Magnesium in PDB 6opd: Crystal Structure of Ilnamivki Peptide Bound to Hla-A2

The structure of Crystal Structure of Ilnamivki Peptide Bound to Hla-A2, PDB code: 6opd was solved by L.M.Davancaze, A.Arbuiso, B.M.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.57 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.561, 74.641, 122.849, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of Ilnamivki Peptide Bound to Hla-A2 (pdb code 6opd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ilnamivki Peptide Bound to Hla-A2, PDB code: 6opd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ilnamivki Peptide Bound to Hla-A2


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 Ilnamivki Peptide Bound to Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:6.1 occ:1.00 ND1 A:HIS151 1.9 26.6 1.0 OE1 A:GLU154 2.0 34.1 1.0 OE2 A:GLU154 2.5 35.7 1.0 CD A:GLU154 2.5 18.8 1.0 CE1 A:HIS151 2.8 23.2 1.0 CG A:HIS151 3.0 25.2 1.0 CB A:HIS151 3.5 19.3 1.0 NE2 A:HIS151 4.0 24.2 1.0 CG A:GLU154 4.1 22.0 1.0 CD2 A:HIS151 4.1 25.4 1.0 O A:HOH523 4.5 35.1 1.0 CB A:GLU154 4.9 19.9 1.0 CA A:HIS151 5.0 15.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ilnamivki Peptide Bound to Hla-A2


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 Ilnamivki Peptide Bound to Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:30.0 occ:1.00 O B:HOH322 3.3 45.8 1.0 CG B:LYS59 3.3 44.1 1.0 N B:LYS59 3.6 19.9 1.0 O A:HOH602 3.7 49.3 1.0 CD B:LYS59 3.8 55.0 1.0 CE B:LYS59 4.0 25.9 1.0 CB B:LYS59 4.0 25.7 1.0 CA B:SER58 4.2 18.6 1.0 CB B:SER58 4.2 19.9 1.0 C B:SER58 4.3 21.7 1.0 CA B:LYS59 4.4 25.6 1.0 OG B:SER58 4.6 23.1 1.0 O B:HOH395 4.7 28.1 1.0 O A:HOH623 4.7 48.1 1.0 O A:HOH454 4.8 48.8 1.0

T.P.Riley, G.L.J.Keller, A.R.Smith, L.M.Davancaze, A.G.Arbuiso, J.R.Devlin, B.M.Baker. Structure Based Prediction of Neoantigen Immunogenicity. Front Immunol V. 10 2047 2019.
ISSN: ESSN 1664-3224
PubMed: 31555277
DOI: 10.3389/FIMMU.2019.02047