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

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

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

Cadmium	(Cd)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop, PDB code: 4yiv:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co506 b:44.1 occ:1.00 OD1 A:ASP102 2.3 28.2 1.0 O A:HOH604 2.4 30.8 1.0 NE2 A:HIS363 2.4 40.8 1.0 CE1 A:HIS363 2.7 51.5 1.0 O A:HOH648 2.7 36.3 1.0 OD2 A:ASP102 2.7 30.1 1.0 CG A:ASP102 2.8 25.1 1.0 O A:HOH630 3.0 48.9 1.0 CD2 A:HIS363 3.7 36.9 1.0 ND1 A:HIS363 3.9 52.2 1.0 NE A:ARG111 4.0 23.3 1.0 O A:HOH606 4.2 41.9 1.0 O A:GLN101 4.3 22.5 1.0 NH2 A:ARG111 4.3 28.6 1.0 CB A:ASP102 4.3 25.5 1.0 CG A:HIS363 4.4 39.9 1.0 C A:GLN101 4.5 24.4 1.0 O A:LEU99 4.5 23.5 1.0 CZ A:ARG111 4.6 24.9 1.0 CG A:ARG111 4.9 25.1 1.0 N A:ASP102 4.9 22.1 1.0 CD A:ARG111 5.0 24.8 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co507 b:33.8 occ:0.75 O A:HOH725 2.1 43.7 1.0 O A:HOH693 2.2 38.1 1.0 ND1 A:HIS266 2.5 25.4 1.0 O A:HOH724 2.5 46.9 1.0 CE1 A:HIS266 3.4 29.4 1.0 CG A:HIS266 3.5 29.3 1.0 O A:HOH765 3.5 44.9 1.0 CB A:HIS266 3.8 27.0 1.0 O A:HOH691 4.1 27.1 1.0 O A:HOH687 4.3 31.7 1.0 NE2 A:HIS266 4.5 29.8 1.0 CD2 A:HIS266 4.6 26.0 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Engineered TGAMA1 Lacking the Dii Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Co508 b:56.8 occ:0.75 NE2 A:HIS89 1.7 23.3 1.0 O A:HOH611 2.1 41.1 1.0 O A:HOH643 2.1 49.2 1.0 OE1 A:GLU83 2.2 43.2 1.0 CD2 A:HIS89 2.4 48.9 1.0 O A:HOH622 2.5 53.2 1.0 NE2 A:HIS90 2.8 39.2 0.6 CE1 A:HIS89 2.9 41.5 1.0 NZ A:LYS285 3.1 48.8 1.0 CD A:GLU83 3.3 49.7 1.0 CD2 A:HIS90 3.5 34.8 0.6 CG A:HIS89 3.6 43.6 1.0 OE2 A:GLU83 3.7 59.5 1.0 ND1 A:HIS89 3.8 43.4 1.0 O A:HOH621 3.9 42.1 1.0 CE1 A:HIS90 4.0 34.6 0.6 CE A:LYS285 4.0 40.5 1.0 CG A:GLU83 4.6 52.4 1.0 CG A:HIS90 4.8 30.9 0.6 CD A:LYS285 4.8 34.3 1.0 CB A:HIS89 4.9 40.5 1.0 ND1 A:HIS90 5.0 26.4 0.6

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