Zinc in PDB 2vhf: Structure of the Cyld Usp Domain

All present enzymatic activity of Structure of the Cyld Usp Domain:
3.1.2.15;

The structure of Structure of the Cyld Usp Domain, PDB code: 2vhf was solved by D.Komander, C.J.Lord, H.Scheel, S.Swift, K.Hofmann, A.Ashworth, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.79 / 2.8
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.494, 89.083, 171.806, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.1

The binding sites of Zinc atom in the Structure of the Cyld Usp Domain (pdb code 2vhf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Cyld Usp Domain, PDB code: 2vhf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Cyld Usp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Cyld Usp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1957 b:63.4 occ:1.00 SG A:CYS817 2.3 36.0 1.0 SG A:CYS791 2.6 48.5 1.0 SG A:CYS820 2.7 35.2 1.0 SG A:CYS788 2.8 36.6 1.0 CB A:CYS820 2.9 41.0 1.0 CB A:CYS788 3.6 34.7 1.0 CB A:CYS817 3.6 47.5 1.0 CB A:CYS791 3.6 26.6 1.0 N A:CYS820 3.9 45.3 1.0 CA A:CYS820 4.0 45.3 1.0 N A:CYS817 4.1 35.9 1.0 N A:CYS791 4.3 36.8 1.0 CA A:CYS817 4.4 48.9 1.0 CA A:CYS791 4.6 35.4 1.0 N A:GLY793 4.8 27.4 1.0 O A:CYS817 4.8 53.3 1.0 C A:CYS817 4.9 56.8 1.0 CB A:ILE790 5.0 33.7 1.0 CA A:CYS788 5.0 39.4 1.0

Zinc binding site 2 out of 4 in the Structure of the Cyld Usp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Cyld Usp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1958 b:44.0 occ:1.00 ND1 A:HIS833 2.4 34.8 1.0 SG A:CYS799 2.6 50.8 1.0 SG A:CYS802 2.7 35.2 1.0 NE2 A:HIS825 2.7 50.8 1.0 CB A:CYS802 3.2 43.3 1.0 CB A:CYS799 3.2 35.2 1.0 CG A:HIS833 3.2 36.0 1.0 CB A:HIS833 3.4 36.4 1.0 CE1 A:HIS833 3.4 34.5 1.0 CE1 A:HIS825 3.5 45.9 1.0 CD2 A:HIS825 3.6 58.5 1.0 N A:CYS802 3.7 44.9 1.0 CA A:CYS802 3.8 45.7 1.0 C A:GLU801 4.2 48.9 1.0 CD2 A:HIS833 4.4 37.3 1.0 NE2 A:HIS833 4.5 35.7 1.0 CB A:GLU801 4.5 61.9 1.0 O A:CYS799 4.5 32.9 1.0 ND1 A:HIS825 4.6 53.8 1.0 CA A:CYS799 4.6 34.2 1.0 CG A:HIS825 4.7 56.6 1.0 CG1 A:VAL824 4.7 39.8 1.0 C A:CYS799 4.8 34.6 1.0 CA A:GLU801 4.8 50.5 1.0 O A:GLU801 4.8 54.7 1.0 CA A:HIS833 4.8 38.9 1.0 CD A:ARG830 4.9 43.5 1.0 N A:GLU801 5.0 42.7 1.0

Zinc binding site 3 out of 4 in the Structure of the Cyld Usp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Cyld Usp Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1956 b:47.9 occ:1.00 SG B:CYS791 2.3 32.6 1.0 SG B:CYS788 2.5 55.4 1.0 SG B:CYS820 2.6 40.8 1.0 CB B:CYS788 2.8 37.1 1.0 SG B:CYS817 2.8 47.9 1.0 CB B:CYS820 3.3 32.8 1.0 CB B:CYS817 3.4 24.9 1.0 N B:CYS791 3.5 44.1 1.0 CB B:CYS791 3.5 59.1 1.0 N B:CYS817 3.9 31.0 1.0 CA B:CYS791 3.9 48.2 1.0 CA B:CYS788 4.3 45.4 1.0 CA B:CYS817 4.3 29.7 1.0 N B:GLY793 4.3 48.0 1.0 N B:GLY792 4.4 25.1 1.0 CB B:ILE790 4.5 45.5 1.0 C B:CYS791 4.5 41.1 1.0 CA B:CYS820 4.6 26.2 1.0 C B:ILE790 4.6 55.6 1.0 N B:CYS820 4.7 32.3 1.0 C B:CYS788 4.8 46.3 1.0 CA B:GLY793 4.8 26.4 1.0 N B:ILE790 4.8 49.1 1.0 CA B:ILE790 4.9 50.2 1.0 C B:CYS817 5.0 37.0 1.0 O B:CYS788 5.0 29.3 1.0 O B:CYS817 5.0 28.6 1.0

Zinc binding site 4 out of 4 in the Structure of the Cyld Usp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Cyld Usp Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1957 b:67.9 occ:1.00 NE2 B:HIS825 2.2 29.3 1.0 SG B:CYS802 2.7 83.3 1.0 SG B:CYS799 2.7 57.3 1.0 ND1 B:HIS833 2.9 0.5 1.0 CD2 B:HIS825 3.1 30.1 1.0 CE1 B:HIS825 3.2 32.3 1.0 CB B:CYS802 3.3 42.0 1.0 CB B:CYS799 3.4 32.5 1.0 CG B:HIS833 3.6 0.1 1.0 CB B:HIS833 3.7 91.5 1.0 CE1 B:HIS833 3.9 0.8 1.0 CA B:CYS802 4.1 48.6 1.0 N B:CYS802 4.1 57.8 1.0 CG B:HIS825 4.2 30.1 1.0 ND1 B:HIS825 4.3 30.6 1.0 CD B:ARG830 4.4 70.3 1.0 CG1 B:VAL824 4.5 42.8 1.0 CG B:ARG830 4.6 82.0 1.0 C B:GLU801 4.7 61.4 1.0 CB B:ARG830 4.7 92.1 1.0 CD2 B:HIS833 4.7 0.3 1.0 NE2 B:HIS833 4.8 0.3 1.0 CA B:CYS799 4.9 42.2 1.0 CB B:TYR835 4.9 44.0 1.0 CB B:GLU801 5.0 64.9 1.0

D.Komander, C.J.Lord, H.Scheel, S.Swift, K.Hofmann, A.Ashworth, D.Barford. The Structure of the Cyld Usp Domain Explains Its Specificity For LYS63-Linked Polyubiquitin and Reveals A B-Box Module Mol.Cell.Biol. V. 29 451 2008.
ISSN: ISSN 0270-7306
PubMed: 18313383
DOI: 10.1016/J.MOLCEL.2007.12.018