Zinc in PDB 7wt4: Crystal Structure of Hla-A*2402 Complexed with 8-Mer Influenza PB1 Peptide

The structure of Crystal Structure of Hla-A*2402 Complexed with 8-Mer Influenza PB1 Peptide, PDB code: 7wt4 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)	47.71 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.122, 46.434, 141.529, 90, 103.97, 90
R / Rfree (%)	20 / 23.2

The binding sites of Zinc atom in the Crystal Structure of Hla-A*2402 Complexed with 8-Mer Influenza PB1 Peptide (pdb code 7wt4). 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 8-Mer Influenza PB1 Peptide, PDB code: 7wt4:
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 8-Mer Influenza PB1 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*2402 Complexed with 8-Mer Influenza PB1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn324 b:19.4 occ:1.00 N A:ALA0 2.0 17.0 1.0 NE2 A:HIS3 2.1 23.1 1.0 OE1 A:GLN180 2.1 17.0 1.0 O A:ALA0 2.2 19.6 1.0 CA A:ALA0 2.9 24.7 1.0 C A:ALA0 2.9 20.4 1.0 CE1 A:HIS3 3.1 22.1 1.0 CD2 A:HIS3 3.1 18.6 1.0 CD A:GLN180 3.1 16.3 1.0 NE2 A:GLN180 3.4 17.7 1.0 CB A:ALA0 3.7 17.6 1.0 ND1 A:HIS3 4.2 17.8 1.0 N A:GLY1 4.2 20.9 1.0 CG A:HIS3 4.2 16.5 1.0 CG A:GLN180 4.5 19.4 1.0 CB A:SER105 4.8 20.3 1.0 O A:HOH455 4.8 18.9 1.0 CA A:GLN180 4.9 18.1 1.0 CB A:GLN180 4.9 18.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Hla-A*2402 Complexed with 8-Mer Influenza PB1 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*2402 Complexed with 8-Mer Influenza PB1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn325 b:98.8 occ:1.00 NE2 A:HIS197 1.9 56.1 1.0 CE1 A:HIS197 2.7 55.1 1.0 CD2 A:HIS197 3.1 49.1 1.0 ND1 A:HIS197 3.9 52.4 1.0 CG A:HIS197 4.1 52.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Hla-A*2402 Complexed with 8-Mer Influenza PB1 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*2402 Complexed with 8-Mer Influenza PB1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn312 b:20.6 occ:1.00 N D:ALA0 2.0 19.5 1.0 NE2 D:HIS3 2.1 21.2 1.0 O D:ALA0 2.3 18.6 1.0 CA D:ALA0 2.8 22.1 1.0 C D:ALA0 2.9 16.5 1.0 CD2 D:HIS3 3.0 18.2 1.0 CE1 D:HIS3 3.1 23.1 1.0 CB D:ALA0 3.5 21.9 1.0 OE1 D:GLN180 4.0 40.8 1.0 ND1 D:HIS3 4.2 18.8 1.0 N D:GLY1 4.2 18.1 1.0 CG D:HIS3 4.2 20.9 1.0 CB D:SER105 4.9 26.0 1.0 CD D:GLN180 5.0 35.4 1.0 CA D:GLY1 5.0 19.5 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