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

Enzymatic activity of 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;

Protein crystallography data

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

Gadolinium Binding Sites:

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 3cqr

Go back to Gadolinium Binding Sites List in 3cqr
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 3cqr

Go back to Gadolinium Binding Sites List in 3cqr
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 3cqr

Go back to Gadolinium Binding Sites List in 3cqr
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

Reference:

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
Page generated: Sun Dec 13 18:59:25 2020

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