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Calcium in PDB 6hfy: Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).

Enzymatic activity of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).

All present enzymatic activity of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).:
3.2.1.18;

Protein crystallography data

The structure of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56)., PDB code: 6hfy was solved by M.T.Salinger, J.R.Hobbs, J.W.Murray, W.G.Laver, P.Kuhn, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.05 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.995, 75.763, 105.976, 90.00, 90.50, 90.00
R / Rfree (%) 15.6 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56). (pdb code 6hfy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56)., PDB code: 6hfy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6hfy

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Calcium binding site 1 out of 5 in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca514

b:22.4
occ:1.00
 O A:ASP294 2.3 14.6 1.0
OD2 A:ASP325 2.4 15.8 1.0
O A:HOH650 2.4 20.5 1.0
O A:GLY298 2.4 17.2 1.0
O A:PRO348 2.4 17.1 1.0
O A:HOH848 2.7 22.9 1.0
CG A:ASP325 3.4 15.1 1.0
C A:ASP294 3.5 15.2 1.0
C A:PRO348 3.5 17.4 1.0
C A:GLY298 3.5 18.1 1.0
O A:HOH677 3.8 13.6 1.0
CA A:GLY349 4.0 15.2 1.0
CB A:ASP325 4.1 14.8 1.0
CA A:ASN295 4.2 15.8 1.0
O A:HOH738 4.2 27.1 1.0
N A:GLY349 4.2 16.1 1.0
N A:ASN295 4.3 15.0 1.0
OD1 A:ASP325 4.3 13.7 1.0
N A:ALA299 4.3 17.2 1.0
N A:GLY298 4.4 19.7 1.0
CA A:ALA299 4.4 16.5 1.0
CA A:ASP294 4.5 15.0 1.0
CA A:GLY298 4.5 19.1 1.0
CA A:PRO348 4.6 18.9 1.0
C A:ASN295 4.6 16.9 1.0
N A:ASP294 4.6 14.3 1.0
CB A:ASP294 4.7 16.0 1.0
C A:LYS297 4.8 21.6 1.0
OD1 A:ASP294 4.9 17.6 1.0
O A:SER327 4.9 19.0 1.0
O A:ASN295 5.0 17.4 1.0

Calcium binding site 2 out of 5 in 6hfy

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Calcium binding site 2 out of 5 in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca514

b:23.0
occ:1.00
 O B:ASP294 2.3 14.2 1.0
O B:HOH728 2.4 14.9 1.0
OD2 B:ASP325 2.4 15.4 1.0
O B:GLY298 2.4 13.9 1.0
O B:PRO348 2.5 13.7 1.0
O B:HOH823 2.7 19.0 1.0
CG B:ASP325 3.4 14.0 1.0
C B:ASP294 3.4 13.7 1.0
C B:GLY298 3.5 14.5 1.0
C B:PRO348 3.6 13.9 1.0
O B:HOH613 3.7 13.4 1.0
CA B:GLY349 4.0 12.7 1.0
CB B:ASP325 4.0 13.7 1.0
O B:HOH665 4.1 23.1 1.0
N B:ALA299 4.2 14.7 1.0
OD1 B:ASP325 4.2 12.9 1.0
N B:GLY349 4.2 13.4 1.0
CA B:ALA299 4.3 14.3 1.0
CA B:ASN295 4.3 13.6 1.0
N B:ASN295 4.3 13.4 1.0
CA B:ASP294 4.4 13.2 1.0
N B:GLY298 4.5 14.8 1.0
N B:ASP294 4.5 12.9 1.0
CA B:GLY298 4.5 14.8 1.0
CB B:ASP294 4.6 13.6 1.0
CA B:PRO348 4.7 14.7 1.0
C B:ASN295 4.7 14.4 1.0
C B:LYS297 4.7 15.4 1.0
O B:LYS297 4.8 15.2 1.0
O B:HOH897 4.8 30.0 1.0
OD1 B:ASP294 5.0 13.6 1.0

