Nickel in PDB 3vcl: Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl

The structure of Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl, PDB code: 3vcl was solved by J.Petersen, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.28 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.786, 65.786, 237.107, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.7

The binding sites of Nickel atom in the Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl (pdb code 3vcl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl, PDB code: 3vcl:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl


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-B7 with the Hcmv PP65 Peptide Rpherngftvl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:34.5 occ:1.00 OE1 A:GLU180 1.9 27.9 1.0 NE2 A:HIS3 2.1 31.2 1.0 O A:HOH598 2.3 36.5 1.0 O A:HOH548 2.3 33.2 1.0 N A:GLY1 2.3 38.7 1.0 O A:HOH547 2.3 35.2 1.0 CD A:GLU180 3.0 40.0 1.0 CD2 A:HIS3 3.1 35.6 1.0 CE1 A:HIS3 3.1 39.5 1.0 CA A:GLY1 3.2 39.3 1.0 OE2 A:GLU180 3.4 38.5 1.0 C A:GLY1 3.9 43.2 1.0 O A:GLY1 3.9 44.3 1.0 ND1 A:HIS3 4.2 33.6 1.0 O A:HOH662 4.2 58.2 1.0 CG A:HIS3 4.2 31.9 1.0 CG A:GLU180 4.4 35.4 1.0 O A:HOH557 4.5 46.0 1.0 O A:HOH459 4.7 45.2 1.0 CB A:GLU180 4.8 33.9 1.0 N A:SER2 4.9 43.3 1.0 O A:HOH673 5.0 64.5 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl


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-B7 with the Hcmv PP65 Peptide Rpherngftvl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:86.9 occ:0.68 O A:HOH696 2.4 27.9 1.0 O A:GLU275 2.6 33.5 1.0 NE2 A:HIS188 2.9 25.6 0.5 O A:VAL189 3.1 26.8 1.0 CE1 A:HIS188 3.3 30.7 0.5 C A:GLU275 3.7 34.5 1.0 CD1 A:TRP274 3.7 27.3 1.0 O A:HOH564 3.8 45.0 1.0 CD2 A:HIS188 4.0 29.9 0.5 N A:GLU275 4.0 23.6 1.0 NE1 A:TRP274 4.0 25.7 1.0 O A:HOH563 4.2 44.7 1.0 ND1 A:HIS188 4.4 33.1 0.5 C A:VAL189 4.4 24.9 1.0 CA A:GLU275 4.4 26.2 1.0 O A:HOH421 4.5 32.2 1.0 OXT A:GLU275 4.5 31.8 1.0 CG A:HIS188 4.8 28.3 0.5 C A:TRP274 4.9 23.7 1.0 CG A:TRP274 5.0 26.0 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:45.4 occ:1.00 O B:HOH300 2.2 33.2 1.0 O B:HOH348 2.5 49.3 1.0 O B:HOH349 2.7 52.8 1.0 O B:HOH286 3.0 41.5 1.0 N B:ILE1 4.1 39.7 1.0 NE2 B:GLN2 4.3 36.9 1.0 CG B:GLN2 4.5 31.9 1.0 CD B:GLN2 4.7 31.8 1.0 C B:ILE1 4.8 34.1 1.0 CA B:ILE1 4.9 29.2 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Hla-B7 with the Hcmv PP65 Peptide Rpherngftvl within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni102 b:77.3 occ:1.00 NE2 B:HIS51 2.5 42.4 1.0 O B:HOH307 2.5 50.6 1.0 O B:HOH342 2.8 70.3 1.0 CD2 B:HIS51 3.3 42.3 1.0 CE1 B:HIS51 3.5 45.2 1.0 CG B:HIS51 4.5 39.0 1.0 ND1 B:HIS51 4.6 37.3 1.0 O B:HOH308 4.9 52.5 1.0

R.M.Brennan, J.Petersen, M.A.Neller, J.J.Miles, J.M.Burrows, C.Smith, J.Mccluskey, R.Khanna, J.Rossjohn, S.R.Burrows. The Impact of A Large and Frequent Deletion in the Human Tcr Beta Locus on Antiviral Immunity J.Immunol. V. 188 2742 2012.
ISSN: ISSN 0022-1767
PubMed: 22323539
DOI: 10.4049/JIMMUNOL.1102675