Magnesium in PDB 7zak: Crystal Structure of Hla-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide

The structure of Crystal Structure of Hla-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide, PDB code: 7zak was solved by J.Racle, P.Guillaume, A.Larabi, K.Lau, F.Pojer, D.Gfeller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.11 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54, 82.682, 105.977, 90, 90, 90
R / Rfree (%)	20.5 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of Hla-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide (pdb code 7zak). 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-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide, PDB code: 7zak:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hla-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide


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-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:28.1 occ:1.00 O A:HOH486 2.5 51.5 1.0 O A:HOH490 3.2 39.7 1.0 N A:PHE54 3.3 24.1 1.0 NE1 A:TRP43 3.3 26.7 1.0 CA A:SER53 3.5 26.2 1.0 O A:PHE54 3.7 25.9 1.0 CB A:SER53 3.7 27.4 1.0 O A:HOH415 3.8 43.4 1.0 CB A:THR41 3.8 25.4 1.0 C A:SER53 3.9 20.4 1.0 CE2 A:TRP43 4.1 23.6 1.0 CG2 A:THR41 4.1 20.9 1.0 CZ2 A:TRP43 4.2 23.6 1.0 OG1 A:THR41 4.2 27.7 1.0 C A:PHE54 4.3 26.4 1.0 O A:HOH431 4.4 39.8 1.0 CD1 A:TRP43 4.4 27.5 1.0 CA A:PHE54 4.4 24.1 1.0 O A:PHE52 4.5 24.1 1.0 N A:SER53 4.7 23.5 1.0 O A:THR41 4.9 31.0 1.0 CB A:PHE54 4.9 23.6 1.0 O A:HOH464 4.9 36.8 1.0 CA A:THR41 5.0 23.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hla-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide


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-Dp (DPA1*02:01-DPB1*01:01) in Complex with A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg308 b:48.8 occ:1.00 N B:SER142 2.6 30.3 1.0 O B:HOH424 3.0 42.9 1.0 CA B:VAL141 3.1 29.8 1.0 C B:VAL141 3.3 41.7 1.0 O B:SER142 3.4 37.8 1.0 CA B:SER142 3.6 30.8 1.0 CG1 B:VAL141 3.7 38.8 1.0 O B:VAL140 3.8 27.1 1.0 C B:SER142 4.0 45.8 1.0 CB B:SER142 4.0 37.0 1.0 CB B:VAL141 4.1 36.6 1.0 N B:VAL141 4.1 27.3 1.0 C B:VAL140 4.3 25.1 1.0 O B:VAL141 4.5 34.7 1.0

J.Racle, P.Guillaume, J.Schmidt, J.Michaux, A.Larabi, K.Lau, G.Coukos, F.Pojer, M.Bassani-Sternberg, A.Harari, D.Gfeller. Machine Learning Predictions of Mhc-II Specificities Reveal Alternative Binding Modes of Class II Epitopes To Be Published.