Calcium in PDB 9eje: Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs

All present enzymatic activity of Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs:
3.2.1.18;

The binding sites of Calcium atom in the Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs (pdb code 9eje). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs, PDB code: 9eje:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:50.0 occ:1.00 OD2 A:ASP241 2.2 100.0 1.0 O A:TYR266 2.3 100.0 1.0 O A:ASP211 2.4 100.0 1.0 O A:GLY215 2.5 66.4 1.0 HA3 A:GLY267 3.4 50.0 1.0 CG A:ASP241 3.4 100.0 1.0 C A:TYR266 3.4 100.0 1.0 C A:ASP211 3.6 100.0 1.0 HA A:ASN212 3.6 98.7 1.0 C A:GLY215 3.7 66.4 1.0 H A:TYR266 3.7 100.0 1.0 HA2 A:GLY267 3.7 50.0 1.0 HB3 A:ASP211 3.9 100.0 1.0 HA A:MET216 3.9 100.0 1.0 CA A:GLY267 3.9 50.0 1.0 O A:THR263 4.0 100.0 1.0 HB3 A:ASP241 4.1 100.0 1.0 N A:GLY267 4.1 50.0 1.0 H A:GLY215 4.1 66.4 1.0 HD2 A:PRO243 4.2 100.0 1.0 CB A:ASP241 4.3 100.0 1.0 OD1 A:ASP241 4.3 100.0 1.0 CA A:ASN212 4.4 98.7 1.0 HB2 A:ASP241 4.4 100.0 1.0 N A:ASN212 4.4 98.7 1.0 N A:TYR266 4.4 100.0 1.0 CA A:TYR266 4.6 100.0 1.0 N A:MET216 4.6 100.0 1.0 CB A:ASP211 4.6 100.0 1.0 H A:ASP211 4.6 100.0 1.0 CA A:ASP211 4.6 100.0 1.0 CA A:GLY215 4.6 66.4 1.0 CA A:MET216 4.7 100.0 1.0 HA3 A:GLY215 4.7 66.4 1.0 HG2 A:PRO243 4.8 100.0 1.0 N A:GLY215 4.8 66.4 1.0 O A:ASN264 4.8 100.0 1.0 C A:ASN212 4.9 98.7 1.0 H A:TRP213 4.9 100.0 1.0 HB2 A:PRO243 4.9 100.0 1.0 OD1 A:ASP211 5.0 100.0 1.0 H A:GLY267 5.0 50.0 1.0 N A:ASP211 5.0 100.0 1.0

Calcium binding site 2 out of 4 in the Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:50.0 occ:1.00 O D:TYR266 2.2 100.0 1.0 OD2 D:ASP241 2.3 100.0 1.0 O D:GLY215 2.4 66.4 1.0 O D:ASP211 2.6 100.0 1.0 C D:TYR266 3.4 100.0 1.0 HA3 D:GLY267 3.5 50.0 1.0 CG D:ASP241 3.5 100.0 1.0 HA D:ASN212 3.6 98.7 1.0 H D:TYR266 3.6 100.0 1.0 C D:GLY215 3.7 66.4 1.0 C D:ASP211 3.7 100.0 1.0 HA2 D:GLY267 3.8 50.0 1.0 O D:THR263 3.8 100.0 1.0 HA D:MET216 3.9 100.0 1.0 CA D:GLY267 3.9 50.0 1.0 HB3 D:ASP211 4.0 100.0 1.0 H D:GLY215 4.0 66.4 1.0 N D:GLY267 4.1 50.0 1.0 HB3 D:ASP241 4.3 100.0 1.0 HD2 D:PRO243 4.3 100.0 1.0 OD1 D:ASP241 4.3 100.0 1.0 N D:TYR266 4.4 100.0 1.0 CA D:ASN212 4.4 98.7 1.0 CB D:ASP241 4.4 100.0 1.0 N D:ASN212 4.5 98.7 1.0 HB2 D:ASP241 4.5 100.0 1.0 CA D:TYR266 4.5 100.0 1.0 N D:MET216 4.6 100.0 1.0 CA D:GLY215 4.6 66.4 1.0 CA D:MET216 4.6 100.0 1.0 O D:ASN264 4.7 100.0 1.0 HA3 D:GLY215 4.7 66.4 1.0 N D:GLY215 4.7 66.4 1.0 CB D:ASP211 4.7 100.0 1.0 CA D:ASP211 4.8 100.0 1.0 HG2 D:PRO243 4.8 100.0 1.0 H D:ASP211 4.8 100.0 1.0 H D:TRP213 4.8 100.0 1.0 C D:ASN212 4.8 98.7 1.0 C D:THR263 4.9 100.0 1.0 HB2 D:PRO243 4.9 100.0 1.0 H D:GLY267 5.0 50.0 1.0

