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Calcium in PDB 6lxi: Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1)

Enzymatic activity of Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1)

All present enzymatic activity of Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1):
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1), PDB code: 6lxi 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) 47.93 / 2.50
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 163.130, 163.130, 190.757, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1) (pdb code 6lxi). 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 Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1), PDB code: 6lxi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6lxi

Go back to Calcium Binding Sites List in 6lxi
Calcium binding site 1 out of 4 in the Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (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 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:27.2
occ:1.00
 O A:HOH665 2.3 32.0 1.0
OD2 A:ASP324 2.3 26.7 1.0
O A:ASN344 2.3 33.4 1.0
O A:ASP294 2.3 26.4 1.0
O A:GLY298 2.4 29.4 1.0
O A:GLY342 2.4 26.1 1.0
C A:GLY298 3.4 32.7 1.0
CG A:ASP324 3.4 24.6 1.0
C A:ASN344 3.4 33.7 1.0
C A:GLY342 3.5 29.7 1.0
C A:ASP294 3.5 27.9 1.0
CA A:GLY345 3.9 27.3 1.0
O A:ALA343 4.0 28.7 1.0
N A:GLY345 4.1 28.0 1.0
CA A:GLY342 4.1 27.6 1.0
C A:ALA343 4.1 25.6 1.0
N A:GLY298 4.2 32.6 1.0
N A:SER299 4.2 28.1 1.0
CB A:ASP324 4.2 19.6 1.0
CA A:SER299 4.3 25.9 1.0
OD1 A:ASP324 4.3 26.6 1.0
CA A:ASN295 4.3 27.3 1.0
CA A:GLY298 4.3 27.4 1.0
N A:ASN295 4.3 27.3 1.0
N A:ASN344 4.4 34.0 1.0
O A:HOH650 4.4 29.3 1.0
N A:ALA343 4.5 23.8 1.0
CA A:ASP294 4.6 22.5 1.0
CA A:ASN344 4.6 33.0 1.0
O A:ASN341 4.6 31.9 1.0
CA A:ALA343 4.7 22.5 1.0
CB A:ASP294 4.7 25.5 1.0
C A:ASN295 4.7 32.0 1.0
N A:ASP294 4.8 25.6 1.0
OD1 A:ASP294 4.9 28.1 1.0
O A:PRO326 4.9 28.9 1.0

Calcium binding site 2 out of 4 in 6lxi

Go back to Calcium Binding Sites List in 6lxi
Calcium binding site 2 out of 4 in the Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (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 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:33.9
occ:1.00
 O A:HOH619 1.8 32.4 1.0
O A:HOH640 1.9 36.6 1.0
OD1 A:ASN378 2.2 27.6 1.0
OD1 A:ASP376 2.2 31.3 1.0
O A:SER386 2.4 28.9 1.0
OD1 A:ASP384 2.5 33.1 1.0
CG A:ASP376 2.9 29.8 1.0
OD2 A:ASP376 2.9 28.5 1.0
CG A:ASN378 3.3 30.4 1.0
CG A:ASP384 3.4 32.9 1.0
C A:SER386 3.5 27.0 1.0
OD2 A:ASP384 3.6 30.0 1.0
ND2 A:ASN378 3.8 29.1 1.0
N A:SER386 4.0 27.0 1.0
CA A:SER386 4.1 27.2 1.0
O A:ASP384 4.1 30.7 1.0
CB A:SER386 4.2 25.9 1.0
N A:GLY379 4.3 27.2 1.0
CB A:ASP376 4.3 23.7 1.0
N A:ASN378 4.4 25.4 1.0
CA A:GLY379 4.4 23.3 1.0
C A:ASN378 4.5 27.4 1.0
C A:ASP384 4.5 33.5 1.0
N A:PHE387 4.5 29.7 1.0
CB A:ASN378 4.5 23.4 1.0
CB A:ASP384 4.7 24.8 1.0
CA A:ASN378 4.7 23.9 1.0
C A:SER385 4.7 28.3 1.0
O A:HOH804 4.8 32.5 1.0
CA A:PHE387 4.8 27.9 1.0
CA A:ASP376 4.9 24.4 1.0
CD A:PRO377 4.9 34.2 1.0
C A:ASP376 5.0 27.0 1.0
O A:ASN378 5.0 28.9 1.0
N A:PRO377 5.0 28.6 1.0
OG A:SER319 5.0 30.1 1.0

