Calcium in PDB 6d96: Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells

Enzymatic activity of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells

All present enzymatic activity of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells:
3.2.1.18;

Protein crystallography data

The structure of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells, PDB code: 6d96 was solved by A.C.Campbell, K.L.Krause, J.J.Tanner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.96 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.681, 148.189, 127.166, 90.00, 94.80, 90.00
R / Rfree (%) 18.6 / 21.5

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells (pdb code 6d96). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells, PDB code: 6d96:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 6d96

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Calcium binding site 1 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:16.6
occ:1.00
 O A:GLY297 2.3 18.7 1.0
O A:ASP293 2.3 25.4 1.0
OD2 A:ASP324 2.3 19.9 1.0
O A:GLY345 2.3 19.1 1.0
O A:HOH638 2.4 17.2 1.0
O A:ASN347 2.4 17.9 1.0
C A:GLY297 3.4 23.4 1.0
C A:GLY345 3.4 24.3 1.0
CG A:ASP324 3.4 24.3 1.0
C A:ASP293 3.5 24.0 1.0
C A:ASN347 3.6 23.4 1.0
O A:HOH662 4.0 21.4 1.0
CA A:GLY348 4.0 17.1 1.0
CA A:GLY345 4.1 20.0 1.0
O A:ALA346 4.1 19.1 1.0
CB A:ASP324 4.2 25.4 1.0
C A:ALA346 4.2 20.8 1.0
N A:GLY297 4.2 22.1 1.0
N A:SER298 4.2 21.0 1.0
CA A:SER298 4.2 19.8 1.0
N A:GLY348 4.3 17.4 1.0
CA A:ASN294 4.3 20.4 1.0
OD1 A:ASP324 4.3 24.1 1.0
N A:ASN294 4.4 21.8 1.0
CA A:GLY297 4.4 23.8 1.0
N A:ASN347 4.5 18.7 1.0
N A:ALA346 4.5 19.9 1.0
CA A:ASP293 4.5 17.7 1.0
O A:ASN344 4.6 22.2 1.0
CB A:ASP293 4.6 18.2 1.0
C A:ASN294 4.7 19.8 1.0
CA A:ALA346 4.7 22.1 1.0
CA A:ASN347 4.7 25.6 1.0
N A:ASP293 4.7 17.2 1.0
OD1 A:ASP293 4.8 21.1 1.0
O A:PRO326 4.9 18.6 1.0

Calcium binding site 2 out of 18 in 6d96

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Calcium binding site 2 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:28.9
occ:1.00
 OD1 A:ASN381 2.3 28.1 1.0
OD1 A:ASP379 2.3 20.7 1.0
O A:HOH709 2.4 31.8 1.0
O A:SER389 2.4 26.6 1.0
OD1 A:ASP387 2.4 29.3 1.0
O A:HOH667 2.5 27.0 1.0
OD2 A:ASP379 2.8 23.4 1.0
CG A:ASP379 2.9 26.5 1.0
CG A:ASP387 3.2 26.8 1.0
OD2 A:ASP387 3.3 32.1 1.0
CG A:ASN381 3.4 30.5 1.0
C A:SER389 3.5 25.1 1.0
O A:ASP387 3.8 28.8 1.0
ND2 A:ASN381 3.9 25.6 1.0
N A:SER389 4.0 25.5 1.0
CA A:SER389 4.2 27.0 1.0
C A:ASP387 4.3 28.7 1.0
CB A:SER389 4.4 30.6 1.0
N A:GLY382 4.4 20.5 1.0
CB A:ASP379 4.4 25.1 1.0
C A:ASN381 4.4 24.2 1.0
N A:ASN381 4.5 21.2 1.0
CB A:ASP387 4.6 25.8 1.0
CA A:GLY382 4.6 21.8 1.0
N A:PHE390 4.6 25.2 1.0
CB A:ASN381 4.6 22.2 1.0
O A:HOH760 4.8 28.1 1.0
CA A:ASN381 4.8 22.9 1.0
O A:ASN381 4.8 26.1 1.0
C A:SER388 4.8 27.8 1.0
OG A:SER319 4.8 25.5 1.0
CA A:PHE390 4.9 27.2 1.0
CA A:ASP387 4.9 27.7 1.0
N A:SER388 5.0 27.0 1.0

