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Calcium in PDB 6v4n: Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013

Enzymatic activity of Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013

All present enzymatic activity of Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013:
3.2.1.18;

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013 (pdb code 6v4n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013, PDB code: 6v4n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6v4n

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Calcium binding site 1 out of 4 in the Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca509

b:45.3
occ:1.00
 O I:ASP293 2.2 45.1 1.0
O I:HOH618 2.2 44.3 1.0
O I:GLY346 2.3 43.8 1.0
O I:THR297 2.3 46.7 1.0
O I:GLY344 2.4 47.6 1.0
OD2 I:ASP324 3.0 43.6 1.0
C I:ASP293 3.4 45.1 1.0
C I:THR297 3.4 46.7 1.0
C I:GLY344 3.5 47.6 1.0
C I:GLY346 3.5 43.8 1.0
CG I:ASP324 3.9 43.6 1.0
CA I:GLY344 4.0 47.6 1.0
CA I:ALA298 4.1 46.1 1.0
CA I:ASN294 4.1 45.1 1.0
N I:ALA298 4.1 46.1 1.0
N I:ASN294 4.2 45.1 1.0
CA I:GLY347 4.2 42.4 1.0
N I:GLY347 4.3 42.4 1.0
N I:THR297 4.4 46.7 1.0
N I:GLY346 4.4 43.8 1.0
CA I:ASP293 4.5 45.1 1.0
C I:ASN294 4.5 45.1 1.0
CB I:ASP324 4.5 43.6 1.0
CA I:THR297 4.5 46.7 1.0
CA I:GLY346 4.6 43.8 1.0
C I:SER345 4.6 46.6 1.0
N I:SER345 4.6 46.6 1.0
N I:SER295 4.6 46.6 1.0
OD1 I:ASP324 4.6 43.6 1.0
CB I:ASP293 4.7 45.1 1.0
N I:ASP293 4.7 45.1 1.0
CA I:SER345 4.9 46.6 1.0
O I:PRO326 4.9 44.5 1.0
C I:ALA298 4.9 46.1 1.0
O I:SER345 5.0 46.6 1.0

Calcium binding site 2 out of 4 in 6v4n

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Calcium binding site 2 out of 4 in the Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca509

b:46.7
occ:1.00
 O M:ASP293 2.2 45.2 1.0
O M:HOH621 2.2 44.7 1.0
O M:GLY346 2.3 44.4 1.0
O M:THR297 2.3 47.2 1.0
O M:GLY344 2.4 48.3 1.0
OD2 M:ASP324 3.0 43.9 1.0
C M:ASP293 3.4 45.2 1.0
C M:THR297 3.4 47.2 1.0
C M:GLY344 3.5 48.3 1.0
C M:GLY346 3.5 44.4 1.0
CG M:ASP324 3.9 43.9 1.0
CA M:GLY344 4.0 48.3 1.0
CA M:ALA298 4.1 46.5 1.0
CA M:ASN294 4.1 45.3 1.0
N M:ALA298 4.1 46.5 1.0
N M:ASN294 4.2 45.3 1.0
CA M:GLY347 4.2 42.6 1.0
N M:GLY347 4.3 42.6 1.0
N M:GLY346 4.4 44.4 1.0
N M:THR297 4.4 47.2 1.0
CA M:ASP293 4.5 45.2 1.0
C M:ASN294 4.5 45.3 1.0
CB M:ASP324 4.5 43.9 1.0
CA M:THR297 4.5 47.2 1.0
CA M:GLY346 4.6 44.4 1.0
C M:SER345 4.6 47.6 1.0
N M:SER345 4.6 47.6 1.0
N M:SER295 4.6 46.8 1.0
OD1 M:ASP324 4.6 43.9 1.0
CB M:ASP293 4.7 45.2 1.0
N M:ASP293 4.7 45.2 1.0
CA M:SER345 4.9 47.6 1.0
C M:ALA298 4.9 46.5 1.0
O M:PRO326 4.9 45.1 1.0
O M:SER345 4.9 47.6 1.0

