Zinc in PDB 2fif: Crystal Structure of A Bovine Rabex-5 Fragment Complexed with Ubiquitin

The structure of Crystal Structure of A Bovine Rabex-5 Fragment Complexed with Ubiquitin, PDB code: 2fif was solved by S.Lee, J.H.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.91 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.200, 44.420, 69.170, 90.00, 108.98, 90.00
R / Rfree (%)	22.8 / 26.3

The binding sites of Zinc atom in the Crystal Structure of A Bovine Rabex-5 Fragment Complexed with Ubiquitin (pdb code 2fif). 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 A Bovine Rabex-5 Fragment Complexed with Ubiquitin, PDB code: 2fif:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of A Bovine Rabex-5 Fragment Complexed with Ubiquitin


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 A Bovine Rabex-5 Fragment Complexed with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:48.4 occ:1.00 SG B:CYS23 2.3 47.8 1.0 SG B:CYS19 2.3 48.9 1.0 SG B:CYS35 2.3 45.9 1.0 SG B:CYS38 2.4 42.9 1.0 CB B:CYS19 3.2 48.2 1.0 CB B:CYS38 3.3 43.3 1.0 CB B:CYS23 3.3 47.1 1.0 CB B:CYS35 3.5 46.4 1.0 N B:CYS35 4.1 46.5 1.0 N B:CYS38 4.4 43.9 1.0 CA B:CYS35 4.4 46.1 1.0 CB B:LYS21 4.4 47.4 1.0 CA B:CYS38 4.4 43.8 1.0 N B:CYS23 4.5 47.2 1.0 CA B:CYS23 4.5 47.4 1.0 CA B:CYS19 4.7 48.1 1.0 NH1 E:ARG54 5.0 45.9 1.0 C B:CYS35 5.0 46.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of A Bovine Rabex-5 Fragment Complexed with Ubiquitin


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 A Bovine Rabex-5 Fragment Complexed with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn902 b:62.0 occ:1.00 SG D:CYS38 2.3 47.3 1.0 SG D:CYS23 2.4 49.1 1.0 SG D:CYS19 2.4 47.5 1.0 SG D:CYS35 2.5 48.2 1.0 CB D:CYS38 3.1 47.9 1.0 CB D:CYS19 3.3 47.5 1.0 CB D:CYS35 3.5 47.7 1.0 CB D:CYS23 3.5 48.3 1.0 N D:CYS35 4.0 47.6 1.0 CA D:CYS38 4.3 47.9 1.0 CB D:LYS21 4.3 48.5 1.0 N D:CYS38 4.3 48.1 1.0 CA D:CYS35 4.3 47.8 1.0 N D:CYS23 4.5 48.4 1.0 CA D:CYS23 4.6 48.4 1.0 CA D:CYS19 4.8 47.6 1.0 CB D:TYR25 4.9 47.6 1.0 C D:CYS35 5.0 47.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of A Bovine Rabex-5 Fragment Complexed with Ubiquitin


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 A Bovine Rabex-5 Fragment Complexed with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn903 b:0.5 occ:1.00 SG F:CYS35 2.5 47.2 1.0 SG F:CYS38 2.9 47.4 1.0 SG F:CYS23 2.9 48.3 1.0 SG F:CYS19 2.9 50.8 1.0 CB F:CYS35 3.4 47.0 1.0 CB F:CYS38 3.4 46.8 1.0 N F:CYS35 3.5 47.0 1.0 CA F:CYS35 4.0 47.0 1.0 CB F:LYS21 4.1 49.1 1.0 CB F:CYS23 4.3 48.2 1.0 CB F:CYS19 4.5 50.4 1.0 N F:CYS23 4.5 48.4 1.0 C F:PHE34 4.6 47.0 1.0 CA F:CYS38 4.7 46.9 1.0 CA F:PHE34 4.7 46.9 1.0 N F:GLY22 4.7 48.9 1.0 C F:CYS35 4.8 47.0 1.0 N F:CYS38 4.8 46.9 1.0 O F:CYS35 4.8 47.0 1.0 N F:LYS21 4.8 49.4 1.0 CG F:LYS21 4.9 49.0 1.0 CA F:LYS21 4.9 49.1 1.0 CA F:CYS23 5.0 48.2 1.0

S.Lee, Y.C.Tsai, R.Mattera, W.J.Smith, M.S.Kostelansky, A.M.Weissman, J.S.Bonifacino, J.H.Hurley. Structural Basis For Ubiquitin Recognition and Autoubiquitination By Rabex-5 Nat.Struct.Mol.Biol. V. 13 264 2006.
ISSN: ISSN 1545-9993
PubMed: 16462746
DOI: 10.1038/NSMB1064