Calcium binding site 3 out of 18 in 6d96

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Calcium binding site 3 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:60.8
occ:0.93
 O C:HOH711 2.3 47.2 0.9
O D:HOH663 2.4 34.7 0.9
O A:HOH621 2.5 48.9 0.9
O A:HOH731 2.5 52.1 0.9
O B:HOH688 2.5 39.9 0.9
O B:HOH790 2.6 47.5 0.9
OD2 C:ASP113 4.2 27.8 1.0
OD2 A:ASP113 4.2 27.5 1.0
OD2 D:ASP113 4.2 32.8 1.0
OD2 B:ASP113 4.3 31.1 1.0
OD1 C:ASP113 4.3 27.5 1.0
OD1 D:ASP113 4.3 28.1 1.0
OD1 A:ASP113 4.4 33.8 1.0
OD1 B:ASP113 4.6 33.5 1.0
CG C:ASP113 4.6 27.9 1.0
CG D:ASP113 4.7 28.2 1.0
CG A:ASP113 4.7 29.9 1.0
CG B:ASP113 4.8 30.3 1.0

Calcium binding site 4 out of 18 in 6d96

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Calcium binding site 4 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca506

b:20.6
occ:1.00
 O B:ASP293 2.3 23.2 1.0
O B:HOH662 2.3 19.3 1.0
O B:ASN347 2.3 23.6 1.0
O B:GLY345 2.3 18.9 1.0
OD2 B:ASP324 2.4 24.7 1.0
O B:GLY297 2.4 21.0 1.0
C B:GLY345 3.4 19.4 1.0
C B:ASN347 3.5 20.3 1.0
C B:ASP293 3.5 21.2 1.0
CG B:ASP324 3.5 25.5 1.0
C B:GLY297 3.5 21.8 1.0
CA B:GLY348 3.9 17.5 1.0
O B:ALA346 4.1 22.9 1.0
CA B:GLY345 4.1 19.6 1.0
O B:HOH668 4.1 22.0 1.0
C B:ALA346 4.1 22.0 1.0
N B:GLY348 4.2 17.8 1.0
CA B:ASN294 4.3 19.4 1.0
CB B:ASP324 4.3 24.8 1.0
CA B:SER298 4.3 25.1 1.0
N B:GLY297 4.3 19.2 1.0
N B:SER298 4.3 19.0 1.0
N B:ASN294 4.4 21.8 1.0
N B:ALA346 4.4 19.8 1.0
OD1 B:ASP324 4.4 22.8 1.0
N B:ASN347 4.4 20.9 1.0
CA B:GLY297 4.5 19.1 1.0
CA B:ASP293 4.5 20.5 1.0
O B:ASN344 4.5 21.7 1.0
CA B:ALA346 4.6 21.8 1.0
CA B:ASN347 4.6 20.5 1.0
C B:ASN294 4.6 22.5 1.0
CB B:ASP293 4.6 19.6 1.0
N B:ASP293 4.7 21.1 1.0
O B:ASN294 4.8 25.2 1.0
O B:PRO326 4.9 25.2 1.0
OD1 B:ASP293 4.9 24.3 1.0

