Cadmium in PDB 3fqu: 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: 3fqu 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)	29.96 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.911, 80.043, 110.367, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.2

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)

1 atom

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 3fqu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 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: 3fqu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 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:Cd279 b:31.7 occ:0.50 CD A:CD279 0.0 31.7 0.5 CD A:CD279 1.8 38.7 0.5 O A:HOH398 2.3 35.3 1.0 O A:HOH361 2.4 41.3 1.0 O A:HOH425 2.8 50.2 1.0 NE2 A:HIS145 2.9 39.6 1.0 CE1 A:HIS145 3.8 37.4 1.0 CD2 A:HIS145 3.9 46.4 1.0 NE2 A:GLN141 4.1 31.5 1.0 O A:HOH578 4.1 42.8 1.0 O A:HOH377 4.2 54.3 1.0 CG A:GLN141 4.3 31.9 1.0 CD A:GLN141 4.7 34.9 1.0 ND1 A:HIS145 4.9 43.2 1.0

Cadmium binding site 2 out of 7 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:Cd279 b:38.7 occ:0.50 CD A:CD279 0.0 38.7 0.5 CD A:CD279 1.8 31.7 0.5 NE2 A:HIS145 2.3 39.6 1.0 O A:HOH377 2.6 54.3 1.0 O A:HOH361 2.6 41.3 1.0 CE1 A:HIS145 2.7 37.4 1.0 O A:HOH398 2.7 35.3 1.0 O A:HOH578 3.3 42.8 1.0 CD2 A:HIS145 3.4 46.4 1.0 ND1 A:HIS145 3.8 43.2 1.0 O A:HOH425 4.1 50.2 1.0 CG A:HIS145 4.2 39.8 1.0 NE2 A:GLN141 4.4 31.5 1.0

Cadmium binding site 3 out of 7 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:Cd280 b:30.6 occ:1.00 OE1 A:GLU154 2.4 22.9 1.0 OE2 A:GLU154 2.4 41.8 1.0 ND1 A:HIS151 2.6 43.4 1.0 CD A:GLU154 2.7 30.9 1.0 CE1 A:HIS151 3.3 49.9 1.0 CG A:HIS151 3.6 52.2 1.0 CD A:CD283 3.7 39.9 0.3 CB A:HIS151 4.1 46.1 1.0 CG A:GLU154 4.2 25.1 1.0 NE2 A:HIS151 4.4 53.7 1.0 O A:HOH546 4.6 56.9 1.0 CD2 A:HIS151 4.6 54.6 1.0 CB A:GLU154 5.0 22.1 1.0

Cadmium binding site 4 out of 7 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:Cd281 b:33.7 occ:0.80 O A:HOH353 2.2 32.9 1.0 NE2 A:HIS3 2.3 22.0 1.0 O A:HOH339 2.4 42.5 1.0 N A:GLY1 2.5 58.7 1.0 O A:GLY1 2.7 41.8 1.0 CE1 A:HIS3 3.2 25.8 1.0 CD2 A:HIS3 3.2 25.2 1.0 C A:GLY1 3.3 48.6 1.0 CA A:GLY1 3.4 56.8 1.0 ND1 A:HIS3 4.3 23.4 1.0 O A:HOH394 4.3 63.6 1.0 CG A:HIS3 4.3 20.8 1.0 N A:SER2 4.5 45.5 1.0 NE1 A:TRP107 4.6 38.2 1.0 O A:SER2 5.0 26.7 1.0

Cadmium binding site 5 out of 7 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 A:Cd282 b:24.6 occ:0.50 OE1 A:GLU212 2.3 26.8 1.0 OE2 A:GLU212 2.3 44.5 1.0 O A:HOH480 2.4 36.8 1.0 OD1 A:ASP30 2.4 26.0 1.0 OD2 A:ASP30 2.5 20.6 1.0 O A:HOH532 2.5 43.0 1.0 O A:HOH556 2.6 40.3 1.0 CD A:GLU212 2.6 40.2 1.0 CG A:ASP30 2.8 23.9 1.0 O A:HOH359 3.8 54.1 1.0 O A:HOH516 4.0 38.4 1.0 CG A:GLU212 4.1 34.9 1.0 CB A:ASP30 4.3 18.6 1.0 N A:ALA211 4.5 17.4 1.0 N A:GLU212 4.5 17.5 1.0 CB A:ALA211 4.6 21.9 1.0 CB A:PRO210 4.6 25.4 1.0 O A:HOH509 4.8 42.0 1.0 C3 A:GOL277 4.8 39.9 1.0 N A:ASP30 4.8 17.0 1.0 C1 A:GOL277 4.9 48.2 1.0 O A:HOH564 4.9 36.0 1.0 CA A:ASP30 4.9 17.5 1.0 CA A:ALA211 5.0 19.7 1.0

Cadmium binding site 6 out of 7 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 6 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:Cd283 b:39.9 occ:0.30 OE2 A:GLU154 2.3 41.8 1.0 O A:HOH354 2.8 20.1 1.0 O A:HOH546 2.9 56.9 1.0 CD A:GLU154 3.3 30.9 1.0 ND1 A:HIS151 3.6 43.4 1.0 CD A:CD280 3.7 30.6 1.0 O A:HOH483 3.7 34.2 1.0 CG A:GLU154 3.9 25.1 1.0 CA A:HIS151 4.0 38.2 1.0 OE1 A:GLU154 4.2 22.9 1.0 CB A:HIS151 4.2 46.1 1.0 CG A:HIS151 4.2 52.2 1.0 O A:HOH442 4.4 32.2 1.0 CE1 A:HIS151 4.5 49.9 1.0 O A:GLU148 4.6 40.5 1.0 N A:HIS151 4.8 42.2 1.0

Cadmium binding site 7 out of 7 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 7 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:Cd100 b:37.7 occ:0.70 NE2 B:HIS50 2.3 24.2 1.0 O A:HOH461 2.4 35.4 1.0 O B:HOH375 2.5 53.6 1.0 O B:HOH376 2.7 53.1 1.0 O B:HOH374 2.7 57.2 1.0 CE1 B:HIS50 3.2 29.4 1.0 CD2 B:HIS50 3.2 26.3 1.0 ND1 B:HIS50 4.3 25.8 1.0 O A:HOH386 4.4 49.3 1.0 CG B:HIS50 4.4 22.9 1.0 O B:HOH164 4.5 37.4 1.0 O B:HOH269 4.7 45.0 1.0 O A:HOH557 4.9 58.9 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