Calcium binding site 3 out of 4 in the Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca402 b:50.0 occ:1.00 O G:GLY215 2.1 66.4 1.0 OD2 G:ASP241 2.2 100.0 1.0 O G:TYR266 2.5 100.0 1.0 O G:ASP211 2.8 100.0 1.0 C G:GLY215 3.2 66.4 1.0 HA3 G:GLY267 3.3 50.0 1.0 HA G:MET216 3.3 100.0 1.0 CG G:ASP241 3.4 100.0 1.0 C G:TYR266 3.6 100.0 1.0 HA G:ASN212 3.8 98.7 1.0 O G:THR263 3.9 100.0 1.0 C G:ASP211 3.9 100.0 1.0 H G:TYR266 3.9 100.0 1.0 CA G:GLY267 4.1 50.0 1.0 HA3 G:GLY215 4.1 66.4 1.0 N G:MET216 4.1 100.0 1.0 CA G:MET216 4.1 100.0 1.0 HA2 G:GLY267 4.1 50.0 1.0 OD1 G:ASP241 4.2 100.0 1.0 CA G:GLY215 4.2 66.4 1.0 H G:GLY215 4.2 66.4 1.0 HB3 G:ASP241 4.3 100.0 1.0 N G:GLY267 4.3 50.0 1.0 HB3 G:ASP211 4.3 100.0 1.0 CB G:ASP241 4.4 100.0 1.0 HD2 G:PRO243 4.5 100.0 1.0 HB2 G:ASP241 4.5 100.0 1.0 N G:GLY215 4.6 66.4 1.0 CA G:ASN212 4.6 98.7 1.0 HG3 G:MET216 4.6 100.0 1.0 H G:ASP211 4.6 100.0 1.0 N G:TYR266 4.6 100.0 1.0 N G:ASN212 4.7 98.7 1.0 HB2 G:MET216 4.8 100.0 1.0 CA G:TYR266 4.8 100.0 1.0 HB G:THR263 4.8 100.0 1.0 H G:MET216 4.9 100.0 1.0 CB G:MET216 5.0 100.0 1.0 CA G:ASP211 5.0 100.0 1.0

Calcium binding site 4 out of 4 in the Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ncs.1 Fab in Complex with N5 Na of A/Shorebird/Delaware Bay/309/2016 (DB16, H10N5) -- 3 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca402 b:50.0 occ:1.00 O P:GLY215 2.1 66.4 1.0 OD2 P:ASP241 2.2 100.0 1.0 O P:ASP211 2.3 100.0 1.0 O P:TYR266 2.7 100.0 1.0 C P:GLY215 3.4 66.4 1.0 C P:ASP211 3.4 100.0 1.0 CG P:ASP241 3.5 100.0 1.0 HB3 P:ASP211 3.6 100.0 1.0 HA3 P:GLY267 3.6 50.0 1.0 HA P:ASN212 3.6 98.7 1.0 HA P:MET216 3.7 100.0 1.0 C P:TYR266 3.8 100.0 1.0 H P:GLY215 3.9 66.4 1.0 H P:TYR266 4.0 100.0 1.0 HA2 P:GLY267 4.0 50.0 1.0 O P:THR263 4.1 100.0 1.0 HB3 P:ASP241 4.1 100.0 1.0 CA P:GLY267 4.2 50.0 1.0 CA P:GLY215 4.2 66.4 1.0 HA3 P:GLY215 4.3 66.4 1.0 CB P:ASP241 4.3 100.0 1.0 N P:ASN212 4.3 98.7 1.0 N P:MET216 4.3 100.0 1.0 CA P:ASN212 4.3 98.7 1.0 CB P:ASP211 4.3 100.0 1.0 OD1 P:ASP241 4.4 100.0 1.0 HB2 P:ASP241 4.4 100.0 1.0 CA P:ASP211 4.4 100.0 1.0 H P:ASP211 4.4 100.0 1.0 CA P:MET216 4.4 100.0 1.0 N P:GLY267 4.5 50.0 1.0 N P:GLY215 4.5 66.4 1.0 HD2 P:PRO243 4.5 100.0 1.0 H P:TRP213 4.7 100.0 1.0 OD1 P:ASP211 4.7 100.0 1.0 N P:TYR266 4.7 100.0 1.0 C P:ASN212 4.8 98.7 1.0 N P:ASP211 4.8 100.0 1.0 O P:ASN264 4.8 100.0 1.0 CG P:ASP211 4.8 100.0 1.0 N P:TRP213 4.9 100.0 1.0 CA P:TYR266 4.9 100.0 1.0

J.Lederhofer, A.J.Borst, L.Nguyen, R.A.Gillespie, C.J.Williams, E.L.Walker, J.E.Raab, C.Yap, D.Ellis, A.Creanga, H.X.Tan, T.H.T.Do, M.Ravichandran, A.B.Mcdermott, V.Le Sage, S.F.Andrews, B.S.Graham, A.K.Wheatley, D.S.Reed, N.P.King, M.Kanekiyo. Structural Convergence and Water-Mediated Substrate Mimicry Enable Broad Neuraminidase Inhibition By Human Antibodies. Nat Commun V. 16 7068 2025.
ISSN: ESSN 2041-1723
PubMed: 40750617
DOI: 10.1038/S41467-025-62339-Z