Zinc in PDB 7wt5: Crystal Structure of Hla-A*2450 Complexed with 8-Mer Model Peptide

The structure of Crystal Structure of Hla-A*2450 Complexed with 8-Mer Model Peptide, PDB code: 7wt5 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)	45.81 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.239, 46.46, 141.65, 90, 104.01, 90
R / Rfree (%)	18.6 / 22.8

The binding sites of Zinc atom in the Crystal Structure of Hla-A*2450 Complexed with 8-Mer Model Peptide (pdb code 7wt5). 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*2450 Complexed with 8-Mer Model Peptide, PDB code: 7wt5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Hla-A*2450 Complexed with 8-Mer Model Peptide


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*2450 Complexed with 8-Mer Model Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.1 occ:1.00 OE2 A:GLU222 2.2 21.5 1.0 OE1 A:GLU222 2.4 24.6 1.0 CD A:GLU222 2.6 20.1 1.0 O1 A:TRS302 3.9 38.1 1.0 C1 A:EDO308 4.1 30.6 1.0 CG A:GLU222 4.1 29.8 1.0 O2 A:EDO308 4.6 42.5 1.0 C2 A:EDO308 4.7 39.6 1.0 O1 A:EDO308 4.8 54.7 1.0 O A:GLY221 4.8 30.4 1.0 CB A:GLU222 4.9 27.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Hla-A*2450 Complexed with 8-Mer Model Peptide


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*2450 Complexed with 8-Mer Model Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:21.8 occ:1.00 N D:ALA0 1.9 15.5 1.0 NE2 D:HIS3 2.0 22.9 1.0 O D:HOH455 2.1 21.8 1.0 O D:ALA0 2.3 19.8 1.0 CA D:ALA0 2.8 21.4 1.0 C D:ALA0 2.9 23.2 1.0 CE1 D:HIS3 2.9 21.3 1.0 CD2 D:HIS3 3.1 21.9 1.0 CB D:ALA0 3.5 23.0 1.0 OE1 D:GLN180 4.0 47.2 1.0 ND1 D:HIS3 4.1 21.2 1.0 CG D:HIS3 4.2 20.4 1.0 N D:GLY1 4.2 18.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Hla-A*2450 Complexed with 8-Mer Model Peptide


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*2450 Complexed with 8-Mer Model Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:92.5 occ:1.00 ND1 D:HIS151 2.7 48.7 1.0 CG D:HIS151 3.2 43.1 1.0 CB D:HIS151 3.5 35.8 1.0 CE1 D:HIS151 3.5 54.9 1.0 CD2 D:HIS151 4.1 50.3 1.0 NE2 D:HIS151 4.2 58.0 1.0 CA D:HIS151 4.9 35.3 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