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Cadmium in PDB 5nyy: Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II)

Enzymatic activity of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II)

All present enzymatic activity of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II):
2.7.11.1;

Protein crystallography data

The structure of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II), PDB code: 5nyy was solved by M.Meury, M.Knop, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.21 / 1.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.314, 67.648, 100.021, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 16.7

Other elements in 5nyy:

The structure of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) (pdb code 5nyy). 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 Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II), PDB code: 5nyy:

Cadmium binding site 1 out of 1 in 5nyy

Go back to Cadmium Binding Sites List in 5nyy
Cadmium binding site 1 out of 1 in the Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:11.0
occ:0.72
 O A:HOH521 2.3 25.1 0.8
O A:ACT405 2.4 24.3 0.9
OXT A:ACT405 2.4 24.8 0.9
SG A:CYS269 2.5 13.8 1.0
SG A:CYS274 2.5 12.8 1.0
C A:ACT405 2.7 7.3 0.9
CB A:CYS274 3.3 14.0 1.0
CB A:CYS269 3.4 11.5 1.0
CA A:CYS269 3.7 11.0 1.0
OH A:TYR273 3.8 12.3 1.0
CZ A:TYR273 4.1 12.6 1.0
CH3 A:ACT405 4.2 22.2 0.9
CE2 A:TYR273 4.2 12.5 1.0
NE1 A:TRP228 4.3 9.5 1.0
N A:CYS269 4.4 8.8 1.0
CB A:ARG276 4.4 13.1 1.0
CZ2 A:TRP228 4.4 10.8 1.0
O A:HOH513 4.7 22.8 1.0
CE2 A:TRP228 4.8 8.6 1.0
CA A:CYS274 4.8 17.0 1.0
O A:HOH760 4.8 11.5 1.0
OG A:SER266 4.9 9.1 1.0
C A:CYS269 4.9 10.9 1.0
C A:LEU268 4.9 9.6 1.0
CE1 A:TYR273 4.9 12.1 1.0
N A:HIS270 5.0 11.9 1.0
N A:ARG276 5.0 12.0 1.0

Reference:

M.Meury, M.Knop, F.P.Seebeck. Structural Basis For Copper-Oxygen Mediated C-H Bond Activation By the Formylglycine-Generating Enzyme. Angew. Chem. Int. Ed. Engl. V. 56 8115 2017.
ISSN: ESSN 1521-3773
PubMed: 28544744
DOI: 10.1002/ANIE.201702901
Page generated: Thu Jul 10 14:31:12 2025

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