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Calcium in PDB 6lxj: Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9)

Enzymatic activity of Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9)

All present enzymatic activity of Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9):
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9), PDB code: 6lxj 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) 48.91 / 2.90
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 201.307, 207.514, 207.702, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9) (pdb code 6lxj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9), PDB code: 6lxj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6lxj

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Calcium binding site 1 out of 4 in the Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9)


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 Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:65.9
occ:1.00
 O A:GLY298 2.3 44.1 1.0
O A:ASP294 2.6 33.3 1.0
O A:ASN344A 2.6 43.5 1.0
OD2 A:ASP324 3.3 36.9 1.0
C A:GLY298 3.5 38.2 1.0
CG A:ASP324 3.6 34.1 1.0
C A:ASN344A 3.8 39.2 1.0
C A:ASP294 3.8 35.3 1.0
CA A:GLY345 3.9 31.2 1.0
OD1 A:ASP324 4.1 30.8 1.0
CA A:SER299 4.1 30.9 1.0
N A:SER299 4.2 33.6 1.0
CB A:ASP324 4.2 30.1 1.0
N A:GLY345 4.3 35.0 1.0
OG A:SER299 4.4 43.5 1.0
CA A:ASN295 4.5 34.8 1.0
N A:ASN295 4.6 32.2 1.0
O A:PRO326 4.6 34.7 1.0
CA A:GLY298 4.6 36.3 1.0
N A:GLY298 4.6 43.6 1.0
O A:ASN342 4.7 39.2 1.0
CB A:SER299 4.8 38.5 1.0
CA A:ASP294 4.8 39.2 1.0
C A:ASN295 4.8 40.3 1.0
CB A:ASP294 4.9 40.6 1.0
N A:ASN344A 5.0 44.2 1.0

Calcium binding site 2 out of 4 in 6lxj

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Calcium binding site 2 out of 4 in the Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9)


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 Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:79.5
occ:1.00
 O B:GLY298 2.6 52.6 1.0
O B:ASN344A 2.7 62.2 1.0
O B:ASP294 3.3 45.6 1.0
C B:GLY298 3.6 49.2 1.0
OD2 B:ASP324 3.6 46.9 1.0
C B:ASN344A 3.9 56.5 1.0
OG B:SER299 4.0 51.9 1.0
CA B:SER299 4.1 49.8 1.0
O B:ASN342 4.1 53.9 1.0
CG B:ASP324 4.1 45.1 1.0
N B:SER299 4.1 49.8 1.0
O B:PRO326 4.2 41.8 1.0
CA B:GLY345 4.3 41.8 1.0
N B:GLY345 4.5 50.4 1.0
C B:ASP294 4.5 44.7 1.0
CB B:SER299 4.6 50.7 1.0
OD1 B:ASP324 4.6 42.8 1.0
CB B:ASP324 4.7 42.2 1.0
CA B:GLY298 4.8 50.7 1.0
C B:ASN342 4.8 56.4 1.0
N B:GLY298 4.8 52.0 1.0
O B:TRP296 4.8 62.5 1.0
C B:ASN295 4.8 56.6 1.0
CA B:ASN295 4.8 49.6 1.0
CB B:ASN342 4.9 51.9 1.0
N B:ASN344A 4.9 52.4 1.0

Calcium binding site 3 out of 4 in 6lxj

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Calcium binding site 3 out of 4 in the Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9)


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 Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:72.0
occ:1.00
 O C:ASP294 2.3 39.6 1.0
O C:GLY298 2.3 54.3 1.0
O C:ASN344A 2.9 48.2 1.0
OD2 C:ASP324 3.0 42.6 1.0
C C:GLY298 3.5 43.8 1.0
C C:ASP294 3.5 42.0 1.0
CG C:ASP324 3.5 38.4 1.0
C C:ASN344A 3.9 43.8 1.0
OD1 C:ASP324 4.0 33.9 1.0
CA C:GLY345 4.1 39.0 1.0
CB C:ASP324 4.2 34.6 1.0
CA C:SER299 4.2 38.4 1.0
N C:SER299 4.2 42.4 1.0
CA C:ASN295 4.3 43.3 1.0
N C:ASN295 4.3 40.7 1.0
N C:GLY345 4.5 43.0 1.0
N C:GLY298 4.5 43.4 1.0
CA C:ASP294 4.5 39.1 1.0
CA C:GLY298 4.5 40.8 1.0
CB C:ASP294 4.6 44.7 1.0
C C:ASN295 4.7 48.4 1.0
OG C:SER299 4.7 45.2 1.0
O C:ASN342 4.7 57.4 1.0
N C:ASP294 4.8 34.7 1.0
O C:PRO326 4.8 35.3 1.0
N C:TRP296 4.9 48.2 1.0
N C:ASN344A 5.0 47.6 1.0

Calcium binding site 4 out of 4 in 6lxj

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Calcium binding site 4 out of 4 in the Crystal Structure of Human Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9)


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 Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Anhui/1/2013 (H7N9) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:90.7
occ:1.00
 O D:GLY298 2.4 47.3 1.0
O D:ASN344A 2.8 56.0 1.0
O D:ASP294 2.9 43.7 1.0
C D:GLY298 3.4 41.0 1.0
OD2 D:ASP324 3.4 39.5 1.0
CG D:ASP324 3.9 39.6 1.0
O D:ASN342 4.0 54.6 1.0
C D:ASN344A 4.0 47.0 1.0
CA D:SER299 4.0 38.4 1.0
N D:SER299 4.0 39.5 1.0
C D:ASP294 4.1 44.6 1.0
OG D:SER299 4.1 45.8 1.0
OD1 D:ASP324 4.3 36.4 1.0
N D:GLY298 4.4 44.3 1.0
CA D:GLY345 4.4 36.9 1.0
OD1 D:ASN295 4.4 52.9 1.0
CA D:GLY298 4.4 40.3 1.0
O D:PRO326 4.5 37.7 1.0
CB D:ASP324 4.5 35.0 1.0
CA D:ASN295 4.6 46.7 1.0
CB D:SER299 4.6 39.7 1.0
N D:GLY345 4.7 43.2 1.0
C D:GLN297 4.8 47.4 1.0
N D:ASN295 4.8 46.8 1.0
N D:ASN344A 4.9 50.4 1.0
O D:GLN297 5.0 46.3 1.0
C D:ASN342 5.0 54.0 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 11:08:01 2024

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