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Cadmium in PDB 2jdz: Crystal Structure of Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose

Protein crystallography data

The structure of Crystal Structure of Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose, PDB code: 2jdz was solved by C.S.Nagano, L.Sanz, B.S.Cavada, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.14 / 2.10
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.222, 89.222, 106.069, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.9

Other elements in 2jdz:

The structure of Crystal Structure of Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose also contains other interesting chemical elements:

Manganese (Mn) 5 atoms
Bromine (Br) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose (pdb code 2jdz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Crystal Structure of Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose, PDB code: 2jdz:

Cadmium binding site 1 out of 1 in 2jdz

Go back to Cadmium Binding Sites List in 2jdz
Cadmium binding site 1 out of 1 in the Crystal Structure of Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


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 Recombinant Dioclea Guianensis Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd245

b:41.8
occ:1.00
OE1 A:GLU185 2.6 43.8 1.0
OE1 A:GLU89 2.8 23.7 1.0
OE2 A:GLU185 3.0 44.0 1.0
CD A:GLU185 3.2 42.9 1.0
CD A:GLU89 3.5 23.8 1.0
OE2 A:GLU89 3.6 28.8 1.0
O A:HOH2031 4.2 22.4 1.0
O A:HOH2051 4.2 62.5 1.0
CG A:GLU185 4.7 40.5 1.0
N A:LYS186 4.8 39.8 1.0
CG A:GLU89 4.9 24.7 1.0

Reference:

C.S.Nagano, J.J.Calvete, D.Barettino, A.Perez, B.S.Cavada, L.Sanz. Insights Into the Structural Basis of the pH-Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Biochem.J. V. 409 417 2008.
ISSN: ISSN 0264-6021
PubMed: 17937659
DOI: 10.1042/BJ20070942
Page generated: Sat Dec 12 08:17:20 2020

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