Calcium binding site 5 out of 18 in 6d96

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Calcium binding site 5 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca507

b:23.8
occ:1.00
 OD1 B:ASN381 2.3 29.4 1.0
O B:HOH618 2.3 19.5 1.0
O B:HOH682 2.3 26.5 1.0
OD1 B:ASP379 2.4 24.4 1.0
OD1 B:ASP387 2.4 36.2 1.0
O B:SER389 2.4 27.1 1.0
OD2 B:ASP379 2.8 26.9 1.0
CG B:ASP379 3.0 24.6 1.0
CG B:ASP387 3.2 32.7 1.0
OD2 B:ASP387 3.4 31.2 1.0
CG B:ASN381 3.4 29.4 1.0
C B:SER389 3.6 29.3 1.0
OG B:SER389 3.9 41.6 1.0
O B:ASP387 3.9 22.9 1.0
ND2 B:ASN381 4.0 25.9 1.0
N B:SER389 4.1 25.1 1.0
CA B:SER389 4.3 28.9 1.0
C B:ASP387 4.4 21.6 1.0
N B:GLY382 4.4 20.1 1.0
CB B:ASP379 4.5 22.5 1.0
C B:ASN381 4.5 29.6 1.0
N B:ASN381 4.5 20.7 1.0
CA B:GLY382 4.6 19.8 1.0
CB B:ASP387 4.6 27.6 1.0
N B:PHE390 4.6 28.1 1.0
CB B:ASN381 4.7 21.5 1.0
O B:HOH776 4.7 36.4 1.0
CB B:SER389 4.7 33.1 1.0
CA B:ASN381 4.8 20.9 1.0
C B:SER388 4.8 26.6 1.0
O B:HOH775 4.8 43.0 1.0
OG B:SER319 4.9 23.5 1.0
CA B:PHE390 4.9 25.9 1.0
O B:ASN381 4.9 24.3 1.0
CA B:ASP387 4.9 22.1 1.0
N B:SER388 4.9 24.8 1.0

Calcium binding site 6 out of 18 in 6d96

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Calcium binding site 6 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca506

b:21.4
occ:1.00
 O C:ASP293 2.3 19.8 1.0
O C:ASN347 2.3 19.2 1.0
O C:GLY297 2.3 21.6 1.0
OD2 C:ASP324 2.4 17.7 1.0
O C:GLY345 2.4 19.3 1.0
O C:HOH661 2.4 15.2 1.0
C C:GLY297 3.4 20.3 1.0
C C:GLY345 3.5 22.3 1.0
C C:ASN347 3.5 23.1 1.0
C C:ASP293 3.5 18.3 1.0
CG C:ASP324 3.5 23.6 1.0
CA C:GLY348 4.0 17.7 1.0
O C:HOH672 4.0 17.8 1.0
CA C:GLY345 4.1 19.9 1.0
N C:GLY348 4.2 18.1 1.0
N C:GLY297 4.2 22.6 1.0
C C:ALA346 4.2 24.1 1.0
O C:ALA346 4.3 19.5 1.0
CB C:ASP324 4.3 21.0 1.0
CA C:ASN294 4.3 18.5 1.0
N C:SER298 4.3 19.4 1.0
CA C:SER298 4.3 24.7 1.0
N C:ASN294 4.3 20.4 1.0
CA C:GLY297 4.4 20.4 1.0
OD1 C:ASP324 4.4 26.1 1.0
N C:ASN347 4.4 21.9 1.0
N C:ALA346 4.5 23.6 1.0
CA C:ASP293 4.5 21.0 1.0
CA C:ASN347 4.6 25.7 1.0
CB C:ASP293 4.7 20.6 1.0
C C:ASN294 4.7 24.1 1.0
O C:ASN344 4.7 23.2 1.0
CA C:ALA346 4.7 24.2 1.0
N C:ASP293 4.7 17.6 1.0
OD1 C:ASP293 4.8 20.6 1.0
O C:PRO326 4.9 25.7 1.0

