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Cadmium in PDB 3fqw: 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: 3fqw 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) 23.66 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.982, 79.378, 111.292, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.6

Other elements in 3fqw:

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:

Cobalt (Co) 1 atom

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 3fqw). 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: 3fqw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3fqw

Go back to Cadmium Binding Sites List in 3fqw
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:55.5
occ:0.90
NE2 A:HIS145 2.4 31.2 1.0
CD2 A:HIS145 3.3 33.6 1.0
CE1 A:HIS145 3.3 35.2 1.0
NE2 A:GLN141 4.3 28.4 1.0
ND1 A:HIS145 4.4 35.2 1.0
CG A:HIS145 4.4 34.0 1.0
CG A:GLN141 4.8 22.4 1.0

Cadmium binding site 2 out of 5 in 3fqw

Go back to Cadmium Binding Sites List in 3fqw
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:25.3
occ:0.90
O A:HOH402 2.2 26.5 1.0
O A:HOH414 2.3 24.3 1.0
OD1 A:ASP30 2.3 22.2 1.0
OE2 A:GLU212 2.4 27.4 1.0
OD2 A:ASP30 2.5 18.6 1.0
OE1 A:GLU212 2.5 26.0 1.0
O A:HOH413 2.5 27.9 1.0
CG A:ASP30 2.7 20.8 1.0
CD A:GLU212 2.7 27.6 1.0
CB A:ASP30 4.2 18.5 1.0
CG A:GLU212 4.3 25.2 1.0
O A:HOH352 4.4 35.5 1.0
N A:ALA211 4.5 15.8 1.0
CB A:PRO210 4.6 23.3 1.0
N A:GLU212 4.6 18.7 1.0
O A:HOH361 4.6 33.9 1.0
CB A:ALA211 4.6 19.0 1.0
N A:ASP30 4.8 17.7 1.0
O A:HOH301 4.8 40.0 1.0
CA A:ASP30 4.9 17.5 1.0

Cadmium binding site 3 out of 5 in 3fqw

Go back to Cadmium Binding Sites List in 3fqw
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:26.9
occ:1.00
ND1 A:HIS191 1.9 11.6 1.0
O A:HIS191 2.4 18.7 1.0
O A:HOH431 2.5 22.7 1.0
CE1 A:HIS191 2.8 30.5 1.0
CG A:HIS191 3.0 20.6 1.0
C A:HIS191 3.2 24.1 1.0
CB A:HIS191 3.5 19.8 1.0
CA A:HIS191 4.0 21.7 1.0
NE2 A:HIS191 4.0 23.1 1.0
N A:HIS192 4.0 18.8 1.0
CD2 A:HIS191 4.1 21.1 1.0
CA A:HIS192 4.2 19.5 1.0
O A:HOH359 4.4 22.0 1.0
O A:HOH503 4.5 43.0 1.0
N A:ALA193 4.5 20.0 1.0
N A:HIS191 4.6 16.3 1.0
O B:HOH171 4.7 36.2 1.0
C A:HIS192 4.9 22.3 1.0

Cadmium binding site 4 out of 5 in 3fqw

Go back to Cadmium Binding Sites List in 3fqw
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:39.7
occ:1.00
N A:GLY1 2.3 44.0 1.0
O A:HOH507 2.3 28.1 1.0
NE2 A:HIS3 2.4 28.5 1.0
O A:HOH333 2.4 53.0 1.0
O A:GLY1 2.9 46.6 1.0
CD2 A:HIS3 3.2 28.7 1.0
CA A:GLY1 3.4 46.4 1.0
C A:GLY1 3.4 46.7 1.0
CE1 A:HIS3 3.4 31.2 1.0
CG A:HIS3 4.4 24.5 1.0
NE1 A:TRP107 4.4 37.2 1.0
ND1 A:HIS3 4.5 24.6 1.0
N A:SER2 4.6 43.7 1.0
O A:SER2 4.8 30.9 1.0

Cadmium binding site 5 out of 5 in 3fqw

Go back to Cadmium Binding Sites List in 3fqw
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
A:Cd280

b:66.5
occ:0.50
O A:HOH303 2.6 17.7 1.0
OE2 A:GLU154 2.7 34.9 1.0
ND1 A:HIS151 3.5 41.3 1.0
CD A:GLU154 3.7 26.2 1.0
O A:GLU148 3.8 27.2 1.0
CA A:HIS151 4.0 27.9 1.0
CG A:HIS151 4.2 40.9 1.0
CB A:HIS151 4.3 35.2 1.0
CG A:GLU154 4.3 22.5 1.0
CE1 A:HIS151 4.4 41.3 1.0
OE1 A:GLU154 4.5 21.2 1.0
N A:HIS151 4.6 29.2 1.0
C A:GLU148 4.9 24.5 1.0
C A:HIS151 5.0 23.4 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: Wed Oct 28 10:02:58 2020
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