Zinc in PDB 2yhn: The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor

The structure of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor, PDB code: 2yhn was solved by L.Fairall, B.T.Goult, C.J.Millard, P.Tontonoz, J.W.R.Schwabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.37 / 3.00
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.260, 22.770, 87.838, 90.00, 116.82, 90.00
R / Rfree (%)	22.8 / 29.7

The binding sites of Zinc atom in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor (pdb code 2yhn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor, PDB code: 2yhn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:20.0 occ:1.00 SG A:CYS390 2.2 29.1 1.0 SG A:CYS387 2.3 16.3 1.0 SG A:CYS411 2.3 14.7 1.0 SG A:CYS408 2.3 11.0 1.0 CB A:CYS387 3.1 14.4 1.0 CB A:CYS411 3.2 9.5 1.0 CB A:CYS390 3.2 12.3 1.0 CB A:CYS408 3.6 10.3 1.0 N A:CYS390 3.7 18.2 1.0 CG2 A:VAL389 3.9 13.1 1.0 N A:CYS408 4.0 8.7 1.0 CA A:CYS390 4.0 18.4 1.0 N A:CYS411 4.2 10.6 1.0 CA A:CYS411 4.3 9.7 1.0 CA A:CYS408 4.4 7.5 1.0 CA A:CYS387 4.6 18.8 1.0 O A:CYS408 4.6 12.8 1.0 N A:CYS391 4.8 23.9 1.0 CB A:GLU393 4.8 26.9 1.0 C A:CYS390 4.8 25.0 1.0 C A:CYS408 4.8 10.8 1.0 OE2 A:GLU393 4.8 24.8 1.0 C A:VAL389 4.9 27.9 1.0

Zinc binding site 2 out of 4 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:8.1 occ:1.00 SG A:CYS402 1.9 14.8 1.0 ND1 A:HIS404 2.0 22.0 1.0 SG A:CYS421 2.1 14.8 1.0 SG A:CYS418 2.2 8.5 1.0 CE1 A:HIS404 2.9 21.8 1.0 CB A:CYS418 3.1 10.6 1.0 CG A:HIS404 3.1 32.9 1.0 CB A:CYS421 3.4 12.7 1.0 CB A:HIS404 3.5 14.7 1.0 CB A:CYS402 3.6 14.0 1.0 N A:CYS421 3.7 7.0 1.0 NE2 A:HIS404 4.0 16.3 1.0 CA A:CYS421 4.1 9.0 1.0 OG A:SER423 4.1 19.0 1.0 CD2 A:HIS404 4.1 20.2 1.0 N A:HIS404 4.4 15.8 1.0 CB A:VAL420 4.4 17.2 1.0 CA A:CYS402 4.5 6.2 1.0 CA A:CYS418 4.5 9.5 1.0 CA A:HIS404 4.6 11.2 1.0 C A:CYS402 4.7 6.5 1.0 C A:VAL420 4.7 11.5 1.0 C A:CYS421 4.8 13.3 1.0 N A:VAL420 4.9 7.5 1.0 O A:CYS402 4.9 9.0 1.0 N A:ARG422 4.9 25.5 1.0 CA A:VAL420 4.9 11.1 1.0 CD2 A:PHE399 5.0 15.4 1.0 C A:CYS418 5.0 14.7 1.0

Zinc binding site 3 out of 4 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:23.5 occ:1.00 SG B:CYS390 2.2 35.1 1.0 SG B:CYS411 2.3 21.5 1.0 SG B:CYS387 2.3 26.2 1.0 SG B:CYS408 2.3 1.7 1.0 CB B:CYS411 3.1 8.2 1.0 CB B:CYS390 3.2 39.7 1.0 CB B:CYS387 3.2 34.0 1.0 OE1 B:GLU393 3.5 95.2 1.0 CB B:CYS408 3.6 13.6 1.0 N B:CYS390 3.8 28.4 1.0 CG2 B:VAL389 4.0 12.3 1.0 N B:CYS408 4.0 8.0 1.0 CA B:CYS390 4.1 28.9 1.0 N B:CYS411 4.2 11.9 1.0 CA B:CYS411 4.2 6.5 1.0 CA B:CYS408 4.3 10.0 1.0 N B:CYS391 4.7 28.4 1.0 CA B:CYS387 4.7 27.7 1.0 CD B:GLU393 4.7 85.5 1.0 C B:CYS390 4.7 34.2 1.0 OG B:SER410 4.8 51.5 1.0 C B:CYS408 4.9 15.8 1.0

Zinc binding site 4 out of 4 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:10.3 occ:1.00 ND1 B:HIS404 2.0 16.5 1.0 SG B:CYS418 2.1 15.4 1.0 SG B:CYS421 2.2 5.3 1.0 SG B:CYS402 2.3 9.8 1.0 CB B:CYS418 2.9 8.0 1.0 CE1 B:HIS404 3.0 9.6 1.0 CG B:HIS404 3.0 17.1 1.0 CB B:CYS402 3.1 3.2 1.0 CB B:HIS404 3.4 4.5 1.0 CB B:CYS421 3.5 7.1 1.0 N B:CYS421 3.9 12.1 1.0 NE2 B:HIS404 4.1 4.8 1.0 CD2 B:HIS404 4.1 9.6 1.0 CA B:CYS421 4.3 9.8 1.0 OG B:SER423 4.3 37.0 1.0 CA B:CYS402 4.4 6.5 1.0 CA B:CYS418 4.4 8.9 1.0 N B:HIS404 4.4 12.1 1.0 CA B:HIS404 4.5 6.9 1.0 C B:CYS402 4.6 6.0 1.0 CB B:VAL420 4.7 9.1 1.0 O B:CYS402 4.8 8.7 1.0 C B:VAL420 4.9 12.1 1.0 N B:GLY403 5.0 6.0 1.0 C B:CYS421 5.0 7.8 1.0

L.Zhang, L.Fairall, B.T.Goult, A.C.Calkin, C.Hong, C.J.Millard, P.Tontonoz, J.W.R.Schwabe. The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor. Genes Dev. V. 25 1262 2011.
ISSN: ISSN 0890-9369
PubMed: 21685362
DOI: 10.1101/GAD.2056211