Cadmium in PDB 4nnx: Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2

The structure of Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2, PDB code: 4nnx was solved by F.Mohammed, D.H.Stones, B.E.Willcox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.100, 79.800, 111.300, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.6

The binding sites of Cadmium atom in the Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2 (pdb code 4nnx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2, PDB code: 4nnx:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:16.1 occ:1.00 OE2 A:GLU154 2.3 10.5 1.0 ND1 A:HIS151 2.4 15.2 1.0 OE1 A:GLU154 2.5 13.4 1.0 CD A:GLU154 2.7 13.1 1.0 CE1 A:HIS151 3.2 14.9 1.0 CG A:HIS151 3.4 16.0 1.0 CB A:HIS151 3.8 16.8 1.0 CG A:GLU154 4.2 10.5 1.0 NE2 A:HIS151 4.2 16.9 1.0 CD2 A:HIS151 4.4 14.6 1.0 CA A:HIS151 4.8 16.1 1.0 O A:HOH507 4.9 27.1 1.0 CB A:GLU154 5.0 11.1 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:32.4 occ:1.00 OE1 A:GLU212 2.5 25.8 1.0 OD1 A:ASP30 2.5 10.4 1.0 OD2 A:ASP30 2.6 9.4 1.0 O A:HOH523 2.6 20.4 1.0 OE2 A:GLU212 2.7 27.2 1.0 O A:HOH522 2.7 26.2 1.0 CG A:ASP30 2.9 12.7 1.0 CD A:GLU212 2.9 25.4 1.0 CB A:ASP30 4.5 11.7 1.0 CG A:GLU212 4.5 17.8 1.0 N A:ALA211 4.5 9.9 1.0 CB A:ALA211 4.6 10.7 1.0 CB A:PRO210 4.6 11.8 1.0 N A:GLU212 4.7 12.1 1.0 N A:ASP30 5.0 11.3 1.0 CA A:ALA211 5.0 10.8 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:59.9 occ:1.00 NE2 A:HIS197 2.6 37.0 1.0 CD2 A:HIS197 3.0 33.7 1.0 CE1 A:HIS197 3.3 33.4 1.0 CG A:HIS197 3.8 31.3 1.0 ND1 A:HIS197 4.0 36.2 1.0 OE2 A:GLU198 5.0 38.6 1.0 CB A:HIS197 5.0 27.1 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd102 b:40.5 occ:1.00 O B:HOH241 2.3 26.4 1.0 NE2 B:HIS51 2.4 20.4 1.0 O A:HOH530 2.5 14.4 1.0 O B:HOH240 2.5 27.5 1.0 CE1 B:HIS51 3.4 20.1 1.0 CD2 B:HIS51 3.4 17.9 1.0 ND1 B:HIS51 4.5 20.6 1.0 CG B:HIS51 4.6 18.4 1.0 O B:HOH235 4.8 22.1 1.0

F.Mohammed, D.H.Stones, B.E.Willcox. Phosphorylation-Induced Conformational Changes Radically Alter the Antigenic Identity of Human Mhc Class I Phosphopeptides To Be Published.