Zinc in PDB 2c7n: Human Rabex-5 Residues 1-74 in Complex with Ubiquitin

The structure of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin, PDB code: 2c7n was solved by L.Penengo, M.Mapelli, A.G.Murachelli, S.Confalioneri, L.Magri, A.Musacchio, P.P.Di Fiore, S.Polo, T.R.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.300, 68.900, 98.500, 108.20, 102.70, 90.40
R / Rfree (%)	19.5 / 23.8

The binding sites of Zinc atom in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin (pdb code 2c7n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin, PDB code: 2c7n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn499 b:39.7 occ:1.00 SG A:CYS19 2.1 41.8 1.0 SG A:CYS35 2.3 41.6 1.0 SG A:CYS23 2.4 48.0 1.0 SG A:CYS38 2.4 41.7 1.0 CB A:CYS19 3.2 46.1 1.0 CB A:CYS38 3.2 41.2 1.0 CB A:CYS23 3.4 46.7 1.0 CB A:CYS35 3.4 42.7 1.0 N A:CYS35 4.0 43.3 1.0 N A:CYS38 4.3 43.5 1.0 CA A:CYS35 4.3 43.0 1.0 CA A:CYS38 4.4 42.9 1.0 N A:CYS23 4.4 47.5 1.0 CB A:LYS21 4.5 50.0 1.0 CA A:CYS23 4.5 46.4 1.0 CA A:CYS19 4.6 46.1 1.0 C A:CYS35 4.9 43.3 1.0 O A:CYS35 4.9 42.5 1.0 CB A:TYR25 4.9 39.5 1.0

Zinc binding site 2 out of 6 in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn499 b:40.0 occ:1.00 SG C:CYS19 2.0 41.5 1.0 SG C:CYS35 2.3 40.6 1.0 SG C:CYS38 2.4 41.7 1.0 SG C:CYS23 2.4 47.2 1.0 CB C:CYS38 3.1 41.5 1.0 CB C:CYS19 3.2 44.4 1.0 CB C:CYS23 3.3 45.0 1.0 CB C:CYS35 3.5 42.3 1.0 N C:CYS35 4.0 42.0 1.0 N C:CYS38 4.2 45.1 1.0 CA C:CYS38 4.3 44.0 1.0 CA C:CYS35 4.4 41.9 1.0 CB C:LYS21 4.4 50.4 1.0 CA C:CYS23 4.5 45.1 1.0 N C:CYS23 4.5 45.3 1.0 CA C:CYS19 4.6 44.4 1.0 NH2 J:ARG54 4.9 39.9 1.0 C C:CYS35 4.9 42.5 1.0 CB C:TYR25 5.0 41.7 1.0

Zinc binding site 3 out of 6 in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn499 b:42.8 occ:1.00 SG E:CYS23 2.3 40.4 1.0 SG E:CYS38 2.3 45.3 1.0 SG E:CYS19 2.3 45.4 1.0 SG E:CYS35 2.4 41.6 1.0 CB E:CYS38 3.0 44.4 1.0 CB E:CYS19 3.2 46.0 1.0 CB E:CYS35 3.3 42.4 1.0 CB E:CYS23 3.5 43.1 1.0 N E:CYS35 4.0 43.3 1.0 N E:CYS38 4.1 46.6 1.0 CA E:CYS38 4.2 46.0 1.0 CA E:CYS35 4.2 43.9 1.0 CB E:LYS21 4.4 46.7 1.0 NZ E:LYS37 4.4 51.6 1.0 N E:CYS23 4.4 44.8 1.0 CA E:CYS23 4.5 44.0 1.0 CE E:LYS37 4.6 56.9 1.0 CA E:CYS19 4.6 46.0 1.0 C E:CYS35 4.8 45.3 1.0 CB E:TYR25 4.9 41.5 1.0 O E:CYS35 5.0 45.2 1.0

Zinc binding site 4 out of 6 in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn499 b:43.2 occ:1.00 SG G:CYS23 2.3 43.0 1.0 SG G:CYS19 2.4 43.6 1.0 SG G:CYS38 2.4 46.6 1.0 SG G:CYS35 2.5 41.6 1.0 CB G:CYS38 3.1 45.9 1.0 CB G:CYS19 3.2 43.0 1.0 CB G:CYS23 3.4 43.2 1.0 CB G:CYS35 3.5 43.1 1.0 N G:CYS35 4.0 43.3 1.0 N G:CYS38 4.2 45.8 1.0 CA G:CYS38 4.2 45.3 1.0 CA G:CYS35 4.3 44.2 1.0 N G:CYS23 4.5 44.0 1.0 CA G:CYS23 4.5 43.3 1.0 CB G:LYS21 4.5 49.8 1.0 CA G:CYS19 4.6 45.5 1.0 CB G:TYR25 4.9 40.8 1.0 C G:CYS35 4.9 44.2 1.0

Zinc binding site 5 out of 6 in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn499 b:75.8 occ:1.00 SG I:CYS19 2.2 43.9 1.0 SG I:CYS35 2.5 45.0 1.0 SG I:CYS23 2.7 45.8 1.0 SG I:CYS38 2.7 35.9 1.0 CB I:CYS23 2.8 45.2 1.0 CB I:CYS19 3.1 45.0 1.0 CB I:CYS38 3.2 39.1 1.0 CB I:CYS35 3.3 42.2 1.0 N I:CYS35 3.8 42.3 1.0 CA I:CYS35 4.2 42.5 1.0 CA I:CYS23 4.2 45.2 1.0 N I:CYS38 4.2 40.2 1.0 CA I:CYS38 4.3 39.9 1.0 CB I:LYS21 4.4 45.6 1.0 CA I:CYS19 4.5 44.9 1.0 N I:CYS23 4.7 45.3 1.0 C I:CYS35 4.8 42.5 1.0 O I:CYS35 4.9 42.7 1.0 C I:CYS23 4.9 45.2 1.0 C I:PHE34 5.0 42.5 1.0

Zinc binding site 6 out of 6 in the Human Rabex-5 Residues 1-74 in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Rabex-5 Residues 1-74 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn499 b:81.0 occ:1.00 SG K:CYS19 2.4 43.4 1.0 SG K:CYS23 2.5 46.2 1.0 CB K:CYS23 2.6 46.6 1.0 SG K:CYS38 2.7 37.9 1.0 SG K:CYS35 2.7 44.1 1.0 CB K:CYS19 3.1 45.8 1.0 CB K:CYS38 3.7 40.7 1.0 CB K:CYS35 3.7 42.3 1.0 CA K:CYS23 4.1 46.3 1.0 N K:CYS35 4.5 42.4 1.0 CB K:LYS21 4.5 48.3 1.0 N K:CYS38 4.5 41.3 1.0 CA K:CYS19 4.6 45.9 1.0 N K:CYS23 4.6 46.6 1.0 CA K:CYS35 4.7 42.3 1.0 CA K:CYS38 4.8 41.0 1.0 C K:CYS23 4.8 46.2 1.0 N K:GLY24 4.9 45.4 1.0

L.Penengo, M.Mapelli, A.G.Murachelli, S.Confalonieri, L.Magri, A.Musacchio, P.P.Di Fiore, S.Polo, T.R.Schneider. Crystal Structure of the Ubiquitin Binding Domains of Rabex-5 Reveals Two Modes of Interaction with Ubiquitin. Cell(Cambridge,Mass.) V. 124 1183 2006.
ISSN: ISSN 0092-8674
PubMed: 16499958
DOI: 10.1016/J.CELL.2006.02.020