Zinc in PDB 7wt3: Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide

The structure of Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide, PDB code: 7wt3 was solved by M.Asa, D.Morita, M.Sugita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.08 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.069, 46.41, 142.67, 90, 104.87, 90
R / Rfree (%)	19.9 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide (pdb code 7wt3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide, PDB code: 7wt3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:44.1 occ:1.00 O2 A:EDO309 1.8 43.0 1.0 NE2 A:HIS197 2.3 37.7 1.0 O1 A:EDO309 2.3 42.9 1.0 C2 A:EDO309 2.9 50.8 1.0 CD2 A:HIS197 3.0 36.6 1.0 C1 A:EDO309 3.1 43.0 1.0 CE1 A:HIS197 3.4 49.6 1.0 CG A:HIS197 4.2 42.6 1.0 ND1 A:HIS197 4.4 44.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:23.2 occ:1.00 N A:ALA0 2.0 20.6 1.0 O A:ALA0 2.2 22.8 1.0 OE1 A:GLN180 2.2 22.5 1.0 NE2 A:HIS3 2.2 23.0 1.0 C A:ALA0 2.9 23.0 1.0 CA A:ALA0 2.9 26.6 1.0 CD2 A:HIS3 3.1 24.4 1.0 CD A:GLN180 3.1 23.7 1.0 CE1 A:HIS3 3.3 22.6 1.0 NE2 A:GLN180 3.5 24.3 1.0 CB A:ALA0 3.7 21.8 1.0 N A:GLY1 4.2 23.1 1.0 CG A:HIS3 4.3 20.6 1.0 ND1 A:HIS3 4.3 20.5 1.0 CG A:GLN180 4.6 22.2 1.0 CB A:SER105 4.8 27.1 1.0 O A:HOH448 4.8 23.2 1.0 CA A:GLN180 4.9 20.3 1.0 CB A:GLN180 4.9 20.1 1.0 CA A:GLY1 4.9 24.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hla-A*2402 Complexed with 4-Mer Lipopeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:26.4 occ:1.00 N D:ALA0 1.9 22.1 1.0 O D:HOH443 2.0 29.4 1.0 O D:ALA0 2.2 21.6 1.0 NE2 D:HIS3 2.2 28.3 1.0 CA D:ALA0 2.8 24.5 1.0 C D:ALA0 2.8 20.9 1.0 CE1 D:HIS3 3.1 29.4 1.0 CD2 D:HIS3 3.2 26.3 1.0 CB D:ALA0 3.5 29.4 1.0 OE1 D:GLN180 3.9 44.6 1.0 N D:GLY1 4.1 26.2 1.0 ND1 D:HIS3 4.2 27.6 1.0 CG D:HIS3 4.3 26.1 1.0 CA D:GLY1 4.9 31.3 1.0

M.Asa, D.Morita, J.Kuroha, T.Mizutani, N.Mori, B.Mikami, M.Sugita. Crystal Structures of N-Myristoylated Lipopeptide-Bound Hla Class I Complexes Indicate Reorganization of B-Pocket Architecture Upon Ligand Binding. J.Biol.Chem. V. 298 02100 2022.
ISSN: ESSN 1083-351X
PubMed: 35667438
DOI: 10.1016/J.JBC.2022.102100