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

Protein crystallography data

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

Calcium Binding Sites:

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 6tvd

Go back to Calcium Binding Sites List in 6tvd
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 6tvd

Go back to Calcium Binding Sites List in 6tvd
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 6tvd

Go back to Calcium Binding Sites List in 6tvd
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

Reference:

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
Page generated: Sat Dec 12 07:45:36 2020

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