Zinc in PDB 8eqa: Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab

The structure of Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab, PDB code: 8eqa was solved by X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.56 / 2.55
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.558, 110.568, 130.679, 90, 90, 90
R / Rfree (%)	21.5 / 26.4

The binding sites of Zinc atom in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab (pdb code 8eqa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab, PDB code: 8eqa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab


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 Human Anti-N1 Neuraminidase 2H08 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:42.1 occ:1.00 OD1 L:ASN137 2.1 35.3 1.0 OD1 L:ASN138 2.2 36.0 1.0 NE2 H:HIS172 2.3 30.1 1.0 O L:HOH416 2.8 20.3 1.0 CD2 H:HIS172 2.8 25.7 1.0 CG L:ASN137 2.9 31.6 1.0 ND2 L:ASN137 3.0 34.0 1.0 CG L:ASN138 3.3 39.7 1.0 CE1 H:HIS172 3.5 34.9 1.0 OG1 H:THR192 3.6 31.6 1.0 ND2 L:ASN138 4.1 43.2 1.0 O H:GLY169 4.1 32.9 1.0 CG H:HIS172 4.1 29.2 1.0 CB L:ASN137 4.4 38.0 1.0 ND1 H:HIS172 4.4 36.1 1.0 OG L:SER174 4.4 32.9 1.0 CG2 H:THR192 4.5 23.4 1.0 CB L:ASN138 4.5 29.3 1.0 CA H:GLY169 4.5 29.8 1.0 C H:GLY169 4.6 38.2 1.0 N L:ASN138 4.6 33.6 1.0 CB H:THR192 4.7 26.3 1.0 CA L:ASN137 4.9 31.0 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab


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 Human Anti-N1 Neuraminidase 2H08 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:151.5 occ:1.00 NE2 H:HIS102 2.3 83.1 1.0 NE2 H:HIS101 2.3 76.8 1.0 CD2 H:HIS101 2.8 70.0 1.0 CD2 H:HIS102 2.9 58.2 1.0 O H:HOH425 3.2 67.8 1.0 CE1 H:HIS101 3.3 74.2 1.0 CE1 H:HIS102 3.5 79.1 1.0 CG H:HIS101 3.9 71.8 1.0 ND1 H:HIS101 4.2 74.7 1.0 CG H:HIS102 4.2 56.5 1.0 N H:GLN1 4.3 122.2 1.0 ND1 H:HIS102 4.4 63.0 1.0 CA H:GLN1 4.7 118.8 1.0 N H:VAL2 4.7 93.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab


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 Human Anti-N1 Neuraminidase 2H08 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:43.9 occ:1.00 OD1 A:ASN138 1.9 38.8 1.0 O B:HOH414 2.2 47.2 1.0 NE2 B:HIS172 2.3 31.8 1.0 OD1 A:ASN137 2.4 39.9 1.0 O A:HOH417 2.5 29.9 1.0 ND2 A:ASN137 2.9 42.9 1.0 CG A:ASN137 3.0 38.8 1.0 CG A:ASN138 3.0 44.0 1.0 CD2 B:HIS172 3.0 27.0 1.0 CE1 B:HIS172 3.4 27.3 1.0 ND2 A:ASN138 3.7 35.5 1.0 OG1 B:THR192 3.9 35.4 1.0 CB A:ASN138 4.2 40.4 1.0 CG B:HIS172 4.3 26.5 1.0 OG A:SER174 4.3 33.9 1.0 ND1 B:HIS172 4.4 31.1 1.0 CB A:ASN137 4.4 42.8 1.0 O B:GLY169 4.5 28.0 1.0 N A:ASN138 4.5 35.3 1.0 CA B:GLY169 4.6 33.5 1.0 CG2 B:THR192 4.8 32.9 1.0 C B:GLY169 4.8 30.7 1.0 CA A:ASN138 4.9 38.1 1.0 CA A:ASN137 5.0 36.6 1.0 CB B:THR192 5.0 30.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab


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 Human Anti-N1 Neuraminidase 2H08 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:62.5 occ:1.00 O B:HOH402 1.9 52.2 1.0 NE2 B:HIS102 2.3 60.7 1.0 CB B:GLN1 2.6 63.6 1.0 CE1 B:HIS102 2.7 59.4 1.0 OE1 B:GLN1 3.1 62.3 1.0 N B:GLN1 3.3 59.0 1.0 CA B:GLN1 3.5 64.7 1.0 CD2 B:HIS102 3.6 53.4 1.0 CG B:GLN1 3.7 60.7 1.0 CD B:GLN1 3.8 66.9 1.0 ND1 B:HIS102 4.0 46.4 1.0 N B:VAL2 4.2 72.8 1.0 C B:GLN1 4.4 69.8 1.0 CG B:HIS102 4.4 48.3 1.0 CE1 B:HIS101 4.7 55.2 1.0 NE2 B:HIS101 4.9 59.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Human Anti-N1 Neuraminidase 2H08 Fab


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 Human Anti-N1 Neuraminidase 2H08 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:53.9 occ:1.00 NE2 B:HIS101 2.3 59.0 1.0 NE2 B:GLN1 2.3 71.5 1.0 OD2 B:ASP27 2.4 64.6 1.0 CD2 B:HIS101 2.6 46.0 1.0 OE1 B:GLN1 2.6 62.3 1.0 CD B:GLN1 2.8 66.9 1.0 CG2 B:VAL2 2.8 71.6 1.0 OH B:TYR34 2.9 67.6 1.0 O B:HOH415 2.9 41.6 1.0 CG B:ASP27 3.3 58.9 1.0 OD1 B:ASP27 3.6 69.3 1.0 CE1 B:HIS101 3.6 55.2 1.0 CZ B:TYR34 3.7 57.5 1.0 CE1 B:TYR34 3.8 60.3 1.0 CG B:HIS101 3.9 52.3 1.0 CG B:GLN1 4.2 60.7 1.0 CB B:VAL2 4.3 74.3 1.0 ND1 B:HIS101 4.4 52.0 1.0 O B:HOH402 4.4 52.2 1.0 ND2 B:ASN94 4.5 50.4 1.0 CB B:ASP27 4.7 47.5 1.0 CD2 B:HIS102 4.7 53.4 1.0 N B:VAL2 4.7 72.8 1.0 CD1 B:ILE96 4.8 52.4 1.0 CE2 B:TYR34 4.9 51.8 1.0

L.Hansen, M.Mcmahon, H.L.Turner, X.Zhu, J.S.Turner, G.Ozorowski, D.Stadlbauer, J.Vahokoski, A.J.Schmitz, A.A.Rizk, W.B.Alsoussi, S.Strohmeier, W.Yu, J.A.Choreno-Parra, L.Jimenez-Alvarez, A.Cruz-Lagunas, J.Zuniga, P.A.Mudd, R.J.Cox, I.A.Wilson, A.B.Ward, A.H.Ellebedy, F.Krammer. Human Anti-N1 Monoclonal Antibodies Elicited By Pandemic H1N1 Virus Infection Broadly Inhibit HXN1 Viruses in Vitro and in Vivo. Immunity 2023.
ISSN: ISSN 1074-7613
PubMed: 37506693
DOI: 10.1016/J.IMMUNI.2023.07.004