4.6 23.4 1.0
CA B:ALA343 4.7 31.4 1.0
N B:ASP294 4.8 16.7 1.0
CG B:ASP294 4.9 36.0 1.0
O B:PRO326 4.9 29.2 1.0
CB B:SER299 4.9 22.1 1.0

Calcium binding site 4 out of 5 in 4b7q

Go back to Calcium Binding Sites List in 4b7q
Calcium binding site 4 out of 5 in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:26.2
occ:1.00
 O C:GLY342 2.3 22.2 1.0
O C:ASP294 2.4 17.5 1.0
O C:ASN344 2.4 45.5 1.0
O C:GLY298 2.4 21.2 1.0
OD2 C:ASP324 2.4 20.4 1.0
C C:GLY342 3.2 31.9 1.0
C C:ASN344 3.4 44.6 1.0
CG C:ASP324 3.5 26.5 1.0
C C:GLY298 3.5 25.1 1.0
C C:ASP294 3.6 18.8 1.0
O C:ALA343 3.7 32.3 1.0
CA C:GLY345 3.8 27.3 1.0
CA C:GLY342 3.9 14.5 1.0
C C:ALA343 3.9 30.2 1.0
N C:GLY345 4.1 37.7 1.0
CA C:SER299 4.2 20.2 1.0
N C:ALA343 4.2 37.3 1.0
N C:SER299 4.2 20.1 1.0
OD1 C:ASP324 4.2 34.6 1.0
CB C:ASP324 4.3 23.4 1.0
CA C:ASN295 4.4 18.9 1.0
N C:ASN344 4.4 31.4 1.0
N C:GLY298 4.4 27.1 1.0
N C:ASN295 4.4 20.9 1.0
CA C:ALA343 4.4 35.0 1.0
CA C:GLY298 4.5 25.8 1.0
O C:ASN341 4.5 46.6 1.0
CA C:ASN344 4.6 39.8 1.0
CA C:ASP294 4.6 18.5 1.0
O C:PRO326 4.8 31.6 1.0
CB C:ASP294 4.8 19.5 1.0
C C:ASN295 4.8 22.3 1.0
N C:ASP294 4.9 22.8 1.0
CB C:SER299 4.9 18.4 1.0
OD1 C:ASP294 5.0 23.1 1.0
N C:GLY342 5.0 25.0 1.0

Calcium binding site 5 out of 5 in 4b7q

Go back to Calcium Binding Sites List in 4b7q
Calcium binding site 5 out of 5 in the H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:41.4
occ:1.00
 O D:ASN344 2.3 38.1 1.0
O D:GLY298 2.5 43.7 1.0
O D:GLY342 2.5 61.7 1.0
O D:ASP294 2.7 47.5 1.0
OD2 D:ASP324 2.7 39.8 1.0
C D:ASN344 3.4 36.2 1.0
CG D:ASP324 3.4 36.4 1.0
C D:GLY342 3.5 53.0 1.0
C D:GLY298 3.6 28.7 1.0
O D:ALA343 3.8 49.9 1.0
C D:ASP294 3.9 38.7 1.0
CA D:GLY345 4.0 36.7 1.0
OD1 D:ASP324 4.0 34.3 1.0
C D:ALA343 4.0 41.8 1.0
N D:GLY345 4.1 30.4 1.0
CB D:ASP324 4.1 27.6 1.0
CA D:GLY342 4.2 54.5 1.0
O D:ASN341 4.2 62.5 1.0
CA D:SER299 4.2 29.9 1.0
N D:SER299 4.3 28.5 1.0
N D:ASN344 4.3 37.4 1.0
O D:PRO326 4.4 36.5 1.0
N D:GLY298 4.4 26.3 1.0
CA D:ASN344 4.4 39.1 1.0
N D:ALA343 4.5 44.7 1.0
CA D:GLY298 4.6 24.0 1.0
CA D:ASN295 4.6 33.2 1.0
N D:ASN295 4.7 30.5 1.0
CA D:ALA343 4.7 41.8 1.0
OG D:SER299 4.8 43.0 1.0
CA D:ASP294 4.9 39.5 1.0
CB D:ASP294 4.9 44.5 1.0
C D:ASN295 5.0 34.4 1.0
N D:ASP294 5.0 28.4 1.0

Reference:

E.Van Der Vries, P.J.Collins, S.G.Vachieri, X.Xiong, J.Liu, P.A.Walker, L.F.Haire, A.J.Hay, M.Schutten, A.D.M.E.Osterhaus, S.R.Martin, C.A.B.Boucher, J.J.Skehel, S.J.Gamblin. H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained By Kinetic and Structural Analysis Plos Pathog. V. 8 2914 2012.
ISSN: ISSN 1553-7366
PubMed: 23028314
DOI: 10.1371/JOURNAL.PPAT.1002914
Page generated: Sat Jul 13 22:37:31 2024

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