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Calcium in PDB 4b7r: 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: 4b7r 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) 29.818 / 1.90
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 (%) 14.57 / 17.32

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 4b7r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 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: 4b7r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4b7r

Go back to Calcium Binding Sites List in 4b7r
Calcium binding site 1 out of 8 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:Ca501

b:34.9
occ:1.00
 O A:ASP294 2.3 31.0 1.0
O A:ASN344 2.3 32.0 1.0
O A:GLY298 2.4 32.6 1.0
O A:HOH2157 2.4 33.3 1.0
OD2 A:ASP324 2.5 35.0 1.0
O A:GLY342 2.5 33.2 1.0
CG A:ASP324 3.5 36.3 1.0
C A:ASP294 3.5 30.4 1.0
C A:GLY298 3.5 36.9 1.0
C A:GLY342 3.5 35.3 1.0
C A:ASN344 3.5 30.4 1.0
CA A:GLY345 4.0 24.9 1.0
O A:HOH2156 4.0 28.6 1.0
CA A:GLY342 4.2 38.7 1.0
O A:ALA343 4.2 34.1 1.0
N A:GLY298 4.2 33.3 1.0
N A:GLY345 4.2 23.9 1.0
CB A:ASP324 4.2 30.4 1.0
C A:ALA343 4.3 33.3 1.0
CA A:ASN295 4.3 28.1 1.0
N A:ASN295 4.4 28.9 1.0
N A:SER299 4.4 31.4 1.0
CA A:SER299 4.4 33.0 1.0
OD1 A:ASP324 4.4 29.8 1.0
CA A:GLY298 4.4 33.2 1.0
N A:ASN344 4.5 25.6 1.0
CA A:ASP294 4.5 30.7 1.0
N A:ALA343 4.5 33.8 1.0
CB A:ASP294 4.6 28.7 1.0
C A:ASN295 4.6 36.9 1.0
CA A:ASN344 4.7 27.9 1.0
N A:ASP294 4.7 26.8 1.0
CA A:ALA343 4.8 32.4 1.0
O A:ASN341 4.8 40.3 1.0
OD1 A:ASP294 4.8 36.3 1.0
O A:PRO326 4.9 33.7 1.0
CG A:ASP294 5.0 34.7 1.0

Calcium binding site 2 out of 8 in 4b7r

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Calcium binding site 2 out of 8 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:Ca502

b:59.5
occ:1.00
 OD1 A:ASP384 2.3 51.2 1.0
O A:ASN386 2.4 47.4 1.0
OD1 A:ASP376 2.4 40.1 1.0
OD1 A:ASN378 2.4 53.1 1.0
O A:HOH2187 2.5 48.5 1.0
O A:HOH2186 2.7 43.2 1.0
OD2 A:ASP376 3.0 38.5 1.0
CG A:ASP376 3.1 40.2 1.0
CG A:ASP384 3.3 53.9 1.0
C A:ASN386 3.4 48.3 1.0
OD2 A:ASP384 3.5 66.2 1.0
CG A:ASN378 3.6 48.4 1.0
N A:ASN386 3.7 46.8 1.0
O A:ASP384 3.9 42.3 1.0
CA A:ASN386 3.9 49.1 1.0
CB A:ASN386 4.0 53.4 1.0
ND2 A:ASN378 4.1 56.1 1.0
C A:ASP384 4.3 44.8 1.0
CB A:ASP376 4.5 36.4 1.0
CB A:ASP384 4.6 43.8 1.0
N A:PHE387 4.6 45.6 1.0
N A:ASN378 4.6 35.7 1.0
C A:ASN385 4.7 50.5 1.0
N A:GLY379 4.7 39.5 1.0
C A:ASN378 4.7 42.5 1.0
CB A:ASN378 4.8 39.5 1.0
N A:ASN385 4.9 46.9 1.0
CA A:ASP384 4.9 45.8 1.0
CA A:GLY379 4.9 36.1 1.0
CA A:ASN378 5.0 36.4 1.0
CD A:PRO377 5.0 40.4 1.0
CA A:PHE387 5.0 45.9 1.0

Calcium binding site 3 out of 8 in 4b7r

Go back to Calcium Binding Sites List in 4b7r
Calcium binding site 3 out of 8 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:Ca501

b:25.0
occ:1.00
 O B:ASN344 2.3 23.4 1.0
O B:ASP294 2.3 23.1 1.0
OD2 B:ASP324 2.3 23.1 1.0
O B:GLY342 2.4 25.4 1.0
O B:GLY298 2.4 21.5 1.0
O B:HOH2151 2.4 24.4 1.0
C B:GLY342 3.4 27.9 1.0
C B:ASN344 3.5 22.3 1.0
CG B:ASP324 3.5 26.5 1.0
C B:GLY298 3.5 25.7 1.0
C B:ASP294 3.5 26.0 1.0
CA B:GLY345 4.0 22.4 1.0
O B:HOH2149 4.0 22.3 1.0
CA B:GLY342 4.1 23.9 1.0
C B:ALA343 4.2 28.8 1.0
O B:ALA343 4.2 26.5 1.0
N B:GLY345 4.2 19.4 1.0
CA B:ASN295 4.2 26.1 1.0
CB B:ASP324 4.3 24.0 1.0
N B:GLY298 4.3 22.7 1.0
CA B:SER299 4.3 21.7 1.0
N B:ASN344 4.3 26.1 1.0
N B:SER299 4.3 20.6 1.0
N B:ASN295 4.3 23.4 1.0
OD1 B:ASP324 4.4 21.7 1.0
CA B:GLY298 4.5 24.5 1.0
N B:ALA343 4.5 27.2 1.0
CA B:ASN344 4.5 26.1 1.0
CA B:ASP294 4.6 22.3 1.0
C B:ASN295 4.6 27.0 1.0
CB B:ASP294 4.7 19.1 1.0
CA B:ALA343 4.7 29.2 1.0
O B:ASN341 4.7 26.0 1.0
N B:ASP294 4.7 22.3 1.0
OD1 B:ASP294 4.8 25.9 1.0
O B:PRO326 4.9 23.4 1.0

Calcium binding site 4 out of 8 in 4b7r

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Calcium binding site 4 out of 8 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
B:Ca502

b:49.6
occ:1.00
 OD1 B:ASP376 2.3 20.8 1.0
OD1 B:ASP384 2.4 27.6 1.0
OD1 B:ASN378 2.4 31.2 1.0
O B:ASN386 2.4 29.0 1.0
O B:HOH2199 2.5 33.6 1.0
O B:HOH2200 2.9 34.6 1.0
CG B:ASP376 3.0 24.1 1.0
OD2 B:ASP376 3.1 25.0 1.0
C B:ASN386 3.4 28.2 1.0
CG B:ASP384 3.4 34.1 1.0
CG B:ASN378 3.5 35.6 1.0
OD2 B:ASP384 3.7 51.2 1.0
CB B:ASN386 3.7 26.9 1.0
N B:ASN386 3.7 30.8 1.0
CA B:ASN386 3.8 27.7 1.0
O B:HOH2205 3.9 40.5 1.0
O B:ASP384 4.1 26.3 1.0
ND2 B:ASN378 4.2 41.5 1.0
N B:ASN378 4.3 24.4 1.0
CB B:ASP376 4.4 20.6 1.0
O B:HOH2208 4.4 26.1 1.0
N B:PHE387 4.5 24.4 1.0
C B:ASP384 4.5 24.1 1.0
C B:ASN378 4.6 26.3 1.0
CB B:ASN378 4.7 30.8 1.0
N B:GLY379 4.7 24.3 1.0
C B:ASN385 4.7 26.3 1.0
CB B:ASP384 4.7 31.3 1.0
CD B:PRO377 4.7 24.6 1.0
CA B:ASN378 4.7 24.4 1.0
CA B:ASP376 4.8 20.6 1.0
CG B:ASN386 4.9 29.9 1.0
N B:PRO377 4.9 22.2 1.0
O B:ASN378 4.9 24.6 1.0
CA B:PHE387 4.9 29.6 1.0
C B:ASP376 4.9 21.7 1.0

