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Calcium in PDB 6lxk: Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1)

Enzymatic activity of Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1)

All present enzymatic activity of Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1):
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1), PDB code: 6lxk was solved by H.Jiang, W.Peng, J.Qi, Y.Chai, H.Song, Y.Shi, G.F.Gao, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.46 / 3.61
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.442, 214.442, 168.680, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) (pdb code 6lxk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1), PDB code: 6lxk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6lxk

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Calcium binding site 1 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:36.1
occ:1.00
 O A:GLY298 2.4 58.9 1.0
OD2 A:ASP324 2.4 49.7 1.0
O A:ASP294 2.5 58.8 1.0
O A:ALA343 2.7 59.5 1.0
O A:GLY342 3.0 81.9 1.0
C A:GLY298 3.4 59.5 1.0
CG A:ASP324 3.5 51.5 1.0
CA A:GLY345 3.6 54.4 1.0
C A:ALA343 3.6 54.8 1.0
N A:GLY345 3.6 53.1 1.0
C A:GLY342 3.6 74.4 1.0
C A:ASP294 3.7 61.5 1.0
C A:ASN344 3.7 76.7 1.0
O A:ASN344 4.1 85.4 1.0
N A:GLY298 4.2 68.5 1.0
CA A:ASN295 4.2 55.3 1.0
CA A:ASN344 4.3 79.3 1.0
CA A:GLY298 4.3 58.9 1.0
CA A:GLY342 4.3 71.5 1.0
N A:SER299 4.3 49.8 1.0
N A:ALA343 4.3 56.7 1.0
O A:ASN341 4.3 63.8 1.0
OD1 A:ASP324 4.3 53.6 1.0
CB A:ASP324 4.4 46.6 1.0
N A:ASN344 4.4 73.3 1.0
N A:ASN295 4.5 56.1 1.0
CA A:SER299 4.5 50.6 1.0
CA A:ALA343 4.5 57.1 1.0
O A:PRO326 4.6 51.6 1.0
C A:ASN295 4.6 55.4 1.0
O A:ASN295 4.8 54.0 1.0
CA A:ASP294 4.8 56.2 1.0

Calcium binding site 2 out of 8 in 6lxk

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Calcium binding site 2 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:72.7
occ:1.00
 OD1 A:ASN378 2.3 64.7 1.0
O A:LYS386 2.3 65.8 1.0
OD1 A:ASP384 2.3 91.0 1.0
OD1 A:ASP376 2.4 58.5 1.0
OD2 A:ASP376 3.1 67.8 1.0
CG A:ASP376 3.1 57.9 1.0
CG A:ASP384 3.1 87.9 1.0
OD2 A:ASP384 3.3 95.7 1.0
CG A:ASN378 3.4 69.8 1.0
C A:LYS386 3.4 66.8 1.0
ND2 A:ASN378 3.8 74.1 1.0
N A:LYS386 3.8 70.2 1.0
O A:ASP384 4.0 76.6 1.0
CA A:LYS386 4.0 71.2 1.0
CB A:LYS386 4.1 77.9 1.0
C A:ASP384 4.4 81.5 1.0
CB A:ASP384 4.5 76.0 1.0
N A:PHE387 4.6 63.7 1.0
N A:GLY379 4.6 56.2 1.0
CB A:ASP376 4.6 50.1 1.0
C A:ASN378 4.6 54.5 1.0
N A:ASN378 4.7 57.3 1.0
CB A:ASN378 4.7 63.5 1.0
C A:ASN385 4.7 65.1 1.0
CA A:GLY379 4.8 59.9 1.0
CA A:ASN378 4.9 55.6 1.0
CA A:ASP384 4.9 84.8 1.0
CA A:PHE387 4.9 55.9 1.0
N A:ASN385 4.9 60.4 1.0
O A:ASN378 5.0 57.1 1.0

Calcium binding site 3 out of 8 in 6lxk

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Calcium binding site 3 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:54.4
occ:1.00
 O B:GLY298 2.4 41.7 1.0
O B:ASP294 2.5 63.3 1.0
O B:ALA343 2.5 82.5 1.0
OD2 B:ASP324 2.8 57.1 1.0
O B:GLY342 2.9 80.4 1.0
C B:ALA343 3.4 72.1 1.0
C B:GLY298 3.5 40.7 1.0
C B:GLY342 3.5 81.3 1.0
N B:GLY345 3.5 41.2 1.0
C B:ASN344 3.6 85.2 1.0
CA B:GLY345 3.7 38.0 1.0
C B:ASP294 3.7 61.6 1.0
CG B:ASP324 3.8 53.2 1.0
O B:ASN344 4.0 98.2 1.0
CA B:ASN344 4.1 84.7 1.0
N B:GLY298 4.1 41.5 1.0
N B:ALA343 4.1 66.5 1.0
CA B:ASN295 4.1 51.8 1.0
N B:ASN344 4.2 86.9 1.0
CA B:GLY342 4.2 84.1 1.0
CA B:GLY298 4.2 40.2 1.0
CA B:ALA343 4.3 64.9 1.0
O B:ASN341 4.3 63.3 1.0
N B:SER299 4.4 57.1 1.0
N B:ASN295 4.4 51.6 1.0
C B:ASN295 4.5 51.1 1.0
CA B:SER299 4.6 57.1 1.0
OD1 B:ASP324 4.6 48.3 1.0
O B:PRO326 4.6 53.4 1.0
CB B:ASP324 4.7 49.6 1.0
O B:ASN295 4.7 53.0 1.0
CA B:ASP294 4.8 61.5 1.0

Calcium binding site 4 out of 8 in 6lxk

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Calcium binding site 4 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:96.7
occ:1.00
 OD1 B:ASN378 2.3 70.0 1.0
O B:LYS386 2.3 70.2 1.0
OD1 B:ASP376 2.4 66.0 1.0
OD1 B:ASP384 2.4 0.3 1.0
CG B:ASP376 3.1 59.2 1.0
OD2 B:ASP376 3.1 58.3 1.0
CG B:ASP384 3.2 96.6 1.0
C B:LYS386 3.4 67.0 1.0
CG B:ASN378 3.4 74.9 1.0
OD2 B:ASP384 3.4 0.4 1.0
N B:LYS386 3.8 62.0 1.0
ND2 B:ASN378 3.9 72.5 1.0
CA B:LYS386 3.9 64.2 1.0
O B:ASP384 4.0 65.3 1.0
CB B:LYS386 4.0 67.0 1.0
C B:ASP384 4.4 69.6 1.0
N B:PHE387 4.5 67.2 1.0
N B:GLY379 4.6 43.0 1.0
CB B:ASP376 4.6 53.6 1.0
CB B:ASP384 4.6 79.8 1.0
N B:ASN378 4.6 53.7 1.0
C B:ASN378 4.6 54.3 1.0
C B:ASN385 4.7 68.2 1.0
CB B:ASN378 4.7 68.5 1.0
CA B:GLY379 4.8 42.2 1.0
CA B:PHE387 4.9 62.0 1.0
CA B:ASN378 4.9 55.8 1.0
CD B:PRO377 4.9 60.9 1.0
N B:ASN385 5.0 66.5 1.0
CA B:ASP384 5.0 77.3 1.0

Calcium binding site 5 out of 8 in 6lxk

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Calcium binding site 5 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:52.4
occ:1.00
 O C:GLY298 2.4 61.0 1.0
O C:ASP294 2.5 69.7 1.0
OD2 C:ASP324 2.5 57.1 1.0
O C:ALA343 2.7 78.7 1.0
O C:GLY342 3.0 94.9 1.0
C C:GLY298 3.4 60.5 1.0
N C:GLY345 3.5 55.3 1.0
C C:ALA343 3.6 75.5 1.0
CA C:GLY345 3.6 46.7 1.0
CG C:ASP324 3.6 61.7 1.0
C C:ASN344 3.7 92.6 1.0
C C:ASP294 3.7 71.3 1.0
C C:GLY342 3.7 96.1 1.0
O C:ASN344 4.0 98.7 1.0
CA C:ASN344 4.1 85.8 1.0
N C:GLY298 4.2 67.1 1.0
CA C:ASN295 4.2 80.8 1.0
CA C:GLY298 4.3 60.6 1.0
N C:ASN344 4.3 78.2 1.0
N C:SER299 4.3 58.0 1.0
N C:ALA343 4.3 86.0 1.0
O C:ASN341 4.3 71.6 1.0
CA C:GLY342 4.4 90.9 1.0
OD1 C:ASP324 4.4 60.5 1.0
N C:ASN295 4.4 81.3 1.0
CB C:ASP324 4.5 60.9 1.0
CA C:ALA343 4.5 81.5 1.0
C C:ASN295 4.5 80.9 1.0
CA C:SER299 4.5 56.0 1.0
O C:PRO326 4.7 52.7 1.0
O C:ASN295 4.7 89.5 1.0
CA C:ASP294 4.8 62.2 1.0
CB C:ASP294 4.9 68.9 1.0

