Cadmium in PDB 3fqx: Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes

The structure of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes, PDB code: 3fqx 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)	24.01 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.846, 79.684, 110.997, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.7

The structure of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Cadmium atom in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes (pdb code 3fqx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes, PDB code: 3fqx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd276 b:24.2 occ:1.00 ND1 A:HIS191 2.3 21.3 1.0 O A:HIS191 2.5 22.3 1.0 CE1 A:HIS191 3.2 25.8 1.0 C A:HIS191 3.2 21.3 1.0 CG A:HIS191 3.3 23.4 1.0 CB A:HIS191 3.7 20.1 1.0 N A:HIS192 4.0 20.8 1.0 CA A:HIS191 4.0 19.2 1.0 CA A:HIS192 4.2 23.5 1.0 NE2 A:HIS191 4.4 24.4 1.0 N A:ALA193 4.4 21.4 1.0 CD2 A:HIS191 4.4 23.4 1.0 O A:HOH328 4.5 25.3 1.0 N A:HIS191 4.6 20.5 1.0 C A:HIS192 4.8 22.9 1.0

Cadmium binding site 2 out of 5 in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd277 b:39.3 occ:0.60 NE2 A:HIS3 2.3 25.8 1.0 O A:HOH398 2.4 50.1 1.0 N A:GLY1 2.4 39.8 1.0 O A:HOH487 2.4 41.7 1.0 O A:GLY1 2.6 38.7 1.0 O A:HOH414 2.9 59.3 1.0 CE1 A:HIS3 3.2 27.1 1.0 C A:GLY1 3.2 39.0 1.0 CD2 A:HIS3 3.3 28.1 1.0 CA A:GLY1 3.3 44.1 1.0 O A:HOH413 4.0 64.3 1.0 ND1 A:HIS3 4.3 26.4 1.0 CG A:HIS3 4.4 25.2 1.0 NE1 A:TRP107 4.4 35.8 1.0 N A:SER2 4.5 38.8 1.0 O A:SER2 4.8 28.9 1.0

Cadmium binding site 3 out of 5 in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd278 b:31.8 occ:0.80 O A:HOH552 2.2 38.4 1.0 O A:HOH361 2.3 47.0 1.0 O A:HOH301 2.4 32.8 1.0 O A:HOH500 2.5 41.1 1.0 ND1 A:HIS197 2.6 53.4 1.0 CE1 A:HIS197 3.5 52.3 1.0 CG A:HIS197 3.6 46.1 1.0 CB A:HIS197 3.9 32.3 1.0 OE1 A:GLU198 4.3 38.5 1.0 OE2 A:GLU198 4.3 40.1 1.0 O A:HOH340 4.3 43.9 1.0 NE2 A:HIS197 4.6 49.6 1.0 CD2 A:HIS197 4.7 46.8 1.0 CD A:GLU198 4.7 39.6 1.0

Cadmium binding site 4 out of 5 in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd279 b:27.9 occ:0.30 O A:HOH346 2.1 29.6 1.0 O A:HOH415 2.3 55.5 1.0 OD1 A:ASP30 2.5 28.7 1.0 OD2 A:ASP30 2.5 23.3 1.0 O A:HOH416 2.7 50.2 1.0 CG A:ASP30 2.9 27.8 1.0 O A:HOH533 3.3 57.1 1.0 O A:HOH537 3.8 42.4 1.0 O A:HOH550 3.8 50.5 1.0 CB A:ASP30 4.4 22.8 1.0 N A:ALA211 4.5 22.1 1.0 CB A:PRO210 4.6 25.1 1.0 N A:GLU212 4.6 20.9 1.0 CB A:ALA211 4.6 21.5 1.0 O A:HOH518 4.8 39.5 1.0 N A:ASP30 4.8 19.9 1.0 C3 A:GOL281 4.9 51.6 1.0 CA A:ALA211 5.0 23.5 1.0

Cadmium binding site 5 out of 5 in the Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd99 b:37.7 occ:0.50 NE2 B:HIS50 2.3 29.4 1.0 O A:HOH345 2.4 37.8 1.0 O B:HOH418 2.7 61.5 1.0 CD2 B:HIS50 3.2 31.6 1.0 CE1 B:HIS50 3.4 33.0 1.0 CG B:HIS50 4.4 28.0 1.0 ND1 B:HIS50 4.5 28.6 1.0 O B:HOH147 4.5 37.9 1.0 O A:HOH564 4.7 60.2 1.0

J.Petersen, S.J.Wurzbacher, N.A.Williamson, S.H.Ramarathinam, H.H.Reid, A.K.Nair, A.Y.Zhao, R.Nastovska, G.Rudge, J.Rossjohn, A.W.Purcell. Phosphorylated Self-Peptides Alter Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generate Tumor-Specific Epitopes Proc.Natl.Acad.Sci.Usa V. 106 2776 2009.
ISSN: ISSN 0027-8424
PubMed: 19196958
DOI: 10.1073/PNAS.0812901106