Cadmium in PDB 7qst: Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)

The structure of Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A), PDB code: 7qst was solved by H.M.Beyer, H.Iwai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.51 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.08, 81.87, 67.69, 90, 112.85, 90
R / Rfree (%)	18.3 / 24.3

The structure of Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A) also contains other interesting chemical elements:

Nickel

(Ni)

3 atoms

The binding sites of Cadmium atom in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A) (pdb code 7qst). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A), PDB code: 7qst:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)


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 Homing Endonuclease-Associated Phovma Intein (C1A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:79.2 occ:1.00 OE1 A:GLU178 2.5 72.4 1.0 OE2 A:GLU178 2.8 102.3 1.0 CD A:GLU178 3.0 94.1 1.0 CG A:GLU178 4.5 80.2 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Homing Endonuclease-Associated Phovma Intein (C1A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:93.2 occ:0.58 OE2 A:GLU37 2.7 72.8 1.0 OE1 A:GLU37 2.9 68.7 1.0 CD A:GLU37 3.2 65.1 1.0 C A:SER-2 3.3 73.5 1.0 CA A:SER-2 3.6 72.6 1.0 O A:SER-2 3.6 90.0 1.0 N A:GLY-1 3.6 58.4 1.0 N A:SER-2 3.6 59.0 1.0 CA A:GLY-1 4.4 71.6 1.0 OH A:TYR65 4.5 56.4 1.0 CG A:GLU37 4.7 54.2 1.0 CZ2 A:TRP39 5.0 50.3 1.0

H.M.Beyer, H.Iwai. Structural Basis For the Propagation of Homing Endonuclease-Associated Inteins. Front Mol Biosci V. 9 55511 2022.
ISSN: ESSN 2296-889X
PubMed: 35372505
DOI: 10.3389/FMOLB.2022.855511