Zinc in PDB 5kzz: Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form

The structure of Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form, PDB code: 5kzz was solved by P.Huang, Y.Kim, A.Salic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.63 / 1.33
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.656, 37.352, 43.151, 90.00, 97.46, 90.00
R / Rfree (%)	15.6 / 18.7

The binding sites of Zinc atom in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form (pdb code 5kzz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form, PDB code: 5kzz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:14.3 occ:0.70 O2 A:GOL207 2.0 18.5 1.0 OE1 A:GLU154 2.0 21.3 1.0 OXT A:ACT201 2.0 19.0 1.0 OE1 A:GLU149 2.1 20.1 1.0 O1 A:GOL207 2.3 23.6 1.0 OE2 A:GLU154 2.4 23.0 1.0 CD A:GLU154 2.5 22.6 1.0 C2 A:GOL207 2.9 22.0 1.0 CD A:GLU149 3.0 21.8 1.0 C1 A:GOL207 3.0 22.9 1.0 C A:ACT201 3.0 20.7 1.0 ZN A:ZN203 3.1 14.2 0.7 OE2 A:GLU149 3.3 20.5 1.0 O A:ACT201 3.3 20.3 1.0 O A:HOH315 3.8 31.2 1.0 CG A:GLU154 4.0 26.5 1.0 O A:HOH340 4.0 20.0 1.0 N A:GLY118 4.1 15.6 1.0 C3 A:GOL207 4.2 23.0 1.0 O3 A:GOL207 4.3 22.1 1.0 CG A:GLU149 4.3 24.5 1.0 CA A:GLY118 4.4 16.4 1.0 CH3 A:ACT201 4.4 20.9 1.0 N A:GLY150 4.4 22.4 1.0 CB A:GLN117 4.6 14.5 1.0 CA A:GLU149 4.8 18.4 1.0 CB A:GLU154 4.8 33.5 1.0 CB A:GLU149 4.9 22.6 1.0 C A:GLN117 4.9 14.5 1.0 CG A:GLN117 5.0 15.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:14.2 occ:0.72 OE2 A:GLU149 1.9 20.5 1.0 O2 A:GOL207 2.0 18.5 1.0 O A:ACT201 2.1 20.3 1.0 O3 A:GOL207 2.2 22.1 1.0 CD A:GLU149 2.9 21.8 1.0 C2 A:GOL207 3.0 22.0 1.0 C3 A:GOL207 3.0 23.0 1.0 C A:ACT201 3.1 20.7 1.0 ZN A:ZN202 3.1 14.3 0.7 OE1 A:GLU149 3.2 20.1 1.0 OXT A:ACT201 3.3 19.0 1.0 C1 A:GOL207 3.6 22.9 1.0 O A:HOH315 3.8 31.2 1.0 O A:HOH357 4.1 28.6 1.0 O1 A:GOL207 4.1 23.6 1.0 CG A:GLU149 4.2 24.5 1.0 CH3 A:ACT201 4.4 20.9 1.0 OE2 A:GLU154 4.9 23.0 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:27.9 occ:0.67 OD1 A:ASP73 2.0 21.4 1.0 NZ A:LYS47 2.0 23.3 1.0 O A:HOH369 2.2 38.7 1.0 O A:HOH366 2.4 35.9 1.0 CG A:ASP73 2.9 20.1 1.0 CE A:LYS47 3.1 24.1 1.0 OD2 A:ASP73 3.1 22.8 1.0 CD A:LYS47 3.4 22.6 1.0 O A:HOH360 3.9 22.7 1.0 CG A:LYS47 4.0 19.8 1.0 CB A:ASP73 4.3 16.1 1.0 CA A:ASP73 4.7 13.4 1.0 N A:ASP73 4.8 12.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:20.3 occ:0.79 OD1 A:ASP93 2.0 16.1 1.0 CG A:ASP93 2.8 13.8 1.0 OD2 A:ASP93 2.9 16.2 1.0 O A:HOH361 3.3 44.2 1.0 O A:HOH337 3.6 29.8 1.0 CB A:ASP93 4.2 14.1 1.0 O A:HOH331 4.3 26.1 1.0 NH1 A:ARG96 4.5 28.4 1.0 CA A:ASP93 4.9 13.3 1.0 O A:ASP93 4.9 12.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Xenopus Smoothened Cysteine-Rich Domain (Crd) in Its Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:28.7 occ:0.66 O A:HOH302 2.1 28.7 1.0 OD2 A:ASP138 2.1 31.1 1.0 O A:HOH354 2.6 41.8 1.0 CG A:ASP138 2.8 31.0 1.0 OD1 A:ASP138 2.8 31.3 1.0 OD2 A:ASP145 3.9 32.0 1.0 OG1 A:THR143 4.1 20.6 1.0 OD1 A:ASP145 4.1 28.6 1.0 CB A:ASP138 4.2 29.0 1.0 CG A:ASP145 4.4 28.4 1.0 CB A:THR143 4.8 18.8 1.0 CB A:TYR146 4.9 20.2 1.0 CG2 A:THR143 4.9 20.0 1.0 O A:HOH358 5.0 34.6 1.0

P.Huang, D.Nedelcu, M.Watanabe, C.Jao, Y.Kim, J.Liu, A.Salic. Cellular Cholesterol Directly Activates Smoothened in Hedgehog Signaling. Cell V. 166 1176 2016.
ISSN: ISSN 1097-4172
PubMed: 27545348
DOI: 10.1016/J.CELL.2016.08.003