Calcium binding site 6 out of 8 in 6lxk

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Calcium binding site 6 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:70.4
occ:1.00
 O C:LYS386 2.3 75.7 1.0
OD1 C:ASN378 2.3 69.9 1.0
OD1 C:ASP376 2.4 58.8 1.0
OD1 C:ASP384 2.5 77.2 1.0
CG C:ASP376 3.1 61.0 1.0
OD2 C:ASP376 3.1 61.8 1.0
CG C:ASP384 3.2 75.2 1.0
OD2 C:ASP384 3.4 88.8 1.0
CG C:ASN378 3.4 69.1 1.0
C C:LYS386 3.4 74.7 1.0
ND2 C:ASN378 3.8 74.9 1.0
N C:LYS386 3.9 73.1 1.0
CA C:LYS386 4.0 71.8 1.0
O C:ASP384 4.0 68.0 1.0
CB C:LYS386 4.1 81.7 1.0
C C:ASP384 4.4 67.3 1.0
N C:PHE387 4.5 75.3 1.0
N C:GLY379 4.6 52.2 1.0
CB C:ASP376 4.6 58.3 1.0
C C:ASN378 4.6 64.5 1.0
CB C:ASP384 4.6 61.6 1.0
N C:ASN378 4.6 63.1 1.0
CB C:ASN378 4.7 60.7 1.0
C C:ASN385 4.7 70.3 1.0
CA C:GLY379 4.8 55.1 1.0
CA C:ASN378 4.9 59.9 1.0
CA C:PHE387 4.9 70.2 1.0
CD C:PRO377 4.9 56.6 1.0
O C:ASN378 4.9 71.2 1.0
CA C:ASP384 5.0 64.8 1.0

Calcium binding site 7 out of 8 in 6lxk

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Calcium binding site 7 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:46.0
occ:1.00
 O D:GLY298 2.4 68.0 1.0
OD2 D:ASP324 2.4 55.5 1.0
O D:ASP294 2.6 50.5 1.0
O D:ALA343 2.6 67.7 1.0
O D:GLY342 3.1 0.5 1.0
C D:GLY298 3.4 65.3 1.0
CG D:ASP324 3.5 57.5 1.0
C D:ALA343 3.6 60.3 1.0
N D:GLY345 3.6 60.5 1.0
C D:GLY342 3.7 0.1 1.0
CA D:GLY345 3.7 56.9 1.0
C D:ASN344 3.7 84.1 1.0
C D:ASP294 3.8 57.6 1.0
O D:ASN344 4.1 94.0 1.0
N D:GLY298 4.2 64.6 1.0
CA D:ASN344 4.2 80.1 1.0
O D:ASN341 4.3 65.6 1.0
N D:SER299 4.3 44.6 1.0
N D:ALA343 4.3 64.2 1.0
CA D:ASN295 4.3 62.0 1.0
OD1 D:ASP324 4.3 62.0 1.0
CA D:GLY298 4.3 60.2 1.0
CA D:GLY342 4.3 0.9 1.0
N D:ASN344 4.3 74.3 1.0
CB D:ASP324 4.4 54.8 1.0
CA D:SER299 4.4 43.8 1.0
CA D:ALA343 4.5 60.9 1.0
O D:PRO326 4.5 65.9 1.0
N D:ASN295 4.5 63.4 1.0
C D:ASN295 4.6 66.2 1.0
O D:ASN295 4.8 72.5 1.0
CA D:ASP294 4.9 58.7 1.0

Calcium binding site 8 out of 8 in 6lxk

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Calcium binding site 8 out of 8 in the Crystal Structure of Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (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 Z2B3 D102R Fab in Complex with Influenza Virus Neuraminidase From A/Serbia/Ns-601/2014 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:81.7
occ:1.00
 OD1 D:ASN378 2.2 68.1 1.0
O D:LYS386 2.3 61.3 1.0
OD1 D:ASP376 2.4 64.9 1.0
OD1 D:ASP384 2.4 87.0 1.0
CG D:ASP376 3.2 62.7 1.0
OD2 D:ASP376 3.3 72.4 1.0
CG D:ASN378 3.3 81.1 1.0
CG D:ASP384 3.3 79.0 1.0
C D:LYS386 3.4 63.2 1.0
OD2 D:ASP384 3.5 84.3 1.0
ND2 D:ASN378 3.8 83.2 1.0
N D:LYS386 3.9 61.6 1.0
CA D:LYS386 3.9 63.9 1.0
CB D:LYS386 4.0 68.2 1.0
O D:ASP384 4.2 64.8 1.0
N D:PHE387 4.5 79.6 1.0
N D:ASN378 4.5 67.3 1.0
CB D:ASN378 4.6 84.7 1.0
C D:ASP384 4.6 67.5 1.0
CB D:ASP376 4.6 51.3 1.0
N D:GLY379 4.6 58.2 1.0
C D:ASN378 4.6 75.5 1.0
CB D:ASP384 4.7 77.2 1.0
CA D:ASN378 4.8 76.5 1.0
C D:ASN385 4.8 69.2 1.0
CA D:PHE387 4.8 77.8 1.0
CD D:PRO377 4.8 61.3 1.0
CA D:GLY379 4.9 55.8 1.0

Reference:

H.Jiang, W.Peng, J.Qi, Y.Chai, H.Song, Y.Bi, P.Rijal, H.Wang, B.O.Oladejo, J.Liu, Y.Shi, G.F.Gao, A.R.Townsend, Y.Wu. Structure-Based Modification of An Anti-Neuraminidase Human Antibody Restores Protection Efficacy Against the Drifted Influenza Virus. Mbio V. 11 2020.
ISSN: ESSN 2150-7511
PubMed: 33024040
DOI: 10.1128/MBIO.02315-20
Page generated: Tue Jul 16 11:08:05 2024

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