Magnesium in PDB 6ntf: Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin

The structure of Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin, PDB code: 6ntf was solved by J.Huang, Y.Bar-Peled, J.J.Mousa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.08 / 2.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	101.518, 101.518, 450.084, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 27.5

The binding sites of Magnesium atom in the Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin (pdb code 6ntf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin, PDB code: 6ntf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1012 b:87.1 occ:1.00 O A:HIS8 2.7 76.2 1.0 OG A:SER320 2.9 75.9 1.0 O A:ARG318 3.0 78.6 1.0 N A:SER320 3.2 89.1 1.0 CB A:ALA9 3.3 75.2 1.0 CE1 A:TYR7 3.3 74.2 1.0 CD1 A:TYR7 3.5 75.4 1.0 CA A:ALA9 3.5 80.4 1.0 CD1 A:LEU317 3.5 71.0 1.0 CA A:ASN319 3.5 75.6 1.0 C A:HIS8 3.7 78.2 1.0 OD1 A:ASN319 3.9 86.0 1.0 C A:ASN319 3.9 82.4 1.0 C A:ARG318 3.9 73.5 1.0 N A:ALA9 4.0 78.6 1.0 CB A:SER320 4.0 84.3 1.0 CG2 A:THR27 4.1 75.4 1.0 CA A:GLY343 4.1 84.8 1.0 N A:ASN319 4.2 72.5 1.0 CA A:SER320 4.2 94.4 1.0 N A:GLY343 4.5 83.3 1.0 CZ A:TYR7 4.6 78.6 1.0 CB A:ASN319 4.6 75.5 1.0 CG A:ASN319 4.7 78.6 1.0 O A:LEU317 4.8 68.2 1.0 CG A:TYR7 4.9 75.9 1.0 CG A:LEU317 4.9 71.1 1.0 C A:ALA9 4.9 83.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1013 b:82.3 occ:1.00 N A:TYR7 2.7 77.7 1.0 O A:GLY342 2.8 74.9 1.0 CA A:GLY6 2.9 72.2 1.0 C A:GLY6 3.3 75.3 1.0 CD2 A:TYR7 3.5 73.7 1.0 O A:TYR7 3.6 74.5 1.0 CA A:GLY343 3.7 84.8 1.0 CG2 A:ILE340 3.7 71.0 1.0 CE2 A:TRP344 3.7 81.1 1.0 CD2 A:TRP344 3.7 81.0 1.0 CE2 A:TYR7 3.8 76.4 1.0 CG A:TYR7 3.8 75.9 1.0 NE1 A:TRP344 3.8 82.9 1.0 CA A:TYR7 3.8 76.6 1.0 C A:GLY342 3.8 75.0 1.0 CG A:TRP344 3.9 82.7 1.0 CD1 A:TRP344 4.0 81.4 1.0 C A:GLY343 4.1 79.7 1.0 N A:TRP344 4.1 80.8 1.0 C A:TYR7 4.1 78.5 1.0 CZ2 A:TRP344 4.2 82.3 1.0 CE3 A:TRP344 4.2 77.7 1.0 N A:GLY343 4.2 83.3 1.0 CZ A:TYR7 4.2 78.6 1.0 N A:GLY6 4.3 77.5 1.0 CD1 A:TYR7 4.3 75.4 1.0 CB A:TYR7 4.4 77.5 1.0 CE1 A:TYR7 4.5 74.2 1.0 O A:ILE5 4.5 79.4 1.0 O A:GLY6 4.5 74.8 1.0 CH2 A:TRP344 4.6 79.0 1.0 CZ3 A:TRP344 4.6 73.8 1.0 CB A:TRP344 4.7 82.8 1.0 C A:ILE5 4.8 78.4 1.0 O A:GLY343 4.9 78.1 1.0 CA A:TRP344 4.9 83.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1014 b:96.0 occ:1.00 N A:GLY464 2.5 95.3 1.0 OH A:TYR449 2.9 87.1 1.0 O A:CYS467 2.9 89.0 1.0 N A:ASN465 3.0 86.6 1.0 N A:GLY466 3.1 83.5 1.0 CA A:GLY464 3.1 93.1 1.0 N A:CYS467 3.2 93.6 1.0 C A:GLY464 3.2 91.2 1.0 N A:LEU463 3.4 93.4 1.0 C A:LEU463 3.6 93.5 1.0 CA A:GLY466 3.7 81.9 1.0 C A:GLY466 3.7 86.2 1.0 CE1 A:TYR449 3.7 86.1 1.0 CZ A:TYR449 3.7 84.1 1.0 C A:CYS467 3.8 85.7 1.0 CA A:LEU463 3.9 94.0 1.0 C A:ASN465 3.9 83.1 1.0 CA A:ASN465 4.1 86.9 1.0 CA A:CYS467 4.1 89.4 1.0 CG A:GLU462 4.1 94.7 1.0 O A:GLY464 4.1 97.6 1.0 CB A:LEU463 4.1 92.6 1.0 C A:GLU462 4.1 95.8 1.0 OD1 A:ASN465 4.2 86.1 1.0 O A:GLY466 4.6 84.0 1.0 CA A:GLU462 4.7 94.2 1.0 O A:LEU463 4.7 92.4 1.0 O A:GLU462 4.8 0.2 1.0 CB A:GLU462 5.0 92.4 1.0 CD1 A:TYR449 5.0 82.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Computationally Optimized H5 Influenza Hemagglutinin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1015 b:94.7 occ:1.00 O A:LEU52 2.5 97.3 1.0 O A:ARG53 2.7 93.3 1.0 N A:LYS82 2.7 81.9 1.0 O A:CYS55 2.9 95.3 1.0 CB A:LYS82 3.2 86.8 1.0 C A:ARG53 3.5 94.9 1.0 CA A:LYS82 3.5 85.0 1.0 CB A:PRO85 3.6 93.7 1.0 C A:GLU81 3.6 86.1 1.0 CA A:GLU81 3.7 81.9 1.0 CG A:LYS82 3.7 87.7 1.0 C A:LEU52 3.8 94.2 1.0 C A:CYS55 4.0 83.1 1.0 C A:ASP54 4.0 88.3 1.0 CD A:LYS82 4.1 87.0 1.0 N A:ASP54 4.1 90.4 1.0 CG A:GLU81 4.1 92.5 1.0 CA A:ASP54 4.1 86.6 1.0 N A:CYS55 4.1 85.9 1.0 CG A:PRO85 4.3 93.7 1.0 CA A:ARG53 4.3 93.8 1.0 O A:VAL80 4.4 82.6 1.0 O A:ASP54 4.5 90.4 1.0 CB A:GLU81 4.5 82.2 1.0 N A:ARG53 4.6 92.6 1.0 CB A:LEU52 4.6 80.9 1.0 C A:LYS82 4.6 90.2 1.0 CA A:PRO85 4.7 91.5 1.0 CA A:CYS55 4.7 81.9 1.0 O A:GLU81 4.8 89.3 1.0 CA A:LEU52 4.8 90.7 1.0 O A:LYS82 4.9 87.6 1.0 N A:GLU81 4.9 86.0 1.0 N A:SER56 5.0 81.5 1.0

Y.Bar-Peled, J.Huang, I.A.Nunez, S.R.Pierce, J.W.Ecker, T.M.Ross, J.J.Mousa. Structural and Antigenic Characterization of A Computationally-Optimized H5 Hemagglutinin Influenza Vaccine. Vaccine V. 37 6022 2019.
ISSN: ESSN 1873-2518
PubMed: 31481254
DOI: 10.1016/J.VACCINE.2019.08.062