Calcium binding site 7 out of 18 in 6d96

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Calcium binding site 7 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca507

b:23.7
occ:1.00
 O C:HOH687 2.3 22.5 1.0
OD1 C:ASN381 2.4 25.7 1.0
O C:SER389 2.4 23.3 1.0
OD1 C:ASP379 2.4 24.7 1.0
OD1 C:ASP387 2.4 30.0 1.0
O C:HOH611 2.5 20.8 1.0
OD2 C:ASP379 2.6 25.7 1.0
CG C:ASP379 2.9 25.2 1.0
CG C:ASP387 3.2 31.8 1.0
OD2 C:ASP387 3.4 30.1 1.0
C C:SER389 3.5 23.9 1.0
CG C:ASN381 3.5 23.9 1.0
O C:ASP387 3.8 20.5 1.0
ND2 C:ASN381 4.0 21.4 1.0
N C:SER389 4.0 24.5 1.0
CA C:SER389 4.2 24.9 1.0
CB C:ASP379 4.3 23.4 1.0
C C:ASP387 4.4 26.4 1.0
CB C:SER389 4.4 25.2 1.0
N C:GLY382 4.5 19.3 1.0
N C:PHE390 4.5 20.1 1.0
CA C:GLY382 4.6 19.1 1.0
C C:ASN381 4.6 20.9 1.0
CB C:ASP387 4.6 21.9 1.0
N C:ASN381 4.6 19.9 1.0
O C:HOH704 4.6 27.9 1.0
OG C:SER319 4.7 23.4 1.0
CB C:ASN381 4.7 20.7 1.0
CA C:PHE390 4.8 19.6 1.0
C C:SER388 4.8 26.7 1.0
CA C:ASN381 4.9 20.1 1.0
CA C:ASP387 4.9 21.5 1.0
OG C:SER389 5.0 35.9 1.0

Calcium binding site 8 out of 18 in 6d96

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Calcium binding site 8 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca505

b:27.2
occ:1.00
 O D:ASN347 2.3 23.3 1.0
O D:GLY297 2.3 30.9 1.0
O D:ASP293 2.3 29.5 1.0
O D:GLY345 2.4 28.7 1.0
O D:HOH628 2.4 24.2 1.0
OD2 D:ASP324 2.5 28.4 1.0
C D:GLY297 3.4 30.7 1.0
C D:GLY345 3.5 28.3 1.0
C D:ASN347 3.5 26.4 1.0
CG D:ASP324 3.5 29.9 1.0
C D:ASP293 3.6 24.9 1.0
O D:ALA346 4.0 33.5 1.0
CA D:GLY348 4.0 22.7 1.0
C D:ALA346 4.1 29.0 1.0
CA D:GLY345 4.2 30.6 1.0
O D:HOH634 4.2 21.1 1.0
N D:GLY297 4.2 28.7 1.0
N D:GLY348 4.2 23.0 1.0
N D:SER298 4.3 31.9 1.0
CA D:ASN294 4.3 24.6 1.0
CA D:SER298 4.3 30.4 1.0
CB D:ASP324 4.3 28.9 1.0
OD1 D:ASP324 4.4 30.7 1.0
N D:ASN347 4.4 27.3 1.0
CA D:GLY297 4.4 27.1 1.0
N D:ASN294 4.4 25.3 1.0
N D:ALA346 4.4 28.9 1.0
CA D:ASN347 4.6 28.2 0.5
CA D:ASN347 4.6 28.2 0.5
CA D:ASP293 4.6 23.9 1.0
O D:ASN344 4.6 37.5 1.0
CA D:ALA346 4.6 27.8 1.0
C D:ASN294 4.6 28.8 1.0
CB D:ASP293 4.7 25.9 1.0
OD1 D:ASP293 4.8 36.7 1.0
N D:ASP293 4.8 21.8 1.0
O D:PRO326 4.9 31.8 1.0
O D:ASN294 4.9 30.7 1.0

