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

Enzymatic activity of 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;

Protein crystallography data

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

Cadmium Binding Sites:

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 2x7k

Go back to Cadmium Binding Sites List in 2x7k
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 2x7k

Go back to Cadmium Binding Sites List in 2x7k
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

Reference:

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
Page generated: Fri Aug 28 13:15:15 2020
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