Atomistry » Calcium » PDB 6lje-6m4l » 6lxi
Atomistry »
  Calcium »
    PDB 6lje-6m4l »
      6lxi »

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

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy