Magnesium in PDB 7jyv: Crystal Structure of Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope

The structure of Crystal Structure of Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope, PDB code: 7jyv was solved by S.Gras, A.T.Nguyen, C.Szeto, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.92 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.952, 75.775, 89.919, 90, 90, 90
R / Rfree (%)	18.7 / 20.6

The binding sites of Magnesium atom in the Crystal Structure of Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope (pdb code 7jyv). 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 Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope, PDB code: 7jyv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope


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 Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.8 occ:1.00 O A:HOH595 2.8 34.8 1.0 OG1 A:THR178 3.0 27.6 1.0 CG2 A:THR178 3.4 33.0 1.0 CA A:GLY175 3.7 20.5 1.0 N A:THR178 3.7 32.3 1.0 O A:GLY175 3.7 29.0 1.0 CB A:THR178 3.7 31.2 1.0 CD1 A:TRP51 3.7 21.8 1.0 C A:GLY175 3.8 27.4 1.0 CB A:GLU177 4.0 37.1 1.0 N A:GLU177 4.0 29.5 1.0 CB A:TRP51 4.1 23.9 1.0 CG A:TRP51 4.2 23.0 1.0 C A:GLU177 4.3 41.7 1.0 CA A:GLU177 4.3 34.5 1.0 CA A:THR178 4.3 30.3 1.0 O A:ASN174 4.4 23.9 1.0 N A:LYS176 4.6 25.0 1.0 CG A:GLU177 4.7 48.6 1.0 NE1 A:TRP51 4.8 20.9 1.0 O A:HOH430 4.9 27.0 1.0 N A:GLY175 4.9 19.5 1.0 C A:LYS176 4.9 37.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope


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 Hla A*2402 in Complex with Yfspirvtf, An 9-Mer Influenza Epitope within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:28.9 occ:1.00 O A:HOH419 2.8 49.0 1.0 O A:HOH708 2.8 39.2 1.0 N A:ALA135 3.0 19.8 1.0 NZ A:LYS144 3.0 35.9 1.0 O A:HOH557 3.4 50.0 1.0 NE2 A:GLN141 3.6 27.4 0.5 O A:ALA135 3.6 30.3 1.0 CA A:THR134 3.7 16.5 1.0 C A:THR134 3.8 16.7 1.0 CA A:ALA135 3.9 19.7 1.0 O A:TRP133 3.9 21.0 1.0 CB A:ALA135 3.9 23.6 1.0 CE A:LYS144 4.2 23.7 1.0 C A:ALA135 4.2 31.3 1.0 CD A:LYS144 4.2 17.9 1.0 O A:HOH596 4.4 42.9 1.0 CD A:GLN141 4.4 24.6 0.5 OE1 A:GLN141 4.4 26.9 0.5 CG2 A:THR134 4.4 20.3 1.0 CB A:THR134 4.7 19.1 1.0 C A:TRP133 4.7 21.4 1.0 N A:THR134 4.7 18.3 1.0 O A:HOH582 4.8 48.2 1.0

A.T.Nguyen, C.Szeto, J.Rossjohn, S.Gras. Crystal Structure of Hla A*2402 in Complex with Iyfspirvtf, An 10-Mer Influenza B Epitope Nat Commun 2021.
ISSN: ESSN 2041-1723