Zinc in PDB 2w9n: Crystal Structure of Linear Di-Ubiquitin

The structure of Crystal Structure of Linear Di-Ubiquitin, PDB code: 2w9n was solved by D.Komander, F.Reyes-Turcu, K.D.Wilkinson, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.25
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.572, 105.572, 105.572, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 27.6

The structure of Crystal Structure of Linear Di-Ubiquitin also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Linear Di-Ubiquitin (pdb code 2w9n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Linear Di-Ubiquitin, PDB code: 2w9n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Linear Di-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 Linear Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1150 b:52.7 occ:1.00 OE2 A:GLU18 2.2 23.2 1.0 OE1 A:GLU18 2.6 30.1 1.0 CD A:GLU18 2.7 29.2 1.0 O A:HOH2003 3.0 57.3 0.3 O A:HOH2002 3.2 64.9 0.3 CG A:GLU18 4.2 29.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Linear Di-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 Linear Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1151 b:44.6 occ:1.00 O A:HOH2026 1.8 20.7 1.0 OD1 A:ASP97 2.0 33.6 1.0 OD2 A:ASP97 2.6 35.4 1.0 CG A:ASP97 2.7 36.0 1.0 NZ A:LYS105 2.9 45.0 1.0 O A:HOH2025 3.0 57.6 1.0 CE A:LYS105 3.9 42.7 1.0 OD1 A:ASN101 4.1 33.3 1.0 CB A:ASP97 4.1 37.1 1.0 OE1 A:GLU94 4.5 34.1 1.0 CG A:GLU94 4.6 37.8 1.0 CB A:ASN101 4.7 34.8 1.0 CG A:ASN101 4.7 32.9 1.0 N A:GLU94 4.8 37.9 1.0 CA A:ASP97 4.9 37.6 1.0 CB A:GLU94 4.9 37.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Linear Di-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 Linear Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1152 b:69.5 occ:1.00 OE1 A:GLU140 2.1 47.1 1.0 OE2 A:GLU140 2.3 46.0 1.0 CD A:GLU140 2.6 45.4 1.0 O A:HOH2023 3.3 44.3 1.0 CG A:GLU140 4.1 43.9 1.0 CE A:LYS139 4.4 56.2 1.0 CB A:GLU140 4.7 43.2 1.0 NZ A:LYS139 4.8 58.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Linear Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Linear Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1153 b:0.7 occ:1.00 OD2 A:ASP128 2.0 53.8 1.0 CG A:ASP128 2.9 51.6 1.0 OD1 A:ASP128 3.2 55.1 1.0 NZ A:LYS103 3.4 50.1 1.0 OD1 A:ASP115 3.9 56.5 1.0 CD A:LYS103 4.0 41.1 1.0 CB A:ASP128 4.2 49.8 1.0 CE A:LYS103 4.3 45.1 1.0 O A:PRO114 4.5 48.0 1.0 C A:PRO114 4.9 47.5 1.0

D.Komander, F.Reyes-Turcu, J.D.Licchesi, P.Odenwaelder, K.D.Wilkinson, D.Barford. Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains. Embo Rep. V. 10 466 2009.
ISSN: ISSN 1469-221X
PubMed: 19373254
DOI: 10.1038/EMBOR.2009.55