Gadolinium in PDB 3cqr: Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5

All present enzymatic activity of Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5:
1.10.99.3;

The structure of Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5, PDB code: 3cqr was solved by P.Arnoux, T.Morosinotto, D.Pignol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.20 / 2.00
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.297, 122.297, 158.337, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 23.4

The binding sites of Gadolinium atom in the Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5 (pdb code 3cqr). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5, PDB code: 3cqr:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in the Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd401 b:24.2 occ:0.29 O A:HOH483 2.3 35.1 1.0 N A:GLU81 2.7 43.8 1.0 O A:GLU81 3.1 40.5 1.0 C A:GLU81 3.4 41.1 1.0 O A:HOH474 3.4 43.5 1.0 CE2 A:PHE82 3.5 30.2 1.0 CZ A:PHE82 3.5 28.4 1.0 CA A:GLU81 3.5 42.8 1.0 NH2 A:ARG237 3.9 38.0 1.0 CD2 A:PHE82 3.9 26.3 1.0 CE1 A:PHE82 3.9 28.8 1.0 CG A:PHE82 4.2 34.1 1.0 CD1 A:PHE82 4.2 32.1 1.0 N A:PHE82 4.2 39.1 1.0 O A:HOH429 4.3 37.6 1.0 NH1 A:ARG237 4.7 31.0 1.0 CZ A:ARG237 4.8 34.1 1.0 CB A:GLU81 5.0 42.5 1.0 CA A:PHE82 5.0 37.9 1.0

Gadolinium binding site 2 out of 3 in the Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd402 b:24.7 occ:0.33 CE2 B:PHE82 3.3 28.5 1.0 CD2 B:PHE82 3.5 30.6 1.0 CZ B:PHE82 3.5 32.4 1.0 N B:PHE82 3.5 35.2 1.0 O B:HOH532 3.8 34.3 1.0 CG B:PHE82 3.8 34.3 1.0 CE1 B:PHE82 3.8 33.9 1.0 CD1 B:PHE82 4.0 34.1 1.0 NH2 B:ARG237 4.1 43.7 1.0 CA B:PHE82 4.6 36.0 1.0 CB B:PHE82 4.7 35.2 1.0 NH1 B:ARG237 4.9 39.0 1.0 CZ B:ARG237 5.0 40.6 1.0

Gadolinium binding site 3 out of 3 in the Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure of the Lipocalin Domain of Violaxanthin De-Epoxidase (Vde) at PH5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd403 b:32.6 occ:0.14 O B:HOH518 4.6 40.2 1.0 NE2 B:GLN176 4.7 21.0 1.0 CE1 B:HIS168 4.9 24.4 1.0 OE1 B:GLN176 4.9 33.8 1.0

P.Arnoux, T.Morosinotto, G.Saga, R.Bassi, D.Pignol. A Structural Basis For the pH-Dependent Xanthophyll Cycle in Arabidopsis Thaliana. Plant Cell V. 21 2036 2009.
ISSN: ISSN 1040-4651
PubMed: 19638474
DOI: 10.1105/TPC.109.068007