Cadmium in PDB 2x7k: The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip

All present enzymatic activity of The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip:
5.2.1.8;

The structure of The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip, PDB code: 2x7k was solved by C.M.Stegmann, R.Luehrmann, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.28 / 1.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.218, 35.701, 45.851, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 14.9

The structure of The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cadmium atom in the The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip (pdb code 2x7k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip, PDB code: 2x7k:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1167 b:7.1 occ:1.00 NE2 A:HIS31 2.3 7.8 1.0 OD2 A:ASP89 2.3 8.0 1.0 OD1 A:ASP89 2.4 7.7 1.0 O A:HOH2190 2.4 9.4 1.0 O A:HOH2087 2.5 33.8 1.0 CG A:ASP89 2.7 8.2 1.0 CE1 A:HIS31 3.3 10.0 1.0 CD2 A:HIS31 3.3 7.0 1.0 HE1 A:HIS31 3.4 12.1 1.0 HD2 A:HIS31 3.4 8.4 1.0 CB A:ASP89 4.2 7.2 1.0 HB3 A:HIS87 4.2 9.3 1.0 ND1 A:HIS31 4.4 9.9 1.0 CG A:HIS31 4.4 6.0 1.0 HG A:LEU90 4.4 12.3 1.0 HB2 A:ASP89 4.5 8.7 1.0 HB3 A:ASP89 4.6 8.7 1.0 ND1 A:HIS87 4.8 7.3 1.0 H A:ASP89 4.9 7.9 1.0 HE3 A:LYS30 4.9 41.5 0.3 CB A:HIS87 5.0 7.8 1.0

Cadmium binding site 2 out of 2 in the The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Crystal Structure of PPIL1 in Complex with Cyclosporine A Suggests A Binding Mode For Skip within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1168 b:7.6 occ:0.99 OE1 A:GLU26 2.2 9.6 1.0 O A:HOH2239 2.5 6.4 1.0 SG A:CYS133 2.5 7.5 1.0 CD A:GLU26 2.8 8.7 1.0 OE2 A:GLU26 2.9 9.9 1.0 HB2 A:CYS133 3.2 8.6 1.0 HH21 A:ARG131 3.2 12.9 1.0 HA A:CYS133 3.3 9.7 1.0 CB A:CYS133 3.4 7.2 1.0 HE A:ARG131 3.6 10.5 1.0 NH2 A:ARG131 3.8 10.7 1.0 CA A:CYS133 3.9 8.1 1.0 NE A:ARG131 4.2 8.7 1.0 HB3 A:CYS133 4.2 8.6 1.0 CG A:GLU26 4.2 8.2 1.0 HH22 A:ARG131 4.3 12.9 1.0 CZ A:ARG131 4.4 9.6 1.0 HG2 A:GLU26 4.4 9.8 1.0 O A:HOH2244 4.5 29.6 1.0 HG3 A:ARG131 4.7 7.9 1.0 HG3 A:GLU26 4.8 9.8 1.0 HB3 A:GLU26 4.8 9.3 1.0 C A:CYS133 4.9 10.0 1.0 N A:CYS133 4.9 6.6 1.0 O A:CYS133 4.9 15.3 1.0

C.M.Stegmann, R.Luehrmann, M.C.Wahl. The Crystal Structure of PPIL1 Bound to Cyclosporine A Suggests A Binding Mode For A Linear Epitope of the Skip Protein. Plos One V. 5 13 2010.
ISSN: ESSN 1932-6203
PubMed: 20368803
DOI: 10.1371/JOURNAL.PONE.0010013