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Cadmium in PDB 4nny: Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2

Protein crystallography data

The structure of Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2, PDB code: 4nny was solved by F.Mohammed, D.H.Stones, B.E.Willcox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.400, 79.800, 110.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 22.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2 (pdb code 4nny). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2, PDB code: 4nny:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 4nny

Go back to Cadmium Binding Sites List in 4nny
Cadmium binding site 1 out of 3 in the Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:14.6
occ:1.00
OE2 A:GLU154 2.3 11.4 1.0
ND1 A:HIS151 2.4 13.8 1.0
OE1 A:GLU154 2.5 14.5 1.0
CD A:GLU154 2.8 13.6 1.0
CE1 A:HIS151 3.1 14.0 1.0
CG A:HIS151 3.5 13.1 1.0
CB A:HIS151 4.0 12.2 1.0
NE2 A:HIS151 4.2 15.7 1.0
CG A:GLU154 4.3 12.1 1.0
CD2 A:HIS151 4.4 13.1 1.0
CA A:HIS151 4.9 12.2 1.0

Cadmium binding site 2 out of 3 in 4nny

Go back to Cadmium Binding Sites List in 4nny
Cadmium binding site 2 out of 3 in the Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:42.7
occ:1.00
O A:HOH598 2.3 18.2 1.0
OD2 A:ASP30 2.5 11.8 1.0
O A:HOH557 2.5 24.1 1.0
OD1 A:ASP30 2.5 12.9 1.0
O A:HOH601 2.7 28.5 1.0
CG A:ASP30 2.9 12.2 1.0
O A:HOH585 4.1 31.5 1.0
CB A:ASP30 4.3 11.3 1.0
N A:ALA211 4.4 11.2 1.0
CB A:ALA211 4.6 11.9 1.0
N A:GLU212 4.6 12.9 1.0
CB A:PRO210 4.6 12.0 1.0
O A:HOH530 4.7 33.5 1.0
O A:HOH527 4.8 24.1 1.0
N A:ASP30 4.8 10.7 1.0
CA A:ALA211 4.9 11.9 1.0
CB A:GLU212 5.0 14.8 1.0

Cadmium binding site 3 out of 3 in 4nny

Go back to Cadmium Binding Sites List in 4nny
Cadmium binding site 3 out of 3 in the Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Non-Phosphorylated Form of PKD2 Phosphopeptide Bound to Hla-A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd103

b:41.9
occ:1.00
NE2 B:HIS51 2.5 17.5 1.0
O B:HOH258 2.6 31.3 1.0
O B:HOH257 2.6 33.3 1.0
O A:HOH606 2.6 23.3 1.0
O B:HOH256 2.6 26.0 1.0
CD2 B:HIS51 3.3 17.6 1.0
CE1 B:HIS51 3.5 18.5 1.0
CG B:HIS51 4.5 16.4 1.0
ND1 B:HIS51 4.6 17.6 1.0
O B:HOH239 4.9 30.6 1.0
O B:HOH262 5.0 28.1 1.0

Reference:

F.Mohammed, D.H.Stones, B.E.Willcox. Phosphorylation-Induced Conformational Changes Radically Alter the Antigenic Identity of Human Mhc Class I Phosphopeptides To Be Published.
Page generated: Sat Dec 12 08:25:18 2020

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