Cadmium in PDB 8vqk: Ycjn From Escherichia Coli

The structure of Ycjn From Escherichia Coli, PDB code: 8vqk was solved by M.A.Trevino, D.Fernandez, N.G.Sharaf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.65 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.216, 63.29, 74.314, 110.01, 91.09, 118.66
R / Rfree (%)	21.5 / 26.4

The structure of Ycjn From Escherichia Coli also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Cadmium atom in the Ycjn From Escherichia Coli (pdb code 8vqk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Ycjn From Escherichia Coli, PDB code: 8vqk:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Ycjn From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Ycjn From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd502 b:57.2 occ:1.00 OE1 B:GLU316 2.6 46.4 1.0 OE2 B:GLU316 2.7 44.2 1.0 O B:HOH717 2.8 52.3 1.0 O B:HOH735 2.8 50.6 1.0 CD B:GLU316 3.0 42.3 1.0 O A:HOH732 3.7 63.7 1.0 CG2 B:THR112 4.0 37.2 1.0 OG1 B:THR112 4.3 33.8 1.0 CG B:GLU316 4.5 33.4 1.0 CB B:THR112 4.5 37.3 1.0

Cadmium binding site 2 out of 2 in the Ycjn From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Ycjn From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd503 b:31.2 occ:1.00 O B:HOH659 2.5 32.3 1.0 NE2 B:HIS403 2.5 25.8 1.0 O B:HOH715 2.7 22.3 1.0 CD2 B:HIS403 3.2 31.9 1.0 CE1 B:HIS403 3.7 35.9 1.0 CG B:HIS403 4.4 27.7 1.0 ND1 B:HIS403 4.7 30.4 1.0 OE1 B:GLU194 4.8 38.0 1.0 O B:HOH606 4.9 39.1 1.0 CG1 B:VAL407 5.0 33.9 1.0

M.A.Trevino, K.A.Amankwah, D.Fernandez, S.A.Weston, C.J.Stewart, J.M.Gallardo, M.Shahgholi, N.G.Sharaf. Expression, Purification, and Characterization of Diacylated Lipo-Ycjn From Escherichia Coli J.Biol.Chem. 2024.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2024.107853