Sodium in PDB 6fyu: Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36

The structure of Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36, PDB code: 6fyu was solved by N.S.Laursen, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.424, 128.159, 192.104, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.6

The binding sites of Sodium atom in the Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36 (pdb code 6fyu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36, PDB code: 6fyu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:66.2 occ:1.00 OD1 D:ASP95 2.7 73.1 1.0 NE D:ARG109 2.7 57.0 1.0 O D:HOH614 2.7 40.1 1.0 O D:HOH635 3.1 49.2 1.0 OD2 D:ASP95 3.2 70.4 1.0 CG D:ASP95 3.3 69.0 1.0 N D:LEU66 3.5 49.9 1.0 NH2 D:ARG109 3.6 60.6 1.0 CZ D:ARG109 3.6 58.9 1.0 CD D:ARG109 3.6 54.2 1.0 N D:LEU67 3.8 47.2 1.0 CG D:LEU67 3.9 47.5 1.0 CB D:LEU66 4.0 49.9 1.0 CA D:LEU66 4.2 50.5 1.0 C D:GLY65 4.3 54.9 1.0 CG D:ARG109 4.3 53.3 1.0 CA D:GLY65 4.4 54.0 1.0 CB D:LEU67 4.4 49.6 1.0 CD1 D:LEU67 4.5 49.4 1.0 C D:LEU66 4.5 52.0 1.0 OE2 D:GLU89 4.5 72.0 1.0 CA D:LEU67 4.7 48.2 1.0 CB D:ASP95 4.8 60.6 1.0 NH1 D:ARG109 4.9 59.6 1.0 CD2 D:LEU67 5.0 43.5 1.0

Sodium binding site 2 out of 4 in the Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na203 b:51.2 occ:1.00 OD1 E:ASP46 2.4 66.8 1.0 OH F:TYR58 2.8 44.7 1.0 O F:HOH214 3.1 33.8 1.0 CG E:ASP46 3.4 62.9 1.0 CE2 F:TYR58 3.4 43.8 1.0 CZ F:TYR58 3.5 43.3 1.0 CA E:ASP46 3.6 38.0 1.0 CB F:ASN52 3.9 36.1 1.0 CB E:ASP46 3.9 47.4 1.0 CB E:THR49 4.0 34.8 1.0 CG2 E:THR49 4.0 34.7 1.0 OG1 E:THR49 4.1 41.9 1.0 N E:ASP46 4.3 33.6 1.0 OD2 E:ASP46 4.4 71.1 1.0 O E:ASP46 4.4 38.4 1.0 O E:HOH321 4.4 28.6 1.0 NE2 E:GLN42 4.5 33.1 1.0 C E:ASP46 4.5 36.0 1.0 ND2 F:ASN52 4.5 36.4 1.0 O E:ILE45 4.6 38.3 1.0 CD F:ARG56 4.6 64.3 1.0 NE2 F:HIS50 4.7 21.6 1.0 CG F:ASN52 4.7 41.0 1.0 CD2 F:TYR58 4.7 45.9 1.0 C E:ILE45 4.7 34.2 1.0 CE1 F:TYR58 4.9 39.2 1.0 CA F:ASN52 4.9 27.0 1.0 CG F:ARG56 5.0 55.3 1.0 CB F:ARG56 5.0 40.1 1.0 CG2 E:ILE45 5.0 32.5 1.0

Sodium binding site 3 out of 4 in the Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na403 b:65.3 occ:1.00 O G:HOH540 3.2 53.8 1.0 OH G:TYR308 3.3 33.5 1.0 OG G:SER299 3.6 45.1 1.0 CZ G:TYR308 3.8 26.9 1.0 CB G:SER299 4.0 36.3 1.0 CE2 G:TYR308 4.1 24.4 1.0 O H:HOH607 4.4 39.5 1.0 O G:HOH513 4.5 36.5 1.0 CE1 G:TYR308 4.7 24.3 1.0 N G:SER299 5.0 32.1 1.0

Sodium binding site 4 out of 4 in the Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in Complex SD36 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na404 b:62.3 occ:1.00 NE G:ARG109 2.7 42.1 1.0 O G:HOH527 2.8 37.1 1.0 OD1 G:ASP95 2.9 68.8 1.0 NH2 G:ARG109 3.2 46.2 1.0 OD2 G:ASP95 3.2 65.7 1.0 CZ G:ARG109 3.3 45.5 1.0 CG G:ASP95 3.5 65.1 1.0 N G:LEU66 3.6 41.4 1.0 CD G:ARG109 3.7 35.8 1.0 CB G:LEU66 4.1 36.6 1.0 N G:LEU67 4.2 39.3 1.0 CA G:GLY65 4.3 41.1 1.0 C G:GLY65 4.3 42.0 1.0 CA G:LEU66 4.4 38.5 1.0 CG G:LEU67 4.5 38.9 1.0 OE2 G:GLU89 4.5 80.4 1.0 O G:HOH506 4.5 50.0 1.0 CG G:ARG109 4.6 34.6 1.0 NH1 G:ARG109 4.6 45.0 1.0 OD1 H:ASN71 4.7 78.0 1.0 CD G:GLU89 4.7 72.8 1.0 C G:LEU66 4.8 41.4 1.0 OE1 G:GLU89 4.9 75.1 1.0 CB G:LEU67 4.9 39.7 1.0 CD1 G:LEU67 4.9 37.7 1.0 CB G:ASP95 5.0 60.4 1.0

N.S.Laursen, R.H.E.Friesen, X.Zhu, M.Jongeneelen, S.Blokland, J.Vermond, A.Van Eijgen, C.Tang, H.Van Diepen, G.Obmolova, M.Van Der Neut Kolfschoten, D.Zuijdgeest, R.Straetemans, R.M.B.Hoffman, T.Nieusma, J.Pallesen, H.L.Turner, S.M.Bernard, A.B.Ward, J.Luo, L.L.M.Poon, A.P.Tretiakova, J.M.Wilson, M.P.Limberis, R.Vogels, B.Brandenburg, J.A.Kolkman, I.A.Wilson. Universal Protection Against Influenza Infection By A Multidomain Antibody to Influenza Hemagglutinin. Science V. 362 598 2018.
ISSN: ESSN 1095-9203
PubMed: 30385580
DOI: 10.1126/SCIENCE.AAQ0620