Atomistry » Cadmium » PDB 3cn6-3haf » 3fqt
Atomistry »
  Cadmium »
    PDB 3cn6-3haf »
      3fqt »

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

Other elements in 3fqt:

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

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

Go back to Cadmium Binding Sites List in 3fqt
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

Go back to Cadmium Binding Sites List in 3fqt
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

Go back to Cadmium Binding Sites List in 3fqt
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

Go back to Cadmium Binding Sites List in 3fqt
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: Sun Jan 24 09:44:40 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy