Zinc in PDB 4fp8: Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit

The structure of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit, PDB code: 4fp8 was solved by D.C.Ekiert, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.794, 247.720, 95.380, 90.00, 91.33, 90.00
R / Rfree (%)	21.2 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit (pdb code 4fp8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit, PDB code: 4fp8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:0.5 occ:1.00 OD2 H:ASP61 2.4 0.5 1.0 OD1 L:ASP1 2.8 0.8 1.0 CG H:ASP61 3.5 0.7 1.0 CG L:ASP1 3.6 0.1 1.0 OD2 L:ASP1 3.8 0.9 1.0 OD1 H:ASP61 4.2 0.7 1.0 CB H:ASP61 4.5 99.7 1.0 N L:ASP1 4.9 99.2 1.0 CB L:ASP1 5.0 97.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:0.1 occ:1.00 NE2 H:HIS164 2.6 46.7 1.0 OD1 L:ASN137 2.7 46.5 1.0 OD1 L:ASN138 2.8 58.2 1.0 ND2 L:ASN137 3.1 45.5 1.0 CD2 H:HIS164 3.1 45.9 1.0 CG L:ASN137 3.2 44.5 1.0 ND2 L:ASN138 3.3 59.2 1.0 CG L:ASN138 3.4 56.4 1.0 CE1 H:HIS164 3.8 46.9 1.0 OG1 H:THR183 3.9 36.8 1.0 O H:GLY162 4.0 38.4 1.0 CA H:GLY162 4.2 42.7 1.0 C H:GLY162 4.4 41.7 1.0 CG H:HIS164 4.4 45.5 1.0 ND1 H:HIS164 4.7 46.7 1.0 CG2 H:THR183 4.7 35.5 1.0 CB L:ASN137 4.7 40.4 1.0 CB L:ASN138 4.8 52.8 1.0 OG L:SER174 4.9 34.8 1.0 CB H:THR183 4.9 36.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:72.7 occ:1.00 ND1 L:HIS189 2.2 75.4 1.0 OD2 B:ASP104 2.4 87.8 1.0 OD1 L:ASP151 2.5 49.5 1.0 OD1 B:ASP104 2.6 89.1 1.0 CG B:ASP104 2.6 88.7 1.0 CE1 L:HIS189 2.8 77.3 1.0 CG L:HIS189 3.2 76.7 1.0 CG L:ASP151 3.4 49.5 1.0 CB L:ASP151 3.7 49.5 1.0 CB B:PRO103 3.7 56.4 1.0 CB L:HIS189 3.8 75.5 1.0 NE2 L:HIS189 3.9 77.6 1.0 CB B:ASP104 3.9 88.5 1.0 O B:PRO103 4.0 59.6 1.0 C B:PRO103 4.0 56.5 1.0 CD2 L:HIS189 4.1 76.4 1.0 CA L:HIS189 4.1 76.1 1.0 N B:ASP104 4.3 84.0 1.0 CA B:ASP104 4.5 85.3 1.0 OD2 L:ASP151 4.5 50.7 1.0 CA B:PRO103 4.5 54.6 1.0 N L:HIS189 4.7 76.1 1.0 O L:LYS188 4.8 75.1 1.0 C L:LYS188 4.9 74.2 1.0 CG B:PRO103 4.9 55.9 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn301 b:94.8 occ:1.00 OD1 M:ASN138 2.5 54.0 1.0 NE2 I:HIS164 2.5 58.7 1.0 ND2 M:ASN137 2.9 51.4 1.0 OD1 M:ASN137 3.0 49.2 1.0 CD2 I:HIS164 3.0 59.2 1.0 CG M:ASN138 3.2 53.1 1.0 ND2 M:ASN138 3.2 51.9 1.0 CG M:ASN137 3.3 50.0 1.0 CE1 I:HIS164 3.7 55.8 1.0 OG1 I:THR183 4.0 66.8 1.0 O I:GLY162 4.3 58.5 1.0 CG I:HIS164 4.3 57.1 1.0 CA I:GLY162 4.4 61.4 1.0 C I:GLY162 4.6 59.7 1.0 CB M:ASN138 4.6 49.3 1.0 ND1 I:HIS164 4.6 55.3 1.0 CB M:ASN137 4.7 49.2 1.0 OG M:SER174 4.8 34.2 1.0 CG2 I:THR183 4.9 65.5 1.0 N M:ASN138 5.0 48.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:0.1 occ:1.00 OD1 N:ASP1 2.4 0.4 1.0 OD1 J:ASP61 2.4 0.5 1.0 CG N:ASP1 3.3 0.7 1.0 CG J:ASP61 3.5 0.9 1.0 OD2 N:ASP1 3.5 0.2 1.0 OD2 J:ASP61 4.0 0.1 1.0 CD N:PRO95 4.5 65.5 1.0 N N:ASP1 4.6 0.7 1.0 CG N:PRO95 4.6 64.7 1.0 CB J:ASP61 4.7 0.0 1.0 CB N:ASP1 4.7 0.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn301 b:0.0 occ:1.00 OD1 N:ASP92 2.3 83.1 1.0 CG N:ASP92 3.0 83.1 1.0 OD2 N:ASP92 3.1 85.0 1.0 O N:ASP92 4.3 75.8 1.0 CB N:ASP92 4.4 76.9 1.0 NE N:ARG30 4.5 0.3 1.0 CE2 N:PHE32 4.7 65.6 1.0 CD N:ARG30 4.8 0.8 1.0 CZ N:ARG30 4.9 0.7 1.0 C N:ASP92 4.9 74.7 1.0 CA N:ASP92 4.9 74.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn302 b:0.4 occ:1.00 NE2 J:HIS164 2.4 68.8 1.0 OD1 N:ASN138 2.7 88.3 1.0 OD1 N:ASN137 2.8 59.5 1.0 CD2 J:HIS164 2.9 68.3 1.0 ND2 N:ASN137 2.9 61.8 1.0 ND2 N:ASN138 3.2 85.8 1.0 CG N:ASN137 3.2 60.2 1.0 CG N:ASN138 3.3 87.2 1.0 CE1 J:HIS164 3.6 68.3 1.0 O J:GLY162 4.1 70.9 1.0 OG1 J:THR183 4.1 75.4 1.0 CG J:HIS164 4.2 66.4 1.0 CA J:GLY162 4.4 75.5 1.0 C J:GLY162 4.4 72.4 1.0 ND1 J:HIS164 4.5 66.3 1.0 CB N:ASN137 4.7 59.0 1.0 CB N:ASN138 4.7 83.1 1.0 OG N:SER174 4.7 53.2 1.0 CG2 J:THR183 4.9 72.5 1.0 N N:ASN138 4.9 81.5 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Broadly Neutralizing Antibody C05 Bound to H3 Influenza Hemagglutinin, HA1 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ O:Zn301 b:0.1 occ:1.00 OD1 O:ASP92 2.6 0.3 1.0 OD2 O:ASP92 3.0 0.3 1.0 CG O:ASP92 3.1 0.4 1.0 O O:ASP92 4.3 0.8 1.0 NE O:ARG30 4.5 0.5 1.0 CB O:ASP92 4.6 0.7 1.0 CZ O:ARG30 4.9 1.0 1.0 CD O:ARG30 4.9 0.6 1.0 C O:ASP92 4.9 0.8 1.0

D.C.Ekiert, A.K.Kashyap, J.Steel, A.Rubrum, G.Bhabha, R.Khayat, J.H.Lee, M.A.Dillon, R.E.O'neil, A.M.Faynboym, M.Horowitz, L.Horowitz, A.B.Ward, P.Palese, R.Webby, R.A.Lerner, R.R.Bhatt, I.A.Wilson. Cross-Neutralization of Influenza A Viruses Mediated By A Single Antibody Loop. Nature V. 489 526 2012.
ISSN: ISSN 0028-0836
PubMed: 22982990
DOI: 10.1038/NATURE11414