Zinc in PDB 3zlz: LYS6-Linked Tri-Ubiquitin

The structure of LYS6-Linked Tri-Ubiquitin, PDB code: 3zlz was solved by M.K.Hospenthal, S.M.V.Freund, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.18 / 2.90
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	104.930, 104.930, 104.930, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 28.8

The binding sites of Zinc atom in the LYS6-Linked Tri-Ubiquitin (pdb code 3zlz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the LYS6-Linked Tri-Ubiquitin, PDB code: 3zlz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of LYS6-Linked Tri-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1074 b:0.1 occ:1.00 OD2 A:ASP32 2.5 0.7 1.0 CG A:ASP32 3.4 0.2 1.0 OD1 A:ASP32 3.9 0.5 1.0 CB A:ASP32 4.4 0.9 1.0

Zinc binding site 2 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of LYS6-Linked Tri-Ubiquitin within 5.0Å range:

Zinc binding site 3 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of LYS6-Linked Tri-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1074 b:78.6 occ:1.00 OD1 B:ASP21 2.1 65.4 1.0 OD2 B:ASP21 2.6 57.8 1.0 CG B:ASP21 2.6 60.3 1.0 NZ B:LYS29 3.6 73.2 1.0 CE B:LYS29 3.8 70.4 1.0 CB B:ASP21 4.1 57.1 1.0 ND2 B:ASN25 4.5 58.5 1.0 CB B:GLU18 4.6 61.7 1.0 CB B:ASN25 4.7 56.2 1.0 CG B:ASN25 4.8 58.1 1.0 CA B:ASP21 4.8 59.3 1.0 N B:GLU18 4.8 60.9 1.0

Zinc binding site 4 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of LYS6-Linked Tri-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1075 b:0.3 occ:1.00 NE2 B:HIS68 2.3 78.5 1.0 CD2 B:HIS68 2.8 76.9 1.0 CE1 B:HIS68 3.5 79.8 1.0 O B:THR66 3.7 67.6 1.0 CG B:HIS68 4.1 77.1 1.0 ND1 B:HIS68 4.4 78.7 1.0 CB B:THR66 4.4 69.4 1.0 CG2 B:THR66 4.6 68.7 1.0 C B:THR66 4.6 64.9 1.0

Zinc binding site 5 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of LYS6-Linked Tri-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1076 b:0.1 occ:1.00 OE2 B:GLU16 2.1 72.0 1.0 N B:MET1 2.1 67.6 1.0 OE1 B:GLU16 2.6 74.0 1.0 CD B:GLU16 2.7 73.0 1.0 CA B:MET1 3.2 65.6 1.0 O B:MET1 3.4 67.6 1.0 C B:MET1 3.6 67.5 1.0 CB B:MET1 3.7 60.7 1.0 O B:VAL17 3.7 62.4 1.0 CG B:GLU16 4.2 72.1 1.0 N B:GLN2 4.8 67.7 1.0 N B:VAL17 4.8 56.7 1.0 C B:VAL17 4.8 60.0 1.0

M.K.Hospenthal, S.M.V.Freund, D.Komander. Assembly, Analysis and Architecture of Atypical Ubiquitin Chains Nat.Struct.Mol.Biol. V. 20 555 2013.
ISSN: ISSN 1545-9993
PubMed: 23563141
DOI: 10.1038/NSMB.2547