Calcium in PDB 6tjy: Crystal Structure of Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus

The structure of Crystal Structure of Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus, PDB code: 6tjy 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)	35.04 / 2.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.421, 212.932, 156.901, 90.00, 101.51, 90.00
R / Rfree (%)	21.6 / 25.7

The binding sites of Calcium atom in the Crystal Structure of Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus (pdb code 6tjy). 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 Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus, PDB code: 6tjy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus


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 Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:57.1 occ:1.00 O7 O:NAG1 2.3 57.8 1.0 OD1 H:ASN79 2.5 52.7 1.0 OE1 B:GLU64 2.6 64.0 1.0 O H:HOH332 2.7 33.3 1.0 OE2 A:GLU104 2.7 63.6 1.0 OE1 A:GLU104 2.9 59.8 1.0 CD A:GLU104 3.0 59.0 1.0 OE2 B:GLU64 3.3 66.1 1.0 CD B:GLU64 3.3 62.2 1.0 C7 O:NAG1 3.4 58.7 1.0 CG H:ASN79 3.6 53.1 1.0 NH2 A:ARG256 4.0 69.0 1.0 ND2 H:ASN79 4.1 54.5 1.0 CG A:GLU104 4.1 56.5 1.0 C2 O:NAG1 4.1 63.1 1.0 N2 O:NAG1 4.1 61.5 1.0 ND2 H:ASN82 4.2 59.7 1.0 O H:HOH310 4.3 37.7 1.0 C8 O:NAG1 4.4 58.3 1.0 O H:HOH340 4.6 31.0 1.0 CG B:GLU64 4.7 59.4 1.0 C1 O:NAG1 4.7 62.7 1.0 NH1 A:ARG256 4.8 70.2 1.0 CB H:ASN79 4.9 52.0 1.0 CZ A:ARG256 4.9 69.9 1.0 CE1 H:HIS75 5.0 63.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus


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 Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:64.9 occ:1.00 OE2 K:GLU104 2.3 58.9 1.0 O7 M:NAG1 2.3 63.7 1.0 OD1 D:ASN79 2.4 45.4 1.0 OE1 L:GLU64 2.7 57.9 1.0 O K:HOH508 2.7 53.4 1.0 CD K:GLU104 3.2 59.1 1.0 C7 M:NAG1 3.3 61.8 1.0 CD L:GLU64 3.4 59.5 1.0 OE1 K:GLU104 3.5 61.9 1.0 OE2 L:GLU64 3.5 63.8 1.0 CG D:ASN79 3.6 45.5 1.0 O D:HOH327 3.7 38.1 1.0 ND2 D:ASN82 3.8 58.9 1.0 N2 M:NAG1 4.0 62.1 1.0 C2 M:NAG1 4.0 64.0 1.0 C8 M:NAG1 4.3 61.8 1.0 ND2 D:ASN79 4.3 45.0 1.0 NH1 K:ARG256 4.5 74.8 1.0 CG K:GLU104 4.5 55.7 1.0 CB D:ASN79 4.6 46.3 1.0 C1 M:NAG1 4.6 63.1 1.0 CA D:ASN79 4.6 46.8 1.0 CB D:ASN82 4.7 51.8 1.0 CG D:ASN82 4.8 53.8 1.0 CG L:GLU64 4.8 56.3 1.0 NH2 K:ARG256 4.8 75.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus


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 Haemagglutinin From (A/Seal/Germany/1/2014) Seal H10N7 Influenza Virus within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:0.1 occ:1.00 O7 P:NAG1 2.3 94.4 1.0 OE1 F:GLU64 2.4 69.9 1.0 OE2 E:GLU104 2.5 88.0 1.0 OD1 L:ASN79 2.6 58.5 1.0 C7 P:NAG1 3.4 91.3 1.0 CD F:GLU64 3.5 70.4 1.0 CG L:ASN79 3.7 56.8 1.0 CD E:GLU104 3.7 84.4 1.0 O L:HOH325 3.8 50.1 1.0 NH2 E:ARG256 4.0 88.4 1.0 OE2 F:GLU64 4.1 71.2 1.0 C8 P:NAG1 4.2 91.3 1.0 CG E:GLU104 4.3 82.9 1.0 N2 P:NAG1 4.4 91.2 1.0 CB L:ASN79 4.5 55.9 1.0 ND2 L:ASN82 4.5 73.7 1.0 ND2 L:ASN79 4.6 59.2 1.0 OE1 E:GLU104 4.6 83.1 1.0 CA L:ASN79 4.6 53.6 1.0 CB F:GLU64 4.6 65.9 1.0 CG F:GLU64 4.7 68.3 1.0 C2 P:NAG1 4.7 90.4 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