Zinc in PDB 5n4w: Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex

The structure of Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex, PDB code: 5n4w was solved by T.A.F.Cardote, M.S.Gadd, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.48 / 3.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	86.038, 190.962, 238.885, 90.00, 90.00, 90.00
R / Rfree (%)	30.2 / 34.6

The binding sites of Zinc atom in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex (pdb code 5n4w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex, PDB code: 5n4w:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase 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 CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:0.4 occ:1.00 SG R:CYS45 2.7 0.4 1.0 SG R:CYS83 2.9 0.7 1.0 ND1 R:HIS80 3.2 0.2 1.0 CB R:CYS83 3.3 0.9 1.0 SG R:CYS42 3.3 0.6 1.0 CB R:HIS80 3.4 0.9 1.0 CG R:HIS80 3.5 0.4 1.0 CB R:CYS45 4.0 0.6 1.0 CE1 R:HIS80 4.1 0.2 1.0 N R:HIS80 4.2 0.1 1.0 CB R:CYS42 4.2 0.0 1.0 O R:CYS42 4.3 0.2 1.0 N R:CYS45 4.3 0.9 1.0 CB R:CYS53 4.3 0.8 1.0 CA R:HIS80 4.4 0.8 1.0 CD2 R:HIS80 4.5 0.3 1.0 CA R:CYS45 4.7 0.6 1.0 CB R:ILE44 4.7 0.8 1.0 NE2 R:HIS80 4.8 0.5 1.0 CA R:CYS83 4.8 0.7 1.0 O R:HIS80 5.0 0.2 1.0 CG2 R:ILE44 5.0 0.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase 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 CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn202 b:0.9 occ:1.00 CE1 R:HIS82 2.2 0.2 1.0 NE2 R:HIS82 2.3 0.7 1.0 SG R:CYS56 2.4 1.0 1.0 SG R:CYS53 2.5 0.4 1.0 CB R:CYS56 3.0 0.3 1.0 SG R:CYS68 3.2 0.1 1.0 ND1 R:HIS82 3.5 1.0 1.0 CD2 R:HIS82 3.7 0.8 1.0 CB R:CYS53 3.9 0.8 1.0 CB R:CYS68 4.1 0.5 1.0 N R:CYS53 4.1 0.1 1.0 CA R:CYS56 4.2 0.3 1.0 N R:CYS56 4.2 0.7 1.0 CG R:HIS82 4.3 0.6 1.0 CA R:CYS53 4.5 0.1 1.0 C R:CYS53 5.0 0.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex


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 CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn203 b:0.4 occ:1.00 SG R:CYS75 2.5 0.2 1.0 CB R:CYS75 3.2 0.0 1.0 CD2 R:HIS77 3.3 0.2 1.0 OD2 R:ASP97 3.3 0.5 1.0 SG R:CYS94 3.4 0.9 1.0 O R:CYS75 3.7 0.9 1.0 CB R:HIS77 3.8 0.7 1.0 CG R:HIS77 3.8 0.4 1.0 CG R:ASP97 4.1 0.1 1.0 C R:CYS75 4.2 0.9 1.0 CB R:ASP97 4.3 0.8 1.0 CA R:CYS75 4.3 0.6 1.0 NE2 R:HIS77 4.5 0.2 1.0 CB R:CYS94 4.5 0.1 1.0 N R:HIS77 4.5 0.3 1.0 CA R:HIS77 4.8 0.0 1.0

T.A.F.Cardote, M.S.Gadd, A.Ciulli. Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex. Structure V. 25 901 2017.
ISSN: ISSN 1878-4186
PubMed: 28591624
DOI: 10.1016/J.STR.2017.04.009