Calcium binding site 5 out of 8 in 4b7r

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Calcium binding site 5 out of 8 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
C:Ca501

b:25.4
occ:1.00
 O C:ASN344 2.3 22.1 1.0
O C:ASP294 2.3 20.8 1.0
OD2 C:ASP324 2.3 24.4 1.0
O C:GLY298 2.3 21.5 1.0
O C:HOH2162 2.4 23.8 1.0
O C:GLY342 2.5 23.4 1.0
C C:GLY298 3.4 25.5 1.0
CG C:ASP324 3.5 26.1 1.0
C C:GLY342 3.5 23.9 1.0
C C:ASN344 3.5 25.3 1.0
C C:ASP294 3.6 26.2 1.0
O C:HOH2159 4.0 20.3 1.0
CA C:GLY345 4.0 17.2 1.0
CA C:GLY342 4.1 25.2 1.0
O C:ALA343 4.2 22.4 1.0
CB C:ASP324 4.2 20.1 1.0
N C:GLY298 4.2 23.2 1.0
C C:ALA343 4.2 23.5 1.0
N C:GLY345 4.2 18.9 1.0
N C:SER299 4.3 19.7 1.0
CA C:ASN295 4.3 22.6 1.0
CA C:SER299 4.3 23.0 1.0
OD1 C:ASP324 4.4 20.6 1.0
N C:ASN295 4.4 26.3 1.0
CA C:GLY298 4.4 24.3 1.0
N C:ASN344 4.4 24.4 1.0
N C:ALA343 4.5 26.2 1.0
CA C:ASP294 4.6 22.8 1.0
CA C:ASN344 4.6 26.2 1.0
C C:ASN295 4.7 24.6 1.0
CB C:ASP294 4.7 20.3 1.0
N C:ASP294 4.7 23.2 1.0
CA C:ALA343 4.8 26.1 1.0
O C:ASN341 4.8 24.9 1.0
O C:PRO326 4.9 22.3 1.0
OD1 C:ASP294 4.9 20.8 1.0

Calcium binding site 6 out of 8 in 4b7r

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Calcium binding site 6 out of 8 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 6 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:Ca502

b:49.3
occ:1.00
 OD1 C:ASP376 2.3 24.4 1.0
OD1 C:ASP384 2.3 38.4 1.0
O C:HOH2210 2.5 43.9 1.0
OD1 C:ASN378 2.5 34.3 1.0
O C:ASN386 2.6 39.2 1.0
O C:HOH2211 2.7 32.7 1.0
CG C:ASP376 3.1 25.5 1.0
OD2 C:ASP376 3.2 28.1 1.0
CG C:ASP384 3.4 43.2 1.0
C C:ASN386 3.6 35.3 1.0
CG C:ASN378 3.6 37.8 1.0
OD2 C:ASP384 3.7 56.3 1.0
N C:ASN386 4.0 30.5 1.0
CB C:ASN386 4.1 46.0 1.0
CA C:ASN386 4.1 39.5 1.0
O C:ASP384 4.2 25.2 1.0
ND2 C:ASN378 4.2 44.4 1.0
N C:ASN378 4.4 24.4 1.0
CB C:ASP376 4.4 19.9 1.0
O C:HOH2218 4.5 44.5 1.0
C C:ASP384 4.5 29.3 1.0
CD C:PRO377 4.6 30.7 1.0
C C:ASN378 4.7 27.8 1.0
O C:HOH2213 4.7 48.6 1.0
N C:GLY379 4.7 23.8 1.0
CB C:ASP384 4.7 33.5 1.0
N C:PHE387 4.7 39.6 1.0
CB C:ASN378 4.8 27.9 1.0
CA C:ASN378 4.8 22.7 1.0
CA C:ASP376 4.8 24.3 1.0
C C:ASN385 4.9 32.3 1.0
N C:PRO377 4.9 25.2 1.0
C C:ASP376 4.9 23.6 1.0
CA C:PHE387 5.0 39.1 1.0

