Zinc in PDB 5vzu: Crystal Structure of the SKP1-FBXO31-Cyclin D1 Complex

The structure of Crystal Structure of the SKP1-FBXO31-Cyclin D1 Complex, PDB code: 5vzu was solved by Y.Li, K.Jin, B.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.679, 156.235, 155.522, 90.00, 104.21, 90.00
R / Rfree (%)	18 / 23.3

The binding sites of Zinc atom in the Crystal Structure of the SKP1-FBXO31-Cyclin D1 Complex (pdb code 5vzu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the SKP1-FBXO31-Cyclin D1 Complex, PDB code: 5vzu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the SKP1-FBXO31-Cyclin D1 Complex


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 SKP1-FBXO31-Cyclin D1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:41.7 occ:1.00 NE2 B:HIS236 2.2 65.3 1.0 NE2 B:HIS214 2.3 75.5 1.0 SG B:CYS206 2.3 60.5 1.0 SG B:CYS230 2.3 57.3 1.0 CB B:CYS206 3.1 59.2 1.0 CB B:CYS230 3.1 58.7 1.0 CE1 B:HIS214 3.1 74.2 1.0 CE1 B:HIS236 3.2 71.2 1.0 CD2 B:HIS214 3.2 80.2 1.0 CD2 B:HIS236 3.3 73.1 1.0 O B:TYR208 4.0 91.0 1.0 ND1 B:HIS214 4.2 83.3 1.0 ND1 B:HIS236 4.3 77.0 1.0 CG B:HIS214 4.3 81.6 1.0 CB B:TYR208 4.3 75.2 1.0 CA B:CYS206 4.4 62.3 1.0 CG B:HIS236 4.4 75.4 1.0 CA B:CYS230 4.4 65.7 1.0 C B:CYS206 4.5 66.2 1.0 O B:CYS206 4.5 75.5 1.0 N B:TYR208 4.6 66.5 1.0 O B:GLN232 4.7 83.4 1.0 C B:TYR208 4.8 73.9 1.0 CA B:TYR208 4.9 71.0 1.0 ND2 B:ASN282 5.0 65.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the SKP1-FBXO31-Cyclin D1 Complex


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 SKP1-FBXO31-Cyclin D1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:38.7 occ:1.00 NE2 D:HIS236 2.3 48.5 1.0 NE2 D:HIS214 2.3 60.0 1.0 SG D:CYS230 2.3 59.5 1.0 SG D:CYS206 2.3 59.0 1.0 CE1 D:HIS236 3.2 55.7 1.0 CD2 D:HIS214 3.2 65.0 1.0 CB D:CYS230 3.2 59.5 1.0 CD2 D:HIS236 3.3 59.2 1.0 CE1 D:HIS214 3.3 60.0 1.0 CB D:CYS206 3.3 63.5 1.0 ND1 D:HIS236 4.3 64.2 1.0 O D:GLN232 4.3 52.0 1.0 CG D:HIS214 4.4 59.2 1.0 ND1 D:HIS214 4.4 66.3 1.0 CG D:HIS236 4.4 60.9 1.0 CB D:TYR208 4.5 70.7 1.0 O D:TYR208 4.6 76.4 1.0 CA D:CYS230 4.6 53.0 1.0 CA D:CYS206 4.6 58.3 1.0 C D:GLN232 4.7 50.8 1.0 CA D:THR233 4.8 55.4 1.0 C D:CYS206 4.8 60.9 1.0 CB D:HIS235 4.9 55.5 1.0 N D:TYR208 4.9 76.4 1.0 O D:CYS206 4.9 80.4 1.0

Y.Li, K.Jin, E.Bunker, X.Zhang, X.Luo, X.Liu, B.Hao. Structural Basis of the Phosphorylation-Independent Recognition of Cyclin D1 By the SCFFBXO31 Ubiquitin Ligase. Proc. Natl. Acad. Sci. V. 115 319 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29279382
DOI: 10.1073/PNAS.1708677115