Nickel in PDB 5ib4: Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel

The structure of Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel, PDB code: 5ib4 was solved by R.Janke, M.Ballaschk, P.Schmieder, B.Uchanska-Ziegler, A.Ziegler, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.12 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.130, 81.740, 65.120, 90.00, 107.83, 90.00
R / Rfree (%)	16.4 / 20.2

The binding sites of Nickel atom in the Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel (pdb code 5ib4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel, PDB code: 5ib4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:39.9 occ:1.00 O A:HOH440 1.9 35.9 1.0 N A:GLY1 1.9 33.6 1.0 O A:HOH523 2.1 41.9 1.0 NE2 A:HIS3 2.2 18.0 1.0 O A:GLY1 2.4 47.4 1.0 O A:HOH521 2.4 43.2 1.0 CA A:GLY1 2.6 41.4 1.0 C A:GLY1 2.7 39.6 1.0 CD2 A:HIS3 3.0 17.3 1.0 CE1 A:HIS3 3.3 24.3 1.0 O A:HOH509 3.7 52.0 1.0 N A:SER2 4.0 36.4 1.0 O A:HOH502 4.1 37.4 1.0 NE2 A:GLN180 4.2 40.2 1.0 CG A:HIS3 4.2 17.2 1.0 ND1 A:HIS3 4.3 16.6 1.0 CA A:SER2 4.7 32.9 0.4 CA A:SER2 4.8 33.1 0.6 C A:SER2 4.9 29.7 1.0 O A:SER2 4.9 30.8 1.0 CA A:PRO105 5.0 46.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Hla-B*27:05 Complexed with the Self-Peptide Pvipr and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:23.2 occ:0.37 NE2 C:HIS8 2.1 40.7 1.0 CD2 C:HIS8 3.1 30.1 1.0 OE1 A:GLU76 3.1 26.6 0.4 CE1 C:HIS8 3.1 34.3 1.0 OE2 A:GLU76 3.4 35.2 0.4 CD A:GLU76 3.5 31.3 0.4 CG C:HIS8 4.2 28.5 1.0 ND1 C:HIS8 4.2 27.4 1.0 CG A:GLU76 4.8 27.3 0.4

R.Driller, M.Ballaschk, P.Schmieder, B.Uchanska-Ziegler, A.Ziegler, B.Loll. Metal-Triggered Conformational Reorientation of A Self-Peptide Bound to A Disease-Associated Hla-B*27 Subtype. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31296658
DOI: 10.1074/JBC.RA119.008937