Zinc in PDB 6lks: Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin

The structure of Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin, PDB code: 6lks was solved by J.Seok, K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 3.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.710, 124.270, 214.530, 90.00, 102.91, 90.00
R / Rfree (%)	26.5 / 29.5

The binding sites of Zinc atom in the Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin (pdb code 6lks). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin, PDB code: 6lks:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn415 b:47.0 occ:1.00 OE1 A:GLU68 1.9 63.0 1.0 NE2 A:HIS137 2.0 42.7 1.0 OE1 K:GLU68 2.0 38.1 1.0 OE2 K:GLU68 2.1 46.4 1.0 NE2 K:HIS137 2.1 49.9 1.0 OE2 A:GLU68 2.2 43.2 1.0 CD K:GLU68 2.3 44.3 1.0 CD A:GLU68 2.3 55.3 1.0 CD2 A:HIS137 2.8 44.4 1.0 CE1 K:HIS137 3.1 51.8 1.0 CE1 A:HIS137 3.1 43.9 1.0 CD2 K:HIS137 3.2 45.7 1.0 CG A:GLU68 3.8 53.6 1.0 CG K:GLU68 3.8 45.0 1.0 CG A:HIS137 4.0 42.6 1.0 ND1 A:HIS137 4.1 40.6 1.0 ND1 K:HIS137 4.2 45.7 1.0 CG K:HIS137 4.3 42.6 1.0 CB K:GLU68 4.5 47.7 1.0 CB A:GLU68 4.7 53.5 1.0 CB K:ASN138 4.8 42.9 1.0 CB A:ASN138 4.9 54.2 1.0

Zinc binding site 2 out of 3 in the Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn414 b:40.7 occ:1.00 OE1 G:GLU68 2.0 40.9 1.0 NE2 G:HIS137 2.1 43.1 1.0 OE2 G:GLU68 2.1 34.2 1.0 CD G:GLU68 2.3 42.2 1.0 CE1 G:HIS137 3.0 46.4 1.0 CD2 G:HIS137 3.1 47.0 1.0 CG G:GLU68 3.8 43.8 1.0 ND1 G:HIS137 4.1 49.1 1.0 CG G:HIS137 4.3 48.5 1.0 CB G:GLU68 4.7 44.2 1.0 CB G:ASN138 4.8 32.2 1.0

Zinc binding site 3 out of 3 in the Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Effects of Zinc Ion on Oligomerization and pH Stability of Influenza Virus Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn411 b:43.8 occ:1.00 OE2 I:GLU68 1.9 36.9 1.0 NE2 I:HIS137 2.1 52.9 1.0 OE1 I:GLU68 2.1 33.6 1.0 CD I:GLU68 2.1 36.0 1.0 CE1 I:HIS137 3.1 54.3 1.0 CD2 I:HIS137 3.1 54.8 1.0 CG I:GLU68 3.5 40.4 1.0 ND1 I:HIS137 4.2 56.0 1.0 CG I:HIS137 4.3 56.6 1.0 CB I:GLU68 4.6 42.0 1.0

J.H.Seok, H.Kim, D.B.Lee, J.S.An, E.J.Kim, J.H.Lee, M.S.Chung, K.H.Kim. Divalent Cation-Induced Conformational Changes of Influenza Virus Hemagglutinin. Sci Rep V. 10 15457 2020.
ISSN: ESSN 2045-2322
PubMed: 32963316
DOI: 10.1038/S41598-020-72368-X