Calcium binding site 9 out of 18 in 6d96

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Calcium binding site 9 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca506

b:35.5
occ:1.00
 O D:HOH656 2.2 36.4 1.0
OD1 D:ASN381 2.3 31.8 1.0
OD1 D:ASP379 2.3 38.6 1.0
O D:HOH673 2.4 29.2 1.0
O D:SER389 2.4 36.6 1.0
OD1 D:ASP387 2.4 43.2 1.0
OD2 D:ASP379 2.9 33.3 1.0
CG D:ASP379 3.0 33.8 1.0
CG D:ASP387 3.2 41.7 1.0
OD2 D:ASP387 3.3 41.7 1.0
CG D:ASN381 3.4 32.9 1.0
C D:SER389 3.6 36.0 1.0
OG D:SER389 3.8 45.0 1.0
ND2 D:ASN381 3.9 33.9 1.0
O D:ASP387 4.1 36.7 1.0
N D:SER389 4.2 34.2 1.0
CA D:SER389 4.3 37.5 1.0
CB D:ASP379 4.4 23.9 1.0
N D:GLY382 4.4 28.5 1.0
C D:ASP387 4.5 34.5 1.0
C D:ASN381 4.5 30.2 1.0
N D:ASN381 4.5 30.1 1.0
N D:PHE390 4.6 37.4 1.0
CB D:ASP387 4.6 35.5 1.0
CA D:GLY382 4.7 30.7 1.0
CB D:ASN381 4.7 31.1 1.0
CB D:SER389 4.7 41.0 1.0
CA D:PHE390 4.8 34.0 1.0
CA D:ASN381 4.8 30.3 1.0
O D:ASN381 4.9 30.2 1.0
CA D:ASP379 4.9 25.7 1.0
C D:SER388 5.0 33.8 1.0
OG D:SER319 5.0 32.0 1.0

Calcium binding site 10 out of 18 in 6d96

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Calcium binding site 10 out of 18 in the Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Influenza Neuraminidase From Strain A/Brevigmission/1/1918(H1N1) Expressed in Hek-293E Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca506

b:20.8
occ:1.00
 O E:ASP293 2.3 21.7 1.0
O E:GLY345 2.3 20.3 1.0
O E:GLY297 2.4 25.6 1.0
O E:ASN347 2.4 19.4 1.0
OD2 E:ASP324 2.4 26.1 1.0
O E:HOH628 2.5 17.4 1.0
C E:GLY345 3.5 21.1 1.0
C E:GLY297 3.5 24.8 1.0
CG E:ASP324 3.5 26.6 1.0
C E:ASN347 3.5 19.6 1.0
C E:ASP293 3.6 22.4 1.0
CA E:GLY348 4.0 18.6 1.0
O E:HOH695 4.1 19.7 1.0
CA E:GLY345 4.2 19.7 1.0
C E:ALA346 4.2 24.2 1.0
O E:ALA346 4.2 23.4 1.0
N E:GLY297 4.2 19.0 1.0
N E:GLY348 4.2 17.4 1.0
CB E:ASP324 4.2 25.0 1.0
CA E:SER298 4.3 18.7 1.0
N E:SER298 4.3 22.4 1.0
CA E:ASN294 4.4 22.8 1.0
CA E:GLY297 4.4 25.8 1.0
OD1 E:ASP324 4.4 24.6 1.0
N E:ASN347 4.4 22.7 1.0
N E:ASN294 4.4 22.8 1.0
N E:ALA346 4.5 22.6 1.0
CA E:ASP293 4.6 21.5 1.0
O E:ASN344 4.6 24.1 1.0
CA E:ASN347 4.6 20.6 1.0
CA E:ALA346 4.7 24.5 1.0
CB E:ASP293 4.7 20.5 1.0
C E:ASN294 4.7 23.6 1.0
N E:ASP293 4.8 24.0 1.0
OD1 E:ASP293 4.9 25.6 1.0
O E:PRO326 5.0 26.8 1.0

Reference:

A.C.Campbell, J.J.Tanner, K.L.Krause. Optimisation of Neuraminidase Expression By Hek-293E Cells For Use in Structural Biology To Be Published.
Page generated: Sat Dec 12 06:02:47 2020

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