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Cadmium in PDB 3fqr: 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: 3fqr 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) 24.27 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.678, 79.706, 111.558, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.9

Other elements in 3fqr:

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

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 3fqr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 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: 3fqr:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 3fqr

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Cadmium binding site 1 out of 8 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:Cd278

b:32.4
occ:0.80
 NE2 A:HIS3 2.3 18.1 1.0
O A:HOH513 2.4 29.7 1.0
O A:HOH478 2.5 46.6 1.0
N A:GLY1 2.5 42.2 1.0
O A:GLY1 2.7 36.8 1.0
CE1 A:HIS3 3.2 24.1 1.0
CD2 A:HIS3 3.3 21.9 1.0
C A:GLY1 3.4 35.7 1.0
CA A:GLY1 3.5 42.3 1.0
O A:HOH447 3.9 50.0 1.0
ND1 A:HIS3 4.3 21.7 1.0
CG A:HIS3 4.3 20.8 1.0
NE1 A:TRP107 4.5 30.0 1.0
N A:SER2 4.6 35.5 1.0
O A:SER2 4.8 23.9 1.0
O A:HOH512 4.9 57.8 1.0

Cadmium binding site 2 out of 8 in 3fqr

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Cadmium binding site 2 out of 8 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:23.7
occ:0.60
 OE1 A:GLU212 2.3 10.2 0.5
OE2 A:GLU212 2.4 21.4 0.5
O A:HOH309 2.4 32.4 1.0
O A:HOH301 2.4 30.3 1.0
OD1 A:ASP30 2.5 22.5 1.0
OD2 A:ASP30 2.5 16.7 1.0
O A:HOH551 2.6 37.8 1.0
CD A:GLU212 2.7 19.9 0.5
CG A:ASP30 2.8 20.0 1.0
O A:HOH570 4.0 31.8 1.0
CG A:GLU212 4.2 22.1 0.5
CB A:ASP30 4.3 17.0 1.0
N A:ALA211 4.5 15.8 1.0
CB A:PRO210 4.5 24.2 1.0
N A:GLU212 4.6 18.3 1.0
CB A:ALA211 4.7 16.3 1.0
O A:HOH507 4.8 40.8 1.0
C3 A:GOL276 4.9 33.1 1.0
N A:ASP30 5.0 17.7 1.0
O3 A:GOL276 5.0 37.9 1.0

Cadmium binding site 3 out of 8 in 3fqr

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Cadmium binding site 3 out of 8 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:20.8
occ:1.00
 ND1 A:HIS191 2.3 19.5 1.0
O A:HOH401 2.4 18.2 1.0
O A:HIS191 2.4 16.7 1.0
CE1 A:HIS191 3.2 23.1 1.0
C A:HIS191 3.3 18.7 1.0
CG A:HIS191 3.3 15.8 1.0
CB A:HIS191 3.7 16.1 1.0
N A:HIS192 4.0 15.4 1.0
CA A:HIS191 4.0 14.1 1.0
CA A:HIS192 4.2 16.2 1.0
NE2 A:HIS191 4.3 21.5 1.0
O A:HOH467 4.4 22.1 1.0
CD2 A:HIS191 4.4 24.0 1.0
N A:ALA193 4.6 18.7 1.0
N A:HIS191 4.6 15.2 1.0
C A:HIS192 4.9 19.7 1.0

Cadmium binding site 4 out of 8 in 3fqr

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Cadmium binding site 4 out of 8 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:28.5
occ:0.50
 CD A:CD281 0.0 28.5 0.5
CD A:CD281 1.6 39.6 0.5
NE2 A:HIS197 2.2 37.6 1.0
CE1 A:HIS197 2.9 35.0 1.0
O A:HOH407 2.9 36.5 1.0
CD2 A:HIS197 3.3 29.7 1.0
O A:HOH400 3.6 39.9 1.0
OE2 A:GLU198 3.9 43.7 1.0
ND1 A:HIS197 4.0 36.8 1.0
CG A:HIS197 4.2 33.7 1.0
CD A:GLU198 4.4 39.6 1.0
OE1 A:GLU198 4.5 36.4 1.0

