Zinc in PDB 4d10: Crystal Structure of the COP9 Signalosome

The structure of Crystal Structure of the COP9 Signalosome, PDB code: 4d10 was solved by R.D.Bunker, G.M.Lingaraju, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.87 / 3.80
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	151.615, 151.615, 343.069, 90.00, 90.00, 120.00
R / Rfree (%)	19.94 / 22.75

The binding sites of Zinc atom in the Crystal Structure of the COP9 Signalosome (pdb code 4d10). 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 COP9 Signalosome, PDB code: 4d10:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the COP9 Signalosome


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 COP9 Signalosome within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn999 b:0.1 occ:1.00 OD2 E:ASP151 2.0 0.6 1.0 OE1 E:GLU104 2.0 0.6 1.0 NE2 E:HIS140 2.0 0.3 1.0 NE2 E:HIS138 2.1 0.2 1.0 CG E:ASP151 2.7 0.9 1.0 CD E:GLU104 2.7 0.4 1.0 OE2 E:GLU104 2.8 0.3 1.0 OD1 E:ASP151 2.8 0.8 1.0 CD2 E:HIS138 3.0 0.9 1.0 CD2 E:HIS140 3.0 0.8 1.0 CE1 E:HIS140 3.1 0.5 1.0 CE1 E:HIS138 3.2 0.2 1.0 OG E:SER148 4.0 0.7 1.0 CG E:HIS140 4.1 0.1 1.0 CG E:HIS138 4.1 0.8 1.0 CB E:ASP151 4.1 0.3 1.0 ND1 E:HIS140 4.1 0.5 1.0 CG E:GLU104 4.2 0.7 1.0 ND1 E:HIS138 4.2 0.1 1.0 O E:TRP146 4.6 0.7 1.0 CB E:SER148 4.6 0.0 1.0 N E:SER148 4.6 0.0 1.0 OH E:TYR143 4.7 0.8 1.0 CB E:GLU104 4.8 0.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the COP9 Signalosome


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 COP9 Signalosome within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn999 b:0.3 occ:1.00 OD2 M:ASP151 2.0 0.8 1.0 OE1 M:GLU104 2.0 0.5 1.0 NE2 M:HIS140 2.1 0.3 1.0 NE2 M:HIS138 2.1 0.3 1.0 CG M:ASP151 2.7 0.4 1.0 CD M:GLU104 2.7 0.2 1.0 OD1 M:ASP151 2.7 0.1 1.0 OE2 M:GLU104 2.8 0.3 1.0 CD2 M:HIS138 2.9 0.1 1.0 CD2 M:HIS140 3.0 0.5 1.0 CE1 M:HIS140 3.1 1.0 1.0 CE1 M:HIS138 3.1 1.0 1.0 OG M:SER148 4.0 0.2 1.0 CG M:HIS138 4.1 0.4 1.0 CG M:HIS140 4.1 0.8 1.0 CB M:ASP151 4.1 0.2 1.0 ND1 M:HIS140 4.2 0.4 1.0 ND1 M:HIS138 4.2 0.2 1.0 CG M:GLU104 4.2 0.1 1.0 O M:TRP146 4.6 0.5 1.0 N M:SER148 4.6 0.1 1.0 CB M:SER148 4.6 0.8 1.0 OH M:TYR143 4.7 0.3 1.0 CB M:GLU104 4.8 0.0 1.0

G.M.Lingaraju, R.D.Bunker, S.Cavadini, D.Hess, U.Hassiepen, M.Renatus, E.S.Fischer, N.H.Thoma. Crystal Structure of the Human COP9 Signalosome Nature V. 512 161 2014.
ISSN: ISSN 0028-0836
PubMed: 25043011
DOI: 10.1038/NATURE13566