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Calcium in PDB 6q23: Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)

Enzymatic activity of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)

All present enzymatic activity of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1):
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1), PDB code: 6q23 was solved by X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.30 / 3.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.594, 234.985, 106.275, 90.00, 106.40, 90.00
R / Rfree (%) 19.6 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) (pdb code 6q23). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1), PDB code: 6q23:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6q23

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Calcium binding site 1 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:68.9
occ:1.00
 O C:GLY345 2.3 0.3 1.0
O C:GLY297 2.5 77.3 1.0
O C:ASN347 2.5 81.5 1.0
O C:ASP293 2.8 63.0 1.0
OD2 C:ASP324 3.0 61.1 1.0
C C:GLY345 3.2 0.9 1.0
C C:GLY297 3.5 71.8 1.0
C C:ASN347 3.6 73.6 1.0
CA C:GLY345 3.7 0.4 1.0
O C:ALA346 3.8 0.9 1.0
CG C:ASP324 3.9 61.0 1.0
C C:ALA346 4.0 99.3 1.0
CA C:GLY348 4.0 54.3 1.0
C C:ASP293 4.1 65.5 1.0
N C:ALA346 4.2 0.3 1.0
O C:ASN344 4.2 73.7 1.0
N C:GLY297 4.2 72.9 1.0
N C:SER298 4.2 68.4 1.0
N C:GLY348 4.3 60.4 1.0
CA C:SER298 4.3 64.1 1.0
CA C:GLY297 4.4 73.6 1.0
N C:ASN347 4.5 87.2 1.0
CB C:ASP324 4.5 65.1 1.0
O C:PRO326 4.5 53.8 1.0
CA C:ASN294 4.6 75.0 1.0
CA C:ALA346 4.6 0.3 1.0
OD1 C:ASP324 4.7 53.1 1.0
CA C:ASN347 4.7 77.3 1.0
N C:ASN294 4.8 70.5 1.0
N C:GLY345 4.8 95.3 1.0
C C:ASN294 4.9 73.2 1.0
C C:ASN344 4.9 85.5 1.0

Calcium binding site 2 out of 9 in 6q23

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Calcium binding site 2 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:0.8
occ:1.00
 O C:ASN389 2.3 0.2 1.0
OD1 C:ASP379 2.5 60.7 1.0
OD2 C:ASP379 2.5 65.4 1.0
CG C:ASP379 2.8 69.3 1.0
C C:ASN389 3.4 98.4 1.0
O C:ASP387 3.5 0.2 1.0
N C:ASN389 3.7 96.5 1.0
C C:ASP387 3.8 0.7 1.0
CA C:ASN389 4.0 92.6 1.0
CB C:ASP387 4.1 0.1 1.0
CB C:ASN389 4.2 85.0 1.0
CB C:ASP379 4.3 72.1 1.0
N C:ASN388 4.4 0.6 1.0
CB C:ASN381 4.4 73.3 1.0
CA C:ASP387 4.4 0.2 1.0
C C:ASN388 4.4 94.8 1.0
N C:PHE390 4.6 94.7 1.0
N C:ASP387 4.6 1.0 1.0
C C:ASN381 4.6 68.6 1.0
CA C:ASN388 4.8 0.4 1.0
N C:ASN381 4.8 72.6 1.0
N C:GLY382 4.8 74.1 1.0
O C:ASN381 4.8 62.0 1.0
CA C:ASN381 4.9 69.0 1.0
OG C:SER319 4.9 54.6 1.0

