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

Protein crystallography data

The structure of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes, PDB code: 3fqt 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) 24.93 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.680, 79.840, 110.207, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.4

Cadmium Binding Sites:

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 3fqt). 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: 3fqt:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 3fqt

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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:Cd276

b:34.9
occ:0.60
CD A:CD276 0.0 34.9 0.6
CD A:CD276 1.8 31.5 0.4
O A:HOH331 2.4 52.1 1.0
O A:HOH304 2.7 57.2 1.0
NE2 A:HIS145 3.1 34.8 1.0
CD2 A:HIS145 3.8 35.0 1.0
CE1 A:HIS145 4.1 38.0 1.0
NE2 A:GLN141 4.2 28.8 1.0
CG A:GLN141 4.3 27.4 1.0
CD A:GLN141 4.7 30.9 1.0

Cadmium binding site 2 out of 7 in 3fqt

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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:Cd276

b:31.5
occ:0.40
CD A:CD276 0.0 31.5 0.4
CD A:CD276 1.8 34.9 0.6
NE2 A:HIS145 2.2 34.8 1.0
O A:HOH304 2.4 57.2 1.0
CE1 A:HIS145 2.9 38.0 1.0
CD2 A:HIS145 3.2 35.0 1.0
O A:HOH331 3.6 52.1 1.0
ND1 A:HIS145 3.9 40.4 1.0
CG A:HIS145 4.1 36.2 1.0
NE2 A:GLN141 4.4 28.8 1.0
O A:HOH575 4.7 54.5 1.0

Cadmium binding site 3 out of 7 in 3fqt

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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:Cd277

b:30.3
occ:1.00
ND1 A:HIS191 1.7 5.7 0.5
O A:HIS191 2.4 23.8 1.0
O A:HOH292 2.5 21.4 1.0
CE1 A:HIS191 2.6 28.3 0.5
CG A:HIS191 2.8 21.6 0.5
ND1 A:HIS191 2.9 23.2 0.5
C A:HIS191 3.2 22.9 1.0
CB A:HIS191 3.3 22.8 0.5
CG A:HIS191 3.7 16.3 0.5
NE2 A:HIS191 3.7 22.8 0.5
CB A:HIS191 3.8 18.4 0.5
CD2 A:HIS191 3.8 18.9 0.5
CE1 A:HIS191 3.9 19.6 0.5
CA A:HIS191 3.9 22.6 0.5
CA A:HIS191 4.0 20.4 0.5
N A:HIS192 4.1 24.7 1.0
CA A:HIS192 4.3 21.6 1.0
O A:HOH451 4.5 28.4 1.0
N A:HIS191 4.6 20.9 1.0
N A:ALA193 4.6 24.2 1.0
CD2 A:HIS191 4.9 14.9 0.5
C A:HIS192 5.0 25.3 1.0
NE2 A:HIS191 5.0 18.4 0.5

Cadmium binding site 4 out of 7 in 3fqt

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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:Cd278

b:27.3
occ:0.50
OE1 A:GLU212 2.3 32.8 1.0
OE2 A:GLU212 2.3 43.7 1.0
O A:HOH487 2.4 39.4 1.0
OD1 A:ASP30 2.4 25.2 1.0
O A:HOH509 2.4 43.4 1.0
OD2 A:ASP30 2.5 20.5 1.0
O A:HOH300 2.6 47.6 1.0
CD A:GLU212 2.6 42.5 1.0
CG A:ASP30 2.8 25.1 1.0
O A:HOH303 3.8 57.8 1.0
O A:HOH532 3.9 42.2 1.0
CG A:GLU212 4.1 37.3 1.0
CB A:ASP30 4.3 19.8 1.0
N A:ALA211 4.4 18.0 1.0
CB A:PRO210 4.5 26.4 1.0
N A:GLU212 4.5 20.2 1.0
CB A:ALA211 4.6 23.3 1.0
O A:HOH302 4.7 55.3 1.0
C3 A:GOL284 4.8 40.8 1.0
N A:ASP30 4.8 19.2 1.0
O A:HOH530 4.8 48.4 1.0
CA A:ASP30 4.9 18.6 1.0
O A:HOH547 5.0 34.6 1.0
CB A:GLU212 5.0 26.3 1.0
CA A:ALA211 5.0 20.5 1.0

Cadmium binding site 5 out of 7 in 3fqt

Go back to Cadmium Binding Sites List in 3fqt
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:Cd279

b:35.9
occ:0.80
O A:HOH550 2.3 37.6 1.0
NE2 A:HIS3 2.3 20.1 1.0
O A:HOH573 2.3 43.0 1.0
N A:GLY1 2.6 54.0 1.0
O A:GLY1 2.6 43.3 1.0
CD2 A:HIS3 3.2 27.5 1.0
CE1 A:HIS3 3.2 27.8 1.0
C A:GLY1 3.3 46.0 1.0
CA A:GLY1 3.4 51.8 1.0
ND1 A:HIS3 4.3 24.2 1.0
CG A:HIS3 4.3 23.4 1.0
O A:HOH333 4.5 60.3 1.0
N A:SER2 4.5 43.9 1.0
NE1 A:TRP107 4.6 40.3 1.0
O A:SER2 4.9 30.1 1.0

Cadmium binding site 6 out of 7 in 3fqt

Go back to Cadmium Binding Sites List in 3fqt
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:Cd280

b:79.2
occ:0.50
O A:HOH385 2.6 22.0 1.0
O A:HOH386 3.1 56.7 1.0
OE2 A:GLU154 3.2 37.9 1.0
O A:GLU148 3.7 40.0 1.0
CD A:GLU154 4.2 33.1 1.0
ND1 A:HIS151 4.2 43.1 1.0
CA A:HIS151 4.2 36.0 1.0
O A:HOH497 4.3 37.8 1.0
O A:HOH413 4.4 34.9 1.0
CG A:GLU154 4.6 25.1 1.0
C A:GLU148 4.7 41.8 1.0
N A:HIS151 4.7 36.4 1.0
CG A:HIS151 4.7 44.4 1.0
CB A:HIS151 4.8 43.0 1.0
CE1 A:HIS151 4.9 45.8 1.0

Cadmium binding site 7 out of 7 in 3fqt

Go back to Cadmium Binding Sites List in 3fqt
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:Cd99

b:40.4
occ:0.70
NE2 B:HIS50 2.3 25.9 1.0
O B:HOH330 2.4 51.1 1.0
O A:HOH443 2.4 37.1 1.0
O B:HOH336 2.6 57.4 1.0
O B:HOH337 2.7 60.1 1.0
CD2 B:HIS50 3.2 28.8 1.0
CE1 B:HIS50 3.3 30.0 1.0
ND1 B:HIS50 4.4 27.2 1.0
CG B:HIS50 4.4 24.9 1.0
O B:HOH157 4.4 42.0 1.0
O B:HOH391 4.8 48.0 1.0
O A:HOH527 4.9 53.5 1.0

Reference:

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
Page generated: Fri Aug 28 13:38:06 2020
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