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Cadmium in PDB 3fqn: 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: 3fqn 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) 23.71 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.716, 79.708, 110.871, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.7

Other elements in 3fqn:

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

Cadmium binding site 1 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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:26.7
occ:0.50
 OE1 A:GLU212 2.3 14.8 0.5
OE2 A:GLU212 2.4 28.2 0.5
OD1 A:ASP30 2.5 24.7 1.0
O A:HOH629 2.5 42.8 1.0
O A:HOH327 2.5 38.5 1.0
OD2 A:ASP30 2.5 19.2 1.0
O A:HOH604 2.5 46.0 1.0
CD A:GLU212 2.6 23.0 0.5
CG A:ASP30 2.8 22.2 1.0
O A:HOH573 3.9 33.5 1.0
CG A:GLU212 4.2 27.5 0.5
CB A:ASP30 4.4 20.4 1.0
N A:ALA211 4.5 19.1 1.0
N A:GLU212 4.5 20.7 1.0
CB A:PRO210 4.6 23.6 1.0
CB A:ALA211 4.6 20.8 1.0
O A:HOH291 4.7 46.4 1.0
CA A:ALA211 5.0 21.8 1.0
C1 A:GOL282 5.0 41.9 1.0
CB A:GLU212 5.0 24.4 0.5
CB A:GLU212 5.0 24.2 0.5
N A:ASP30 5.0 18.6 1.0

Cadmium binding site 2 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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:Cd277

b:34.7
occ:0.70
 NE2 A:HIS3 2.3 21.3 1.0
O A:HOH395 2.4 52.8 1.0
O A:HOH528 2.4 36.4 1.0
N A:GLY1 2.6 46.8 1.0
O A:GLY1 2.7 37.3 1.0
CE1 A:HIS3 3.1 25.6 1.0
CD2 A:HIS3 3.2 25.3 1.0
O A:HOH434 3.3 50.8 1.0
C A:GLY1 3.4 39.4 1.0
CA A:GLY1 3.5 44.9 1.0
ND1 A:HIS3 4.3 23.8 1.0
CG A:HIS3 4.3 24.8 1.0
NE1 A:TRP107 4.5 33.8 1.0
N A:SER2 4.6 37.8 1.0
O A:SER2 4.9 26.5 1.0

Cadmium binding site 3 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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:Cd278

b:32.0
occ:0.50
 CD A:CD278 0.0 32.0 0.5
CD A:CD278 1.7 32.5 0.5
O A:HOH465 2.1 35.5 1.0
OE2 A:GLU198 2.4 41.9 1.0
NE2 A:HIS197 2.4 37.1 1.0
O A:HOH363 2.6 43.6 1.0
CD A:GLU198 3.1 38.1 1.0
CD2 A:HIS197 3.3 28.7 1.0
OE1 A:GLU198 3.3 33.7 1.0
CE1 A:HIS197 3.5 33.2 1.0
O A:HOH393 4.1 47.0 1.0
CG A:GLU198 4.3 36.4 1.0
CG A:HIS197 4.5 32.8 1.0
ND1 A:HIS197 4.5 37.6 1.0

Cadmium binding site 4 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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:32.5
occ:0.50
 CD A:CD278 0.0 32.5 0.5
CD A:CD278 1.7 32.0 0.5
NE2 A:HIS197 2.3 37.1 1.0
O A:HOH393 2.5 47.0 1.0
O A:HOH363 2.6 43.6 1.0
O A:HOH465 2.8 35.5 1.0
CE1 A:HIS197 2.8 33.2 1.0
CD2 A:HIS197 3.5 28.7 1.0
OE2 A:GLU198 4.0 41.9 1.0
ND1 A:HIS197 4.1 37.6 1.0
CG A:HIS197 4.4 32.8 1.0
OE1 A:GLU198 4.4 33.7 1.0
CD A:GLU198 4.5 38.1 1.0
O A:HOH347 4.6 46.8 1.0

Cadmium binding site 5 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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:23.4
occ:1.00
 ND1 A:HIS191 2.3 22.5 1.0
O A:HIS191 2.4 21.0 1.0
CE1 A:HIS191 3.2 24.6 1.0
C A:HIS191 3.2 21.8 1.0
CG A:HIS191 3.4 18.5 1.0
CB A:HIS191 3.7 19.3 1.0
N A:HIS192 4.0 18.4 1.0
CA A:HIS191 4.0 17.9 1.0
CA A:HIS192 4.2 19.1 1.0
NE2 A:HIS191 4.4 24.2 1.0
O A:HOH480 4.4 26.2 1.0
CD2 A:HIS191 4.5 26.0 1.0
N A:ALA193 4.5 21.8 1.0
N A:HIS191 4.6 19.1 1.0
C A:HIS192 4.9 22.6 1.0

Cadmium binding site 6 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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
B:Cd99

b:33.1
occ:0.50
 NE2 B:HIS50 2.3 26.7 1.0
O A:HOH486 2.5 34.2 1.0
O B:HOH388 2.6 57.4 1.0
O B:HOH415 2.6 65.1 1.0
O B:HOH339 2.7 51.3 1.0
CD2 B:HIS50 3.2 31.6 1.0
CE1 B:HIS50 3.3 30.4 1.0
O A:HOH357 4.0 59.6 1.0
ND1 B:HIS50 4.4 27.5 1.0
O B:HOH370 4.4 54.0 1.0
CG B:HIS50 4.4 26.0 1.0
O B:HOH115 4.5 35.6 1.0
O B:HOH250 4.7 45.5 1.0

Cadmium binding site 7 out of 7 in 3fqn

Go back to Cadmium Binding Sites List in 3fqn
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
C:Cd11

b:23.0
occ:0.40
 OD1 C:ASP3 2.3 19.5 0.4
CE2 A:TYR99 2.4 14.9 0.6
O A:HOH381 2.5 25.9 1.0
OD2 C:ASP3 2.5 25.4 0.4
NE2 A:HIS70 2.6 25.1 1.0
CG C:ASP3 2.7 20.5 0.4
CZ A:TYR99 3.0 17.4 0.6
OH A:TYR99 3.0 18.8 0.6
CD2 A:HIS70 3.3 25.4 1.0
CD2 A:TYR99 3.3 13.5 0.6
CE1 A:HIS70 3.5 24.9 1.0
O C:SER4 3.7 21.5 0.4
CB C:ASP3 3.8 21.2 0.6
CE2 A:TYR99 3.8 16.1 0.4
CD2 A:TYR99 4.0 16.9 0.4
CE1 A:TYR99 4.1 16.7 0.6
CE1 A:HIS114 4.1 25.2 1.0
O C:HOH74 4.2 24.0 1.0
CB C:ASP3 4.3 20.8 0.4
OD2 C:ASP3 4.3 25.2 0.6
CG A:TYR99 4.4 16.8 0.6
CG A:HIS70 4.4 20.1 1.0
CG C:ASP3 4.4 24.0 0.6
CD A:ARG97 4.5 17.9 0.5
ND1 A:HIS70 4.5 23.0 1.0
C C:SER4 4.7 26.1 0.4
CD1 A:TYR99 4.7 17.3 0.6
CE2 A:PHE9 4.8 17.8 1.0
C C:ASP3 4.8 24.2 0.4
CZ A:PHE9 4.8 18.2 1.0
ND1 A:HIS114 4.8 19.0 1.0
O C:ASP3 4.9 22.4 0.6
CA C:ASP3 4.9 20.3 0.6
CZ A:TYR99 4.9 19.8 0.4
O C:ASP3 5.0 22.1 0.4
CA C:ASP3 5.0 20.6 0.4

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 15:57:05 2024

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