Calcium binding site 3 out of 5 in 6hfy

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Calcium binding site 3 out of 5 in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca515

b:32.2
occ:1.00
 CE1 B:HIS113 2.5 16.1 1.0
CE1 D:HIS113 2.6 15.9 1.0
CE1 C:HIS113 2.7 15.7 1.0
CE1 A:HIS113 2.7 16.7 1.0
NE2 B:HIS113 2.9 15.1 1.0
NE2 D:HIS113 2.9 15.1 1.0
NE2 A:HIS113 3.0 15.2 1.0
NE2 C:HIS113 3.1 15.0 1.0
ND1 B:HIS113 3.4 15.4 1.0
ND1 D:HIS113 3.4 15.5 1.0
ND1 C:HIS113 3.5 15.1 1.0
ND1 A:HIS113 3.6 16.1 1.0
CD2 B:HIS113 4.0 14.7 1.0
CD2 D:HIS113 4.0 14.4 1.0
CD2 A:HIS113 4.1 14.5 1.0
CD2 C:HIS113 4.1 14.1 1.0
CG B:HIS113 4.2 14.0 1.0
CG D:HIS113 4.2 14.2 1.0
CG A:HIS113 4.3 14.5 1.0
CG C:HIS113 4.3 13.9 1.0
O2 A:GOL513 5.0 35.5 1.0

Calcium binding site 4 out of 5 in 6hfy

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Calcium binding site 4 out of 5 in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca512

b:21.8
occ:1.00
 O C:ASP294 2.2 13.6 1.0
OD2 C:ASP325 2.3 13.4 1.0
O C:GLY298 2.4 13.6 1.0
O C:HOH711 2.5 21.5 1.0
O C:PRO348 2.5 14.6 1.0
O C:HOH799 2.5 23.7 1.0
CG C:ASP325 3.4 12.9 1.0
C C:ASP294 3.4 13.7 1.0
C C:GLY298 3.5 14.9 1.0
C C:PRO348 3.6 14.8 1.0
O C:HOH739 3.8 12.0 1.0
CA C:GLY349 4.0 13.7 1.0
CB C:ASP325 4.1 12.7 1.0
CA C:ASN295 4.2 14.2 1.0
N C:ASN295 4.2 13.8 1.0
O C:HOH679 4.3 28.2 1.0
N C:GLY349 4.3 14.2 1.0
OD1 C:ASP325 4.3 12.9 1.0
N C:ALA299 4.3 14.3 1.0
CA C:ASP294 4.4 13.1 1.0
CA C:ALA299 4.4 14.5 1.0
N C:GLY298 4.5 16.4 1.0
N C:ASP294 4.5 12.7 1.0
CA C:GLY298 4.6 15.8 1.0
C C:ASN295 4.6 15.5 1.0
CB C:ASP294 4.7 13.8 1.0
CA C:PRO348 4.7 16.8 1.0
C C:LYS297 4.8 17.8 1.0
OD1 C:ASP294 4.9 14.1 1.0
O C:LYS297 4.9 20.0 1.0
O C:ASN295 5.0 17.3 1.0

Calcium binding site 5 out of 5 in 6hfy

Go back to Calcium Binding Sites List in 6hfy
Calcium binding site 5 out of 5 in the Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Influenza A Virus N6 Neuraminidase Complex with Dana (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca511

b:23.7
occ:1.00
 O D:ASP294 2.3 14.4 1.0
O D:GLY298 2.3 16.3 1.0
O D:HOH695 2.3 19.1 1.0
OD2 D:ASP325 2.4 15.4 1.0
O D:PRO348 2.4 15.9 1.0
O D:HOH740 2.7 23.0 1.0
CG D:ASP325 3.4 15.0 1.0
C D:GLY298 3.5 17.1 1.0
C D:ASP294 3.5 14.4 1.0
C D:PRO348 3.5 16.4 1.0
O D:HOH669 3.8 11.3 1.0
CA D:GLY349 4.0 14.4 1.0
O D:HOH793 4.0 30.3 1.0
CB D:ASP325 4.0 14.8 1.0
N D:GLY349 4.2 15.0 1.0
OD1 D:ASP325 4.3 14.4 1.0
N D:ALA299 4.3 17.1 1.0
CA D:ASN295 4.3 14.8 1.0
CA D:ALA299 4.3 16.8 1.0
N D:ASN295 4.4 14.5 1.0
CA D:ASP294 4.4 14.0 1.0
N D:GLY298 4.5 17.1 1.0
CA D:GLY298 4.5 17.2 1.0
CB D:ASP294 4.6 14.5 1.0
N D:ASP294 4.6 13.3 1.0
CA D:PRO348 4.6 17.6 1.0
C D:LYS297 4.7 18.0 1.0
C D:ASN295 4.7 15.9 1.0
O D:LYS297 4.8 18.6 1.0
OD1 D:ASP294 4.9 14.7 1.0
O D:SER327 5.0 17.3 1.0

Reference:

M.T.Salinger, J.R.Hobbs, J.W.Murray, W.G.Laver, P.Kuhn, E.F.Garman. High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (in Preparation) To Be Published.
Page generated: Tue Jul 16 08:21:42 2024

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