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Cadmium in PDB 4yiv: Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop

Protein crystallography data

The structure of Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop, PDB code: 4yiv was solved by M.L.Parker, M.J.Boulanger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.82 / 1.93
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.050, 89.050, 124.970, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.5

Other elements in 4yiv:

The structure of Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop (pdb code 4yiv). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop, PDB code: 4yiv:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4yiv

Go back to Cadmium Binding Sites List in 4yiv
Cadmium binding site 1 out of 2 in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop


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 Engineered TGAMA1 Lacking the Dii Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:31.3
occ:1.00
CL A:CL505 2.5 27.6 1.0
OD2 A:ASP250 2.5 29.9 1.0
CL A:CL504 2.6 27.9 1.0
OD1 A:ASP250 2.7 31.8 1.0
CG A:ASP250 2.9 35.1 1.0
O A:HOH651 4.1 43.4 1.0
CB A:ASP250 4.4 33.5 1.0
O A:HOH635 4.8 42.8 1.0

Cadmium binding site 2 out of 2 in 4yiv

Go back to Cadmium Binding Sites List in 4yiv
Cadmium binding site 2 out of 2 in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop


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 Engineered TGAMA1 Lacking the Dii Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:26.0
occ:0.75
OE2 A:GLU180 2.3 35.1 1.0
O A:HOH657 2.5 40.6 1.0
OE2 A:GLU177 2.5 29.3 1.0
OE1 A:GLU177 2.6 29.6 1.0
CD A:GLU177 2.8 32.2 1.0
OE1 A:GLU180 2.9 38.5 1.0
CD A:GLU180 2.9 39.3 1.0
CG A:GLU177 4.3 28.2 1.0
O A:HOH610 4.4 31.6 1.0
CG A:GLU180 4.4 39.6 1.0
O A:HOH662 4.5 46.6 1.0
NZ A:LYS181 4.7 30.1 1.0
CE A:LYS181 4.7 29.9 1.0
NH1 A:ARG224 4.8 31.4 1.0
NH2 A:ARG224 4.9 32.1 1.0

Reference:

M.L.Parker, M.J.Boulanger. An Extended Surface Loop on Toxoplasma Gondii Apical Membrane Antigen 1 (AMA1) Governs Ligand Binding Selectivity. Plos One V. 10 26206 2015.
ISSN: ESSN 1932-6203
PubMed: 25955165
DOI: 10.1371/JOURNAL.PONE.0126206
Page generated: Sat Dec 12 08:26:03 2020

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