Calcium binding site 3 out of 9 in 6q23

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Calcium binding site 3 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:0.6
occ:1.00
 OD2 B:ASP324 2.3 54.1 1.0
O B:ASN347 2.3 45.3 1.0
O B:GLY297 2.5 66.3 1.0
O B:ASP293 2.7 43.8 1.0
O B:GLY345 3.0 81.1 1.0
CG B:ASP324 3.2 61.3 1.0
C B:ASN347 3.4 53.0 1.0
CA B:GLY348 3.5 49.1 1.0
C B:GLY297 3.6 66.4 1.0
CB B:ASP324 3.8 60.2 1.0
C B:GLY345 3.9 82.8 1.0
N B:GLY348 3.9 47.8 1.0
C B:ASP293 3.9 45.8 1.0
O B:ALA346 4.0 88.2 1.0
OD1 B:ASP324 4.1 62.7 1.0
CA B:SER298 4.2 58.2 1.0
N B:SER298 4.3 60.0 1.0
C B:ALA346 4.4 74.7 1.0
O B:PRO326 4.4 72.3 1.0
CA B:GLY345 4.5 79.6 1.0
O B:ASN344 4.6 71.4 1.0
N B:ASN347 4.6 68.3 1.0
CA B:ASN347 4.7 61.6 1.0
CA B:ASN294 4.7 48.6 1.0
N B:GLY297 4.7 73.1 1.0
N B:ASN294 4.7 45.4 1.0
CA B:GLY297 4.8 67.4 1.0
N B:ALA346 4.8 81.8 1.0
CA B:ASP293 4.9 49.8 1.0
C B:GLY348 5.0 49.2 1.0
N B:ASP293 5.0 45.2 1.0

Calcium binding site 4 out of 9 in 6q23

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Calcium binding site 4 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:0.9
occ:1.00
 OD1 B:ASP379 2.2 62.1 1.0
OD2 B:ASP387 2.4 0.5 1.0
O B:ASN389 2.4 0.2 1.0
OD1 B:ASP387 2.5 0.4 1.0
CG B:ASP387 2.7 0.2 1.0
CG B:ASP379 2.9 62.2 1.0
OD2 B:ASP379 3.0 53.8 1.0
C B:ASN389 3.4 0.1 1.0
N B:ASN389 3.5 0.9 1.0
CA B:ASN389 3.7 95.0 1.0
CB B:ASN389 3.7 83.6 1.0
CB B:ASN381 3.8 59.0 1.0
OD1 B:ASN381 3.9 67.8 1.0
O B:ASP387 4.0 0.4 1.0
CB B:ASP387 4.1 0.3 1.0
C B:ASP387 4.2 0.3 1.0
CG B:ASN381 4.3 64.2 1.0
CB B:ASP379 4.3 60.4 1.0
N B:ASN381 4.3 56.4 1.0
CA B:ASN381 4.4 56.6 1.0
C B:ASN388 4.5 0.2 1.0
C B:ASN381 4.5 59.0 1.0
N B:PHE390 4.6 0.5 1.0
N B:ASN388 4.6 0.6 1.0
CA B:ASP387 4.7 0.0 1.0
OD1 B:ASN389 4.7 56.0 1.0
CG B:ASN389 4.7 79.6 1.0
N B:GLY382 4.8 65.4 1.0
CA B:ASP379 4.8 60.4 1.0
O B:ASN381 4.8 60.1 1.0
CA B:ASN388 4.9 0.5 1.0
C B:ASP379 5.0 57.0 1.0

Calcium binding site 5 out of 9 in 6q23

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Calcium binding site 5 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:99.7
occ:1.00
 O A:GLY297 2.5 72.7 1.0
O A:ASN347 2.6 89.7 1.0
OD2 A:ASP324 2.6 55.5 1.0
O A:GLY345 2.8 93.4 1.0
O A:ASP293 2.8 60.2 1.0
CG A:ASP324 3.4 53.2 1.0
C A:GLY297 3.6 69.1 1.0
C A:GLY345 3.6 96.4 1.0
C A:ASN347 3.6 86.7 1.0
CA A:GLY348 3.8 74.4 1.0
O A:ALA346 4.0 0.7 1.0
CB A:ASP324 4.0 55.7 1.0
C A:ASP293 4.0 60.4 1.0
CA A:GLY345 4.1 94.6 1.0
N A:GLY348 4.2 74.8 1.0
OD1 A:ASP324 4.2 51.0 1.0
O A:ASN344 4.3 0.2 1.0
O A:PRO326 4.3 57.7 1.0
CA A:SER298 4.4 64.5 1.0
C A:ALA346 4.4 0.5 1.0
N A:SER298 4.4 64.4 1.0
N A:GLY297 4.6 67.0 1.0
N A:ALA346 4.6 0.0 1.0
CA A:GLY297 4.6 65.4 1.0
N A:ASN347 4.7 0.6 1.0
CA A:ASN294 4.8 59.5 1.0
N A:ASN294 4.8 59.9 1.0
CA A:ASN347 4.8 88.5 1.0

Calcium binding site 6 out of 9 in 6q23

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Calcium binding site 6 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:1.0
occ:1.00
 OD2 A:ASP379 2.5 94.8 1.0
OD1 A:ASP379 2.7 74.9 1.0
OD1 A:ASP387 2.7 89.5 1.0
CG A:ASP379 2.9 84.9 1.0
O A:ASN389 3.1 0.0 1.0
CG A:ASP387 3.4 91.2 1.0
O A:ASP387 3.4 94.6 1.0
OD2 A:ASP387 3.7 0.7 1.0
C A:ASP387 3.9 91.0 1.0
N A:ASN389 4.0 0.1 1.0
C A:ASN389 4.1 0.2 1.0
CB A:ASN381 4.3 80.8 1.0
C A:ASN381 4.3 73.2 1.0
CB A:ASP379 4.4 72.2 1.0
CA A:ASN389 4.4 0.6 1.0
N A:ASP387 4.5 71.7 1.0
CA A:ASP387 4.5 80.8 1.0
CB A:ASP387 4.5 83.8 1.0
CB A:ASN389 4.5 0.5 1.0
N A:GLY382 4.5 71.6 1.0
O A:ASN381 4.5 77.5 1.0
N A:ASN388 4.6 95.4 1.0
O A:GLY385 4.6 63.6 1.0
CA A:ASN381 4.7 79.4 1.0
CA A:GLY382 4.7 74.6 1.0
N A:ASN381 4.7 82.0 1.0
C A:ASN388 4.8 93.2 1.0
C A:GLY385 4.9 65.8 1.0
OG A:SER319 4.9 52.3 1.0
CA A:ASN388 4.9 91.2 1.0
OD1 A:ASN381 5.0 91.3 1.0

Calcium binding site 7 out of 9 in 6q23

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Calcium binding site 7 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:68.7
occ:1.00
 OD1 D:ASP113 3.1 50.5 1.0
OD2 D:ASP113 3.4 41.7 1.0
CG D:ASP113 3.6 48.8 1.0
OD2 C:ASP113 3.9 45.0 1.0
OD1 C:ASP113 4.0 53.7 1.0
CG C:ASP113 4.4 51.3 1.0
NZ A:LYS111 4.4 56.1 1.0
OD2 A:ASP113 4.4 60.8 1.0
OD1 A:ASP113 4.5 69.0 1.0
OD2 B:ASP113 4.6 64.8 1.0
O D:LYS111 4.6 50.8 1.0
OD1 B:ASP113 4.8 55.7 1.0
CG A:ASP113 4.8 59.1 1.0
O A:LYS111 5.0 45.2 1.0

Calcium binding site 8 out of 9 in 6q23

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Calcium binding site 8 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:96.0
occ:1.00
 O D:GLY345 2.3 0.8 1.0
O D:ASN347 2.3 64.9 1.0
O D:ASP293 2.4 65.3 1.0
O D:GLY297 2.5 80.7 1.0
OD2 D:ASP324 2.7 60.2 1.0
C D:GLY345 3.4 0.3 1.0
C D:ASN347 3.5 73.4 1.0
C D:ASP293 3.6 74.3 1.0
C D:GLY297 3.7 76.0 1.0
CG D:ASP324 3.7 59.4 1.0
CA D:GLY348 3.9 61.6 1.0
O D:ALA346 4.0 0.3 1.0
C D:ALA346 4.1 0.9 1.0
N D:GLY348 4.1 68.2 1.0
CA D:GLY345 4.2 94.2 1.0
CA D:ASN294 4.2 73.0 1.0
N D:GLY297 4.3 81.7 1.0
N D:ASN294 4.4 79.6 1.0
N D:ALA346 4.4 0.5 1.0
N D:ASN347 4.4 93.5 1.0
CB D:ASP324 4.4 59.9 1.0
CA D:GLY297 4.5 78.6 1.0
C D:ASN294 4.6 68.5 1.0
OD1 D:ASP324 4.6 49.4 1.0
N D:SER298 4.6 72.5 1.0
CA D:ASN347 4.6 80.3 1.0
CA D:ALA346 4.6 0.4 1.0
CA D:ASP293 4.7 73.4 1.0
CA D:SER298 4.8 71.5 1.0
CB D:ASP293 4.9 85.9 1.0
N D:ASP293 4.9 68.7 1.0
O D:PRO326 4.9 68.7 1.0
N D:TRP295 4.9 69.3 1.0
O D:ASN294 4.9 72.2 1.0
O D:ASN344 5.0 73.0 1.0
OD1 D:ASN294 5.0 52.3 1.0

Calcium binding site 9 out of 9 in 6q23

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Calcium binding site 9 out of 9 in the Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human 1G01 Fab in Complex with Influenza Virus Neuraminidase From A/California/04/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:0.7
occ:1.00
 O D:ASN389 2.5 0.3 1.0
OD1 D:ASP379 2.6 90.5 1.0
OD1 D:ASP387 2.7 0.6 1.0
C D:ASN389 3.3 0.4 1.0
CB D:ASN389 3.3 0.2 1.0
CG D:ASP379 3.5 83.5 1.0
CA D:ASN389 3.6 0.2 1.0
CG D:ASP387 3.6 0.0 1.0
OD2 D:ASP379 3.7 86.2 1.0
N D:ASN389 3.7 0.6 1.0
OD2 D:ASP387 3.8 0.5 1.0
CB D:ASN381 3.9 90.5 1.0
ND2 D:ASN381 3.9 0.7 1.0
CG D:ASN389 4.1 97.2 1.0
CG D:ASN381 4.2 94.2 1.0
N D:ASN381 4.3 88.1 1.0
N D:PHE390 4.4 0.6 1.0
OD1 D:ASN389 4.5 73.7 1.0
CA D:ASN381 4.6 92.5 1.0
O D:ASP387 4.8 0.5 1.0
CB D:ASP379 4.8 81.2 1.0
C D:ASN388 4.8 0.1 1.0
CD D:PRO380 4.8 82.8 1.0
C D:ASP387 4.9 0.7 1.0
C D:ASN381 4.9 87.8 1.0
ND2 D:ASN389 5.0 88.3 1.0
CB D:ASP387 5.0 0.6 1.0
CG D:PRO380 5.0 81.9 1.0

Reference:

D.Stadlbauer, X.Zhu, M.Mcmahon, J.S.Turner, T.J.Wohlbold, A.J.Schmitz, S.Strohmeier, W.Yu, R.Nachbagauer, P.A.Mudd, I.A.Wilson, A.H.Ellebedy, F.Krammer. Broadly Protective Human Antibodies That Target the Active Site of Influenza Virus Neuraminidase. Science V. 366 499 2019.
ISSN: ESSN 1095-9203
PubMed: 31649200
DOI: 10.1126/SCIENCE.AAY0678
Page generated: Tue Jul 16 13:09:59 2024

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