Copper in PDB 5ib5: Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper

The structure of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper, PDB code: 5ib5 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)	43.00 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.004, 81.677, 126.474, 90.00, 96.74, 90.00
R / Rfree (%)	21.4 / 27.2

The structure of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Copper atom in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper (pdb code 5ib5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper, PDB code: 5ib5:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu301 b:63.6 occ:1.00 O A:HOH402 2.0 36.1 1.0 NE2 A:HIS3 2.0 44.4 1.0 N A:GLY1 2.0 45.9 1.0 OE1 A:GLN180 2.8 37.6 1.0 CD2 A:HIS3 3.0 36.2 1.0 O A:HOH455 3.0 48.2 1.0 CE1 A:HIS3 3.0 35.7 1.0 CA A:GLY1 3.3 50.3 1.0 O A:GLY1 3.4 53.0 1.0 C A:GLY1 3.6 53.3 1.0 CD A:GLN180 4.0 41.9 1.0 ND1 A:HIS3 4.1 30.7 1.0 CG A:HIS3 4.1 36.6 1.0 NE2 A:GLN180 4.6 32.3 1.0 N A:SER2 4.6 48.3 1.0

Copper binding site 2 out of 6 in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu302 b:78.3 occ:1.00 NE2 A:HIS191 2.0 61.3 1.0 OE2 A:GLU254 2.0 69.6 1.0 OE2 E:GLU44 2.0 53.4 1.0 CD A:GLU254 2.9 71.1 1.0 CD2 A:HIS191 2.9 57.5 1.0 CD E:GLU44 3.0 40.6 1.0 CE1 A:HIS191 3.1 54.6 1.0 OE1 A:GLU254 3.1 73.0 1.0 OE1 E:GLU44 3.3 33.1 1.0 O E:HOH213 3.9 41.1 1.0 OG A:SER251 4.0 87.4 1.0 CG A:HIS191 4.1 57.9 1.0 ND1 A:HIS191 4.1 61.5 1.0 CG A:GLU254 4.3 74.3 1.0 CB A:ALA199 4.3 72.2 1.0 CG E:GLU44 4.4 43.9 1.0 CB A:SER251 4.5 78.2 1.0 CA A:SER251 4.5 77.4 1.0

Copper binding site 3 out of 6 in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu101 b:68.7 occ:1.00 O C:HOH201 2.0 34.0 1.0 O A:HOH401 2.0 48.0 1.0 NE2 C:HIS8 2.0 14.9 1.0 OE2 A:GLU76 2.0 41.5 1.0 CE1 C:HIS8 2.9 23.4 1.0 O C:HOH205 2.9 34.5 1.0 CD2 C:HIS8 3.0 23.8 1.0 CD A:GLU76 3.2 39.1 1.0 OE1 A:GLU76 3.8 50.7 1.0 ND1 C:HIS8 4.0 18.8 1.0 CG C:HIS8 4.1 21.5 1.0 CG A:GLU76 4.3 33.2 1.0

Copper binding site 4 out of 6 in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu301 b:72.2 occ:1.00 NE2 D:HIS3 2.0 39.1 1.0 N D:GLY1 2.0 57.7 1.0 O D:HOH469 2.9 31.0 1.0 CE1 D:HIS3 3.0 31.5 1.0 CD2 D:HIS3 3.0 30.3 1.0 CA D:GLY1 3.1 49.7 1.0 OE1 D:GLN180 3.1 35.6 1.0 C D:GLY1 3.6 46.6 1.0 O D:GLY1 3.8 50.4 1.0 ND1 D:HIS3 4.0 29.4 1.0 CD D:GLN180 4.1 34.6 1.0 CG D:HIS3 4.1 33.3 1.0 O D:HOH464 4.3 29.1 1.0 O D:HOH452 4.4 30.3 1.0 NE2 D:GLN180 4.4 26.8 1.0 N D:SER2 4.4 43.5 1.0 O D:HOH446 4.6 31.6 1.0

Copper binding site 5 out of 6 in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu101 b:87.1 occ:1.00 OD1 E:ASP96 2.5 73.7 1.0 O D:HOH402 2.5 32.4 1.0 OD2 E:ASP98 2.9 68.6 1.0 OD2 E:ASP96 2.9 64.0 1.0 CG E:ASP96 3.0 69.0 1.0 CG E:ASP98 3.9 69.7 1.0 NE2 D:HIS192 4.2 56.0 1.0 CB E:ASP96 4.4 54.8 1.0 CB E:ASP98 4.4 71.0 1.0 CD2 D:HIS192 4.7 60.6 1.0 OD1 E:ASP98 4.7 74.2 1.0 CE1 D:HIS192 5.0 59.7 1.0

Copper binding site 6 out of 6 in the Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Hla-B*27:09 Complexed with the Self-Peptide Pvipr and Copper within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu101 b:57.8 occ:1.00 O F:HOH207 2.0 61.6 1.0 O F:HOH202 2.0 44.5 1.0 NE2 F:HIS8 2.0 32.6 1.0 CD2 F:HIS8 3.0 28.1 1.0 CE1 F:HIS8 3.0 32.5 1.0 OE1 D:GLU76 3.1 48.2 1.0 OE2 D:GLU76 3.2 39.8 1.0 CD D:GLU76 3.5 42.7 1.0 O F:HOH208 3.5 39.6 1.0 O D:HOH456 3.7 28.9 1.0 CG F:HIS8 4.1 27.9 1.0 ND1 F:HIS8 4.1 24.5 1.0 O D:HOH477 4.6 40.7 1.0 CG D:GLU76 4.9 31.0 1.0

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