Calcium in PDB 6tvr: Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany

The structure of Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany, PDB code: 6tvr 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)	72.33 / 2.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.354, 214.102, 157.165, 90.00, 102.06, 90.00
R / Rfree (%)	24.1 / 26.4

The binding sites of Calcium atom in the Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany (pdb code 6tvr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany, PDB code: 6tvr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany


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 Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:53.5 occ:1.00 O7 H:NAG201 2.3 58.5 1.0 OE2 B:GLU64 2.4 58.2 1.0 OE2 A:GLU106 2.4 54.0 1.0 O H:HOH327 2.4 36.5 1.0 OD1 H:ASN79 2.6 45.0 1.0 CD A:GLU106 3.0 59.9 1.0 CD B:GLU64 3.1 59.3 1.0 OE1 A:GLU106 3.1 61.1 1.0 OE1 B:GLU64 3.1 60.0 1.0 NH2 A:ARG258 3.4 84.9 1.0 C7 H:NAG201 3.4 60.0 1.0 CG H:ASN79 3.8 46.6 1.0 N2 H:NAG201 4.2 60.6 1.0 C2 H:NAG201 4.3 59.7 1.0 O H:HOH311 4.3 42.9 1.0 CZ A:ARG258 4.3 80.2 1.0 NH1 A:ARG258 4.3 79.9 1.0 ND2 H:ASN79 4.4 48.4 1.0 CG A:GLU106 4.4 60.9 1.0 C8 H:NAG201 4.4 58.4 1.0 ND2 H:ASN82 4.5 58.1 1.0 CG B:GLU64 4.5 58.5 1.0 CB A:GLU106 4.9 58.3 1.0 NE2 H:HIS75 5.0 54.3 1.0 C1 H:NAG201 5.0 58.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany


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 Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:0.1 occ:1.00 O7 F:NAG201 2.3 1.0 1.0 O F:HOH303 2.4 71.2 1.0 OD1 F:ASN79 2.5 70.7 1.0 OE1 D:GLU64 2.5 73.8 1.0 OE2 C:GLU106 3.3 0.1 1.0 C7 F:NAG201 3.4 0.4 1.0 CD D:GLU64 3.5 73.0 1.0 O D:HOH528 3.6 47.9 1.0 CG F:ASN79 3.7 69.2 1.0 O F:HOH307 3.8 53.1 1.0 OE2 D:GLU64 3.9 75.5 1.0 CD C:GLU106 4.0 99.9 1.0 NH1 C:ARG258 4.1 1.0 1.0 OE1 C:GLU106 4.1 99.3 1.0 N2 F:NAG201 4.2 98.6 1.0 C2 F:NAG201 4.2 98.1 1.0 ND2 F:ASN82 4.2 84.9 1.0 O D:HOH506 4.3 46.4 1.0 C8 F:NAG201 4.4 99.4 1.0 ND2 F:ASN79 4.4 76.4 1.0 CB F:ASN79 4.8 66.6 1.0 CG D:GLU64 4.8 70.1 1.0 C1 F:NAG201 4.8 94.1 1.0 NH2 C:ARG258 4.9 0.6 1.0 CZ C:ARG258 4.9 0.8 1.0 CA F:ASN79 4.9 64.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany


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 Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca404 b:55.1 occ:1.00 O7 M:NAG1 2.3 63.6 1.0 OE2 K:GLU106 2.3 64.3 1.0 OE2 L:GLU64 2.5 59.5 1.0 O D:HOH523 2.5 41.1 1.0 OD1 D:ASN79 2.6 43.6 1.0 CD K:GLU106 3.0 67.2 1.0 OE1 L:GLU64 3.0 69.5 1.0 OE1 K:GLU106 3.1 71.5 1.0 CD L:GLU64 3.1 62.9 1.0 NH2 K:ARG258 3.3 86.9 1.0 C7 M:NAG1 3.4 63.1 1.0 CG D:ASN79 3.7 47.6 1.0 N2 M:NAG1 4.2 63.1 1.0 C2 M:NAG1 4.2 64.3 1.0 CZ K:ARG258 4.2 83.2 1.0 NH1 K:ARG258 4.2 85.6 1.0 ND2 D:ASN79 4.3 52.4 1.0 C8 M:NAG1 4.3 62.3 1.0 CG K:GLU106 4.3 65.3 1.0 ND2 D:ASN82 4.4 57.4 1.0 O D:HOH507 4.4 39.3 1.0 CG L:GLU64 4.6 61.4 1.0 CB K:GLU106 4.9 60.2 1.0 C1 M:NAG1 4.9 63.1 1.0 CB D:ASN79 4.9 47.2 1.0 NE2 D:HIS75 5.0 65.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Haemagglutinin Mutant (GLN226LEU) From An H10N7 Seal Influenza Virus Isolated in Germany within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:0.6 occ:1.00 O7 J:NAG201 2.3 0.6 1.0 O G:HOH508 2.4 0.3 1.0 O H:HOH318 2.5 68.8 1.0 OD1 J:ASN79 2.8 73.9 1.0 OE1 H:GLU64 2.8 80.9 1.0 OE2 G:GLU105 3.0 0.2 1.0 C7 J:NAG201 3.5 98.8 1.0 CD G:GLU105 3.6 1.0 1.0 OE1 G:GLU105 3.8 0.8 1.0 CD H:GLU64 3.8 80.0 1.0 CG J:ASN79 3.9 71.2 1.0 OE2 H:GLU64 4.0 87.7 1.0 NH1 G:ARG257 4.3 0.7 1.0 N2 J:NAG201 4.3 0.3 1.0 C2 J:NAG201 4.4 0.7 1.0 ND2 J:ASN79 4.4 75.4 1.0 C8 J:NAG201 4.5 96.2 1.0 NH2 G:ARG257 4.7 0.6 1.0 CZ G:ARG257 4.7 0.8 1.0 ND2 J:ASN82 4.8 85.1 1.0 NE2 J:HIS75 4.9 95.7 1.0 CG G:GLU105 4.9 99.6 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