Nickel in PDB 4d00: Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln

The structure of Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln, PDB code: 4d00 was solved by X.Xiong, L.F.Haire, S.G.Vachieri, P.J.Collins, P.A.Walker, S.R.Martin, Y.Zhang, J.W.Mccauley, S.J.Gamblin, J.J.Skehel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	132.58 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.601, 183.169, 192.145, 90.00, 90.00, 90.00
R / Rfree (%)	20.852 / 23.474

The binding sites of Nickel atom in the Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln (pdb code 4d00). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln, PDB code: 4d00:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1321 b:35.4 occ:1.00 O7 F:NAG1174 2.0 32.3 1.0 OE2 A:GLU104 2.1 27.2 1.0 OD1 F:ASN79 2.4 22.8 1.0 OE2 B:GLU64 2.5 25.2 1.0 OE1 B:GLU64 2.6 24.9 1.0 CD A:GLU104 2.7 25.7 1.0 CD B:GLU64 2.9 25.1 1.0 OE1 A:GLU104 3.0 25.4 1.0 C7 F:NAG1174 3.2 31.7 1.0 CG F:ASN79 3.4 22.4 1.0 ND2 F:ASN79 3.9 22.7 1.0 CG A:GLU104 3.9 25.2 1.0 C8 F:NAG1174 4.1 30.7 1.0 N2 F:NAG1174 4.1 33.1 1.0 NH1 A:ARG256 4.2 40.8 1.0 C2 F:NAG1174 4.3 36.1 1.0 O B:HOH2009 4.3 18.2 1.0 O F:HOH2029 4.3 16.1 1.0 CG B:GLU64 4.4 25.2 1.0 O A:HOH2087 4.4 28.6 1.0 ND2 F:ASN82 4.4 36.8 1.0 O B:HOH2027 4.6 18.1 1.0 NH2 A:ARG256 4.6 42.5 1.0 CB F:ASN79 4.7 21.7 1.0 NE2 F:HIS75 4.8 24.7 1.0 C1 F:NAG1174 4.9 33.2 1.0 CZ A:ARG256 4.9 41.8 1.0 CA F:ASN79 5.0 21.5 1.0 CB A:GLU104 5.0 24.2 1.0

Nickel binding site 2 out of 3 in the Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1178 b:38.7 occ:1.00 O7 B:NAG1176 2.0 37.6 1.0 OE2 C:GLU104 2.1 30.1 1.0 OD1 B:ASN79 2.4 22.2 1.0 OE2 D:GLU64 2.5 30.3 1.0 OE1 D:GLU64 2.6 28.4 1.0 CD C:GLU104 2.7 29.1 1.0 O B:HOH2047 2.7 33.6 1.0 CD D:GLU64 2.9 28.7 1.0 OE1 C:GLU104 3.0 28.7 1.0 C7 B:NAG1176 3.2 35.6 1.0 CG B:ASN79 3.4 21.9 1.0 CG C:GLU104 3.9 29.2 1.0 ND2 B:ASN79 3.9 22.2 1.0 C8 B:NAG1176 4.1 35.9 1.0 N2 B:NAG1176 4.1 35.9 1.0 NH2 C:ARG256 4.1 44.8 1.0 O B:HOH2046 4.2 18.9 1.0 C2 B:NAG1176 4.3 36.3 1.0 CG D:GLU64 4.3 28.1 1.0 ND2 B:ASN82 4.4 34.3 1.0 O B:HOH2048 4.6 22.9 1.0 CB B:ASN79 4.7 21.5 1.0 NE2 B:HIS75 4.8 25.5 1.0 C1 B:NAG1176 4.8 32.9 1.0 CB C:GLU104 4.9 28.4 1.0 O B:HOH2049 4.9 15.0 1.0 CA B:ASN79 4.9 21.2 1.0 CZ C:ARG256 5.0 45.4 1.0

Nickel binding site 3 out of 3 in the Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Haemagglutinin of H10N8 Influenza Virus Isolated From Humans in Complex with Human Receptor Analogue 6'Sln within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1179 b:39.5 occ:1.00 O7 D:NAG1177 2.0 36.1 1.0 OE2 E:GLU104 2.2 26.9 1.0 OD1 D:ASN79 2.4 23.1 1.0 OE1 F:GLU64 2.5 25.8 1.0 OE2 F:GLU64 2.5 25.6 1.0 CD E:GLU104 2.8 26.5 1.0 CD F:GLU64 2.8 26.0 1.0 OE1 E:GLU104 3.1 26.3 1.0 C7 D:NAG1177 3.1 33.4 1.0 CG D:ASN79 3.4 22.9 1.0 ND2 D:ASN79 3.8 23.5 1.0 CG E:GLU104 3.9 26.6 1.0 C8 D:NAG1177 4.0 33.3 1.0 N2 D:NAG1177 4.1 34.1 1.0 NH1 E:ARG256 4.2 49.9 1.0 O D:HOH2042 4.2 23.8 1.0 O D:HOH2041 4.2 23.0 1.0 CG F:GLU64 4.3 26.2 1.0 C2 D:NAG1177 4.3 36.2 1.0 O D:HOH2018 4.4 34.1 1.0 ND2 D:ASN82 4.5 33.8 1.0 NE2 D:HIS75 4.7 24.9 1.0 CB D:ASN79 4.7 22.4 1.0 NH2 E:ARG256 4.8 51.5 1.0 C1 D:NAG1177 4.9 32.7 1.0 CB E:GLU104 5.0 26.1 1.0 CE1 D:HIS75 5.0 24.9 1.0 CZ E:ARG256 5.0 51.0 1.0

S.G.Vachieri, X.Xiong, P.J.Collins, P.A.Walker, S.R.Martin, L.F.Haire, Y.Zhang, J.W.Mccauley, S.J.Gamblin, J.J.Skehel. Receptor Binding By H10 Influenza Viruses. Nature V. 511 475 2014.
ISSN: ISSN 0028-0836
PubMed: 24870229
DOI: 10.1038/NATURE13443