Calcium in PDB 6tvd: Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln

The structure of Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln, PDB code: 6tvd was solved by J.Zhang, X.Xiong, A.Purkiss, P.Walker, S.Gamblin, J.J.Skehel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.55 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.741, 214.956, 157.781, 90.00, 100.60, 90.00
R / Rfree (%)	24.3 / 31.3

The binding sites of Calcium atom in the Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln (pdb code 6tvd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln, PDB code: 6tvd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:76.8 occ:1.00 O7 S:NAG1 2.3 94.7 1.0 OE1 B:GLU64 2.4 89.7 1.0 OE1 A:GLU104 2.4 96.8 1.0 OD1 H:ASN79 2.8 72.6 1.0 CD A:GLU104 3.1 93.4 1.0 NH2 A:ARG256 3.4 0.9 1.0 C7 S:NAG1 3.5 93.4 1.0 CD B:GLU64 3.5 96.6 1.0 OE2 A:GLU104 3.7 92.2 1.0 CG H:ASN79 3.8 79.0 1.0 NH1 A:ARG256 3.8 95.8 1.0 CG A:GLU104 4.0 89.9 1.0 OE2 B:GLU64 4.1 0.5 1.0 CZ A:ARG256 4.1 0.5 1.0 ND2 H:ASN79 4.3 82.0 1.0 C8 S:NAG1 4.4 86.6 1.0 N2 S:NAG1 4.4 97.6 1.0 C2 S:NAG1 4.5 89.1 1.0 CG B:GLU64 4.7 83.5 1.0 ND2 H:ASN82 4.8 73.6 1.0 CB A:GLU104 5.0 76.3 1.0 CB B:GLU64 5.0 70.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca203 b:0.6 occ:1.00 OE2 H:GLU64 2.2 89.8 1.0 O7 U:NAG1 2.3 0.4 1.0 OD1 J:ASN79 2.9 97.5 1.0 OE1 G:GLU104 3.3 0.7 1.0 CD H:GLU64 3.3 96.5 1.0 CD G:GLU104 3.5 0.4 1.0 C7 U:NAG1 3.5 0.1 1.0 OE1 H:GLU64 3.7 99.6 1.0 OE2 G:GLU104 3.9 0.7 1.0 CG J:ASN79 4.0 1.0 1.0 CG G:GLU104 4.1 0.4 1.0 C2 U:NAG1 4.3 0.9 1.0 N2 U:NAG1 4.3 0.7 1.0 ND2 J:ASN82 4.3 0.0 1.0 C8 U:NAG1 4.6 0.6 1.0 CG H:GLU64 4.6 95.2 1.0 ND2 J:ASN79 4.7 0.1 1.0 C1 U:NAG1 4.9 0.8 1.0 NH2 G:ARG256 4.9 0.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Haemagglutinin From A H10N7 Seal Influenza Virus Isolated in Germany in Complex with Avian Receptor Analogue, 3'-Sln within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca405 b:77.7 occ:1.00 O7 O:NAG1 2.3 0.1 1.0 OE2 K:GLU104 2.6 0.2 1.0 OE1 L:GLU64 2.7 0.0 1.0 OD1 D:ASN79 2.7 68.4 1.0 CD K:GLU104 3.0 98.8 1.0 OE1 K:GLU104 3.2 93.0 1.0 OE2 L:GLU64 3.2 0.0 1.0 CD L:GLU64 3.3 0.4 1.0 C7 O:NAG1 3.4 0.2 1.0 NH2 K:ARG256 3.6 0.9 1.0 NH1 K:ARG256 3.7 0.0 1.0 CG D:ASN79 3.7 74.1 1.0 CG K:GLU104 4.0 93.7 1.0 ND2 D:ASN79 4.0 77.8 1.0 CZ K:ARG256 4.1 1.0 1.0 N2 O:NAG1 4.2 0.7 1.0 C8 O:NAG1 4.2 99.4 1.0 C2 O:NAG1 4.3 96.8 1.0 ND2 D:ASN82 4.6 76.1 1.0 NE2 D:HIS75 4.6 94.7 1.0 CG L:GLU64 4.7 93.5 1.0 CB K:GLU104 4.9 84.1 1.0

S.Herfst, J.Zhang, M.Richard, R.Mcbride, P.Lexmond, T.M.Bestebroer, M.I.J.Spronken, D.De Meulder, J.M.Van Den Brand, M.E.Rosu, S.R.Martin, S.J.Gamblin, X.Xiong, W.Peng, R.Bodewes, E.Van Der Vries, A.D.M.E.Osterhaus, J.C.Paulson, J.J.Skehel, R.A.M.Fouchier. Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus Between Mammals. Cell Host Microbe V. 28 602 2020.
ISSN: ESSN 1934-6069
PubMed: 33031770
DOI: 10.1016/J.CHOM.2020.08.011