Calcium in PDB 6hgb: Influenza A Virus N6 Neuraminidase Native Structure (Duck/England/56).

Enzymatic activity of Influenza A Virus N6 Neuraminidase Native Structure (Duck/England/56).

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

Protein crystallography data

The structure of Influenza A Virus N6 Neuraminidase Native Structure (Duck/England/56)., PDB code: 6hgb 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) 30.68 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.200, 73.900, 106.400, 90.00, 90.30, 90.00
R / Rfree (%) 13.9 / 16.1

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 6hgb

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Calcium binding site 1 out of 4 in the Influenza A Virus N6 Neuraminidase Native Structure (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 Native Structure (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca519

b:15.5
occ:0.70
O A:ASP294 2.3 12.2 1.0
OD2 A:ASP325 2.4 13.7 1.0
O A:GLY298 2.4 14.8 1.0
O A:PRO348 2.4 12.7 1.0
O A:HOH659 2.5 19.3 1.0
O A:HOH806 2.8 25.9 1.0
CG A:ASP325 3.4 14.4 1.0
C A:ASP294 3.5 11.3 1.0
C A:GLY298 3.5 14.2 1.0
C A:PRO348 3.5 13.8 1.0
O A:HOH739 3.8 13.4 1.0
CA A:GLY349 3.9 11.0 1.0
CB A:ASP325 4.0 12.7 1.0
O A:HOH779 4.2 29.2 1.0
N A:GLY349 4.2 12.2 1.0
CA A:ASN295 4.2 12.8 1.0
OD1 A:ASP325 4.2 12.3 1.0
N A:ALA299 4.3 12.7 1.0
N A:ASN295 4.3 12.0 1.0
N A:GLY298 4.4 14.7 1.0
CA A:ALA299 4.4 12.4 1.0
CA A:ASP294 4.5 11.3 1.0
CA A:GLY298 4.5 14.7 1.0
N A:ASP294 4.5 12.0 1.0
CA A:PRO348 4.6 13.6 1.0
C A:ASN295 4.7 13.2 1.0
CB A:ASP294 4.8 11.8 1.0
C A:LYS297 4.9 16.3 1.0
OD1 A:ASP294 4.9 13.6 1.0
O A:HOH958 5.0 35.4 1.0

Calcium binding site 2 out of 4 in 6hgb

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Calcium binding site 2 out of 4 in the Influenza A Virus N6 Neuraminidase Native Structure (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 Native Structure (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca517

b:7.7
occ:0.50
O B:ASP294 2.2 11.0 1.0
O B:GLY298 2.3 10.1 1.0
O B:HOH809 2.4 13.6 1.0
OD2 B:ASP325 2.4 11.8 1.0
O B:PRO348 2.5 10.7 1.0
O B:HOH775 2.7 18.1 1.0
CG B:ASP325 3.4 10.8 1.0
C B:GLY298 3.5 11.8 1.0
C B:ASP294 3.5 10.0 1.0
C B:PRO348 3.6 10.7 1.0
O B:HOH734 3.8 12.1 1.0
CB B:ASP325 4.0 10.6 1.0
CA B:GLY349 4.0 9.9 1.0
O B:HOH762 4.1 18.4 1.0
N B:ALA299 4.2 11.0 1.0
CA B:ASN295 4.3 10.1 1.0
OD1 B:ASP325 4.3 9.7 1.0
CA B:ALA299 4.3 11.2 1.0
N B:GLY349 4.3 10.1 1.0
N B:ASN295 4.3 10.4 1.0
CA B:ASP294 4.4 9.4 1.0
N B:GLY298 4.5 11.0 1.0
N B:ASP294 4.5 9.5 1.0
CA B:GLY298 4.5 11.4 1.0
CB B:ASP294 4.7 9.4 1.0
CA B:PRO348 4.7 11.0 1.0
C B:ASN295 4.7 11.5 1.0
C B:LYS297 4.7 11.6 1.0
O B:LYS297 4.8 11.2 1.0
O B:HOH955 4.9 31.9 1.0

Calcium binding site 3 out of 4 in 6hgb

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Calcium binding site 3 out of 4 in the Influenza A Virus N6 Neuraminidase Native Structure (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 Native Structure (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca519

b:19.7
occ:1.00
O C:ASP294 2.2 9.3 1.0
O C:GLY298 2.3 11.4 1.0
O C:HOH752 2.3 16.9 1.0
OD2 C:ASP325 2.5 11.7 1.0
O C:PRO348 2.5 12.0 1.0
O C:HOH783 2.6 12.1 0.5
C C:GLY298 3.4 11.6 1.0
CG C:ASP325 3.4 10.7 1.0
C C:ASP294 3.5 9.4 1.0
C C:PRO348 3.6 12.1 1.0
O C:HOH736 3.8 11.8 1.0
O C:HOH783 3.9 17.8 0.5
CA C:GLY349 4.0 10.0 1.0
CB C:ASP325 4.0 9.7 1.0
CA C:ASN295 4.2 10.0 1.0
N C:ALA299 4.2 10.9 1.0
N C:GLY349 4.3 10.8 1.0
N C:ASN295 4.3 9.8 1.0
O C:HOH606 4.3 31.3 1.0
CA C:ALA299 4.3 11.5 1.0
OD1 C:ASP325 4.3 10.4 1.0
N C:GLY298 4.3 13.1 1.0
CA C:GLY298 4.4 12.1 1.0
CA C:ASP294 4.5 9.1 1.0
N C:ASP294 4.6 9.5 1.0
C C:ASN295 4.6 11.0 1.0
CB C:ASP294 4.7 10.1 1.0
CA C:PRO348 4.8 12.4 1.0
C C:LYS297 4.8 14.6 1.0
OD1 C:ASP294 4.9 11.6 1.0

Calcium binding site 4 out of 4 in 6hgb

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Calcium binding site 4 out of 4 in the Influenza A Virus N6 Neuraminidase Native Structure (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 Native Structure (Duck/England/56). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca515

b:9.9
occ:0.50
O D:ASP294 2.3 10.3 1.0
O D:PRO348 2.3 10.3 1.0
O D:GLY298 2.4 11.0 1.0
OD2 D:ASP325 2.4 12.6 1.0
O D:HOH673 2.4 16.5 1.0
O D:HOH781 2.7 18.7 1.0
CG D:ASP325 3.4 11.8 1.0
C D:ASP294 3.5 10.5 1.0
C D:GLY298 3.5 12.5 1.0
C D:PRO348 3.5 11.0 1.0
O D:HOH778 3.8 11.2 1.0
CA D:GLY349 3.9 10.3 1.0
CB D:ASP325 4.0 10.3 1.0
O D:HOH696 4.1 24.4 1.0
N D:GLY349 4.2 10.4 1.0
OD1 D:ASP325 4.3 10.9 1.0
N D:ALA299 4.3 11.5 1.0
CA D:ASN295 4.3 10.6 1.0
CA D:ALA299 4.3 11.9 1.0
N D:ASN295 4.3 10.1 1.0
CA D:ASP294 4.5 10.1 1.0
N D:GLY298 4.5 12.0 1.0
N D:ASP294 4.5 10.6 1.0
CA D:GLY298 4.6 11.2 1.0
CA D:PRO348 4.6 11.8 1.0
CB D:ASP294 4.7 10.8 1.0
C D:ASN295 4.7 10.9 1.0
O D:HOH948 4.7 27.6 0.8
C D:LYS297 4.8 12.1 1.0
O D:LYS297 4.8 12.6 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: Sat Dec 12 06:09:43 2020

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