Calcium binding site 3 out of 4 in 6lxi

Go back to Calcium Binding Sites List in 6lxi
Calcium binding site 3 out of 4 in the Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (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 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:32.9
occ:1.00
 OD2 B:ASP324 2.2 36.7 1.0
O B:ASP294 2.2 30.3 1.0
O B:GLY298 2.3 39.1 1.0
O B:GLY342 2.5 33.8 1.0
O B:ASN344 2.5 38.4 1.0
O B:HOH625 2.5 31.1 1.0
CG B:ASP324 3.4 33.6 1.0
C B:GLY298 3.4 37.8 1.0
C B:ASP294 3.5 32.4 1.0
C B:GLY342 3.5 34.3 1.0
C B:ASN344 3.6 34.9 1.0
CA B:GLY345 3.8 26.4 1.0
N B:GLY345 4.1 28.2 1.0
CA B:GLY342 4.1 31.6 1.0
CB B:ASP324 4.2 29.7 1.0
N B:GLY298 4.2 41.0 1.0
N B:SER299 4.2 29.1 1.0
CA B:ASN295 4.2 30.4 1.0
C B:ALA343 4.3 27.9 1.0
O B:HOH646 4.3 31.1 1.0
OD1 B:ASP324 4.3 36.9 1.0
CA B:GLY298 4.3 33.4 1.0
N B:ASN295 4.3 35.1 1.0
CA B:SER299 4.3 30.4 1.0
O B:ALA343 4.3 30.6 1.0
N B:ALA343 4.5 27.3 1.0
CA B:ASP294 4.5 27.3 1.0
N B:ASN344 4.6 34.1 1.0
O B:ASN341 4.6 34.0 1.0
CB B:ASP294 4.6 30.1 1.0
C B:ASN295 4.6 34.7 1.0
CA B:ALA343 4.7 28.9 1.0
CA B:ASN344 4.7 35.1 1.0
N B:ASP294 4.8 30.8 1.0
OD1 B:ASP294 4.9 35.4 1.0
O B:PRO326 4.9 28.6 1.0
O B:ASN295 4.9 32.3 1.0

Calcium binding site 4 out of 4 in 6lxi

Go back to Calcium Binding Sites List in 6lxi
Calcium binding site 4 out of 4 in the Crystal Structure of Z2B3 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (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 Fab in Complex with Influenza Virus Neuraminidase From A/Brevig Mission/1/1918 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:37.5
occ:1.00
 O B:HOH633 2.0 35.4 1.0
OD1 B:ASN378 2.1 37.4 1.0
O B:HOH621 2.3 37.5 1.0
OD1 B:ASP376 2.3 39.9 1.0
O B:SER386 2.4 34.5 1.0
OD1 B:ASP384 2.5 35.5 1.0
OD2 B:ASP376 2.8 37.0 1.0
CG B:ASP376 2.9 37.5 1.0
CG B:ASN378 3.2 40.0 1.0
CG B:ASP384 3.2 36.2 1.0
OD2 B:ASP384 3.4 41.0 1.0
C B:SER386 3.5 34.5 1.0
ND2 B:ASN378 3.7 39.5 1.0
O B:ASP384 3.8 34.4 1.0
N B:SER386 3.9 34.3 1.0
CA B:SER386 4.1 30.2 1.0
C B:ASP384 4.2 33.4 1.0
N B:GLY379 4.3 31.5 1.0
CB B:SER386 4.3 33.3 1.0
CB B:ASP376 4.4 31.1 1.0
CA B:GLY379 4.5 27.9 1.0
C B:ASN378 4.5 35.3 1.0
CB B:ASN378 4.5 35.4 1.0
CB B:ASP384 4.5 30.0 1.0
N B:ASN378 4.6 34.3 1.0
C B:SER385 4.6 39.5 1.0
N B:PHE387 4.6 36.5 1.0
OG B:SER319 4.6 27.6 1.0
CA B:ASN378 4.7 34.6 1.0
CA B:ASP384 4.7 31.0 1.0
N B:SER385 4.8 38.4 1.0
N B:ASP384 4.8 35.6 1.0
O B:ASN378 4.9 39.4 1.0
O B:GLU382 5.0 39.0 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 11:07:52 2024

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