Calcium binding site 7 out of 8 in 4b7r

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Calcium binding site 7 out of 8 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 7 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:Ca501

b:30.6
occ:1.00
 O D:ASN344 2.3 27.0 1.0
O D:ASP294 2.3 25.0 1.0
O D:GLY298 2.4 25.1 1.0
O D:HOH2133 2.4 24.2 1.0
OD2 D:ASP324 2.4 27.6 1.0
O D:GLY342 2.5 30.8 1.0
C D:GLY342 3.5 37.3 1.0
C D:GLY298 3.5 26.1 1.0
C D:ASN344 3.5 27.0 1.0
CG D:ASP324 3.5 26.2 1.0
C D:ASP294 3.6 27.6 1.0
CA D:GLY345 3.9 20.3 1.0
O D:HOH2129 4.0 24.9 1.0
CA D:GLY342 4.1 35.4 1.0
N D:GLY345 4.2 23.8 1.0
N D:GLY298 4.2 24.9 1.0
O D:ALA343 4.2 29.1 1.0
CA D:ASN295 4.2 26.5 1.0
CB D:ASP324 4.3 25.8 1.0
C D:ALA343 4.3 34.9 1.0
N D:SER299 4.3 25.5 1.0
N D:ASN295 4.4 25.1 1.0
OD1 D:ASP324 4.4 22.2 1.0
CA D:GLY298 4.4 23.3 1.0
CA D:SER299 4.4 25.4 1.0
N D:ASN344 4.5 25.3 1.0
N D:ALA343 4.5 37.0 1.0
CA D:ASP294 4.6 22.8 1.0
C D:ASN295 4.6 31.4 1.0
O D:ASN341 4.6 45.5 1.0
CA D:ASN344 4.6 25.9 1.0
N D:ASP294 4.7 22.3 1.0
CB D:ASP294 4.7 23.7 1.0
CA D:ALA343 4.8 31.3 1.0
O D:PRO326 4.8 26.6 1.0
OD1 D:ASP294 4.9 27.5 1.0
O D:ASN295 5.0 31.0 1.0

Calcium binding site 8 out of 8 in 4b7r

Go back to Calcium Binding Sites List in 4b7r
Calcium binding site 8 out of 8 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 8 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:Ca502

b:57.5
occ:1.00
 OD1 D:ASP376 2.3 27.3 1.0
OD1 D:ASP384 2.3 43.0 1.0
O D:HOH2172 2.4 39.2 1.0
OD1 D:ASN378 2.5 52.1 1.0
O D:HOH2171 2.5 37.2 1.0
O D:ASN386 2.6 44.4 1.0
CG D:ASP376 3.0 27.3 1.0
OD2 D:ASP376 3.0 30.9 1.0
CG D:ASP384 3.3 47.1 1.0
C D:ASN386 3.5 42.9 1.0
OD2 D:ASP384 3.6 58.3 1.0
CG D:ASN378 3.6 47.9 1.0
N D:ASN386 3.8 41.1 1.0
O D:ASP384 4.0 31.5 1.0
CA D:ASN386 4.0 39.0 1.0
CB D:ASN386 4.0 40.5 1.0
ND2 D:ASN378 4.3 50.7 1.0
CB D:ASP376 4.4 25.5 1.0
C D:ASP384 4.4 34.4 1.0
N D:ASN378 4.5 30.1 1.0
N D:GLY379 4.6 28.5 1.0
C D:ASN378 4.6 30.8 1.0
N D:PHE387 4.6 33.9 1.0
CB D:ASP384 4.6 36.1 1.0
O D:HOH2176 4.7 45.0 1.0
C D:ASN385 4.8 42.2 1.0
CB D:ASN378 4.8 36.4 1.0
CA D:ASN378 4.8 32.0 1.0
CD D:PRO377 4.8 23.8 1.0
CA D:ASP376 4.8 30.8 1.0
CA D:GLY379 4.8 26.8 1.0
CA D:PHE387 4.9 31.6 1.0
CA D:ASP384 5.0 35.0 1.0
C D:ASP376 5.0 28.1 1.0
O D:ASN378 5.0 33.4 1.0
N D:PRO377 5.0 28.1 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 22:37:54 2024

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