Calcium binding site 3 out of 4 in 6v4n

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Calcium binding site 3 out of 4 in the Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca509

b:45.7
occ:1.00
 O N:ASP293 2.2 45.2 1.0
O N:HOH623 2.2 44.3 1.0
O N:GLY346 2.3 44.0 1.0
O N:THR297 2.3 46.8 1.0
O N:GLY344 2.4 47.8 1.0
OD2 N:ASP324 3.0 43.8 1.0
C N:ASP293 3.4 45.2 1.0
C N:THR297 3.4 46.8 1.0
C N:GLY344 3.5 47.8 1.0
C N:GLY346 3.5 44.0 1.0
CG N:ASP324 3.9 43.8 1.0
CA N:GLY344 4.0 47.8 1.0
CA N:ALA298 4.1 46.1 1.0
CA N:ASN294 4.1 45.2 1.0
N N:ALA298 4.1 46.1 1.0
N N:ASN294 4.2 45.2 1.0
CA N:GLY347 4.2 42.5 1.0
N N:GLY347 4.3 42.5 1.0
N N:THR297 4.4 46.8 1.0
N N:GLY346 4.4 44.0 1.0
C N:ASN294 4.5 45.2 1.0
CA N:ASP293 4.5 45.2 1.0
CB N:ASP324 4.5 43.8 1.0
CA N:THR297 4.5 46.8 1.0
CA N:GLY346 4.6 44.0 1.0
C N:SER345 4.6 47.0 1.0
N N:SER345 4.6 47.0 1.0
OD1 N:ASP324 4.6 43.8 1.0
N N:SER295 4.6 46.7 1.0
N N:ASP293 4.7 45.2 1.0
CB N:ASP293 4.7 45.2 1.0
CA N:SER345 4.9 47.0 1.0
C N:ALA298 4.9 46.1 1.0
O N:PRO326 4.9 44.9 1.0
O N:SER345 5.0 47.0 1.0

Calcium binding site 4 out of 4 in 6v4n

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Calcium binding site 4 out of 4 in the Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Human 1G05 Fab in Complex with Influenza Virus Neuraminidase From B/Phuket/3073/2013 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Ca509

b:45.6
occ:1.00
 O W:ASP293 2.2 44.9 1.0
O W:HOH615 2.2 44.5 1.0
O W:GLY346 2.3 43.7 1.0
O W:THR297 2.3 46.6 1.0
O W:GLY344 2.4 47.8 1.0
OD2 W:ASP324 3.0 43.5 1.0
C W:ASP293 3.4 44.9 1.0
C W:THR297 3.4 46.6 1.0
C W:GLY344 3.5 47.8 1.0
C W:GLY346 3.5 43.7 1.0
CG W:ASP324 3.9 43.5 1.0
CA W:GLY344 4.0 47.8 1.0
CA W:ALA298 4.1 46.0 1.0
CA W:ASN294 4.1 44.8 1.0
N W:ALA298 4.1 46.0 1.0
N W:ASN294 4.2 44.8 1.0
CA W:GLY347 4.2 42.1 1.0
N W:GLY347 4.3 42.1 1.0
N W:THR297 4.4 46.6 1.0
N W:GLY346 4.4 43.7 1.0
CA W:ASP293 4.5 44.9 1.0
C W:ASN294 4.5 44.8 1.0
CB W:ASP324 4.5 43.5 1.0
CA W:THR297 4.5 46.6 1.0
CA W:GLY346 4.6 43.7 1.0
C W:SER345 4.6 47.1 1.0
N W:SER345 4.6 47.1 1.0
OD1 W:ASP324 4.6 43.5 1.0
N W:SER295 4.6 46.6 1.0
CB W:ASP293 4.7 44.9 1.0
N W:ASP293 4.7 44.9 1.0
CA W:SER345 4.9 47.1 1.0
C W:ALA298 4.9 46.0 1.0
O W:PRO326 4.9 44.6 1.0
O W:SER345 4.9 47.1 1.0

Reference:

A.Madsen, Y.N.Dai, M.Mcmahon, A.J.Schmitz, J.S.Turner, J.Tan, T.Lei, W.B.Alsoussi, S.Strohmeier, M.Amor, B.M.Mohammed, P.A.Mudd, V.Simon, R.J.Cox, D.H.Fremont, F.Krammer, A.H.Ellebedy. Human Antibodies Targeting Influenza B Virus Neuraminidase Active Site Are Broadly Protective. Immunity V. 53 852 2020.
ISSN: ISSN 1074-7613
PubMed: 32976769
DOI: 10.1016/J.IMMUNI.2020.08.015
Page generated: Tue Jul 16 16:30:47 2024

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