Cadmium binding site 5 out of 8 in 3fqr

Go back to Cadmium Binding Sites List in 3fqr
Cadmium binding site 5 out of 8 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:Cd281

b:39.6
occ:0.50
 CD A:CD281 0.0 39.6 0.5
CD A:CD281 1.6 28.5 0.5
O A:HOH407 2.4 36.5 1.0
OE2 A:GLU198 2.6 43.7 1.0
NE2 A:HIS197 2.6 37.6 1.0
CD A:GLU198 3.3 39.6 1.0
CD2 A:HIS197 3.4 29.7 1.0
OE1 A:GLU198 3.6 36.4 1.0
CE1 A:HIS197 3.7 35.0 1.0
CG A:GLU198 4.6 37.8 1.0
CG A:HIS197 4.6 33.7 1.0
ND1 A:HIS197 4.7 36.8 1.0
O A:HOH400 5.0 39.9 1.0

Cadmium binding site 6 out of 8 in 3fqr

Go back to Cadmium Binding Sites List in 3fqr
Cadmium binding site 6 out of 8 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
B:Cd102

b:35.8
occ:0.70
 NE2 B:HIS50 2.3 23.9 1.0
O B:HOH409 2.5 48.6 1.0
O B:HOH103 2.5 50.7 1.0
O B:HOH133 2.6 33.5 1.0
O B:HOH261 2.7 41.2 1.0
CD2 B:HIS50 3.2 27.7 1.0
CE1 B:HIS50 3.3 28.5 1.0
CG B:HIS50 4.4 24.4 1.0
ND1 B:HIS50 4.4 25.4 1.0
O A:HOH455 4.5 56.2 1.0
O B:HOH154 4.6 36.4 1.0
O B:HOH356 4.6 51.2 1.0
O B:HOH260 4.8 41.1 1.0

Cadmium binding site 7 out of 8 in 3fqr

Go back to Cadmium Binding Sites List in 3fqr
Cadmium binding site 7 out of 8 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
C:Cd11

b:26.7
occ:0.30
 CD C:CD11 0.0 26.7 0.3
CD C:CD11 1.6 21.4 0.3
O C:SEP4 2.1 29.2 0.6
O C:SEP4 2.4 31.3 0.4
NE2 C:HIS7 2.7 36.3 1.0
O3P C:SEP4 3.1 45.2 0.4
CD2 C:HIS7 3.2 33.4 1.0
O C:HOH511 3.3 16.3 1.0
C C:SEP4 3.3 29.2 0.6
C C:SEP4 3.4 28.5 0.4
O C:HOH510 3.8 24.4 1.0
CE1 C:HIS7 3.9 39.3 1.0
CA C:GLY5 4.0 31.5 1.0
N C:GLY5 4.1 25.8 1.0
CB C:SEP4 4.3 26.3 0.4
P C:SEP4 4.3 34.0 0.4
O1P C:SEP4 4.3 38.9 0.4
CA C:SEP4 4.4 26.4 0.4
CA C:SEP4 4.4 26.5 0.6
CB C:SEP4 4.5 26.2 0.6
CG C:HIS7 4.5 30.3 1.0
OG C:SEP4 4.7 26.4 0.6
ND1 C:HIS7 4.8 34.5 1.0
OG C:SEP4 4.9 33.7 0.4
C C:GLY5 4.9 36.1 1.0

Cadmium binding site 8 out of 8 in 3fqr

Go back to Cadmium Binding Sites List in 3fqr
Cadmium binding site 8 out of 8 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 8 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
C:Cd11

b:21.4
occ:0.30
 CD C:CD11 0.0 21.4 0.3
CD C:CD11 1.6 26.7 0.3
O C:HOH510 2.4 24.4 1.0
O C:SEP4 2.4 31.3 0.4
NE2 C:HIS7 2.4 36.3 1.0
O C:SEP4 2.6 29.2 0.6
O3P C:SEP4 2.7 45.2 0.4
CE1 C:HIS7 3.3 39.3 1.0
CD2 C:HIS7 3.6 33.4 1.0
C C:SEP4 3.6 28.5 0.4
C C:SEP4 3.7 29.2 0.6
NH1 A:ARG65 3.9 38.2 1.0
O C:HOH511 4.1 16.3 1.0
P C:SEP4 4.1 34.0 0.4
CA C:SEP4 4.4 26.4 0.4
CA C:SEP4 4.4 26.5 0.6
O C:HOH136 4.4 28.1 1.0
CB C:SEP4 4.4 26.3 0.4
ND1 C:HIS7 4.5 34.5 1.0
CB C:SEP4 4.5 26.2 0.6
N C:GLY5 4.6 25.8 1.0
CG C:HIS7 4.6 30.3 1.0
OG C:SEP4 4.7 33.7 0.4
O1P C:SEP4 4.7 38.9 0.4
CA C:GLY5 4.7 31.5 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 Jul 19 15:57:16 2024

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