Zinc in PDB 4z4k: Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein

The structure of Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein, PDB code: 4z4k was solved by A.Rohaim, M.Kawasaki, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.885, 83.334, 128.496, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 28

The binding sites of Zinc atom in the Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein (pdb code 4z4k). 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 Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein, PDB code: 4z4k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein


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 Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:45.8 occ:1.00 SG A:CYS241 2.0 37.5 1.0 NE2 A:HIS257 2.1 41.3 1.0 NE2 A:HIS261 2.2 31.0 1.0 SG A:CYS238 2.2 35.3 1.0 CE1 A:HIS257 3.0 42.3 1.0 CD2 A:HIS257 3.0 40.6 1.0 CB A:CYS238 3.0 35.8 1.0 CD2 A:HIS261 3.1 31.6 1.0 CE1 A:HIS261 3.2 31.1 1.0 CB A:CYS241 3.5 37.9 1.0 N A:CYS241 3.9 38.5 1.0 ND1 A:HIS257 4.0 42.5 1.0 CG A:HIS257 4.1 41.1 1.0 CA A:CYS241 4.2 39.4 1.0 ND1 A:HIS261 4.3 30.5 1.0 CG A:HIS261 4.3 31.2 1.0 CA A:CYS238 4.5 35.1 1.0 C A:LEU240 4.6 37.0 1.0 C A:CYS241 4.7 42.1 1.0 CB A:LEU243 4.7 51.9 1.0 O A:CYS241 4.8 40.2 1.0 N A:LEU240 4.9 33.1 1.0 CD2 A:LEU243 5.0 55.5 1.0 CB A:LEU240 5.0 33.7 1.0 O A:HIS257 5.0 41.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein


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 Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:64.5 occ:1.00 NE2 A:HIS288 2.1 80.6 1.0 SG A:CYS265 2.1 56.5 1.0 NE2 A:HIS284 2.4 50.1 1.0 SG A:CYS268 2.6 68.1 1.0 CD2 A:HIS284 2.8 50.5 1.0 CD2 A:HIS288 3.0 80.9 1.0 CB A:CYS265 3.1 55.5 1.0 CE1 A:HIS288 3.1 82.3 1.0 CE1 A:HIS284 3.6 50.9 1.0 N A:CYS268 3.6 69.2 1.0 CB A:CYS268 3.8 69.1 1.0 CB A:MET267 3.9 70.7 1.0 CG A:HIS284 4.1 51.8 1.0 CG A:HIS288 4.1 82.3 1.0 ND1 A:HIS288 4.1 85.8 1.0 CA A:CYS268 4.3 68.9 1.0 ND1 A:HIS284 4.4 51.9 1.0 CA A:CYS265 4.5 55.6 1.0 O A:HIS284 4.6 58.3 1.0 C A:MET267 4.7 67.7 1.0 CA A:MET267 4.7 66.1 1.0 N A:MET267 4.7 60.5 1.0 N A:SER269 4.8 61.2 1.0 C A:CYS268 4.8 64.0 1.0 C A:CYS265 4.9 55.8 1.0 CB A:GLU270 5.0 64.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein


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 Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:52.4 occ:1.00 NE2 B:HIS257 2.0 41.8 1.0 SG B:CYS241 2.1 42.1 1.0 NE2 B:HIS261 2.1 43.4 1.0 SG B:CYS238 2.2 48.8 1.0 CD2 B:HIS257 2.9 43.5 1.0 CE1 B:HIS257 2.9 42.0 1.0 CD2 B:HIS261 3.0 43.0 1.0 CB B:CYS238 3.1 50.2 1.0 CE1 B:HIS261 3.2 43.8 1.0 CB B:CYS241 3.6 42.8 1.0 N B:CYS241 3.9 42.6 1.0 ND1 B:HIS257 4.0 43.0 1.0 CG B:HIS257 4.0 44.5 1.0 CG B:HIS261 4.2 43.3 1.0 ND1 B:HIS261 4.2 44.4 1.0 CA B:CYS241 4.2 43.2 1.0 CB B:LEU243 4.5 52.1 1.0 CA B:CYS238 4.5 47.1 1.0 C B:CYS241 4.7 45.1 1.0 O B:CYS241 4.8 45.1 1.0 CD2 B:LEU243 4.8 53.5 1.0 O B:HIS257 4.8 46.4 1.0 CB B:LEU240 4.9 44.1 1.0 C B:LEU240 4.9 40.7 1.0 N B:LEU240 4.9 43.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein


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 Gfp-TAX1BP1 UBZ1+2 Domain Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:75.7 occ:1.00 NE2 B:HIS288 2.1 90.7 1.0 SG B:CYS265 2.2 73.8 1.0 SG B:CYS268 2.3 67.7 1.0 NE2 B:HIS284 2.4 85.9 1.0 CE1 B:HIS288 3.0 89.4 1.0 CD2 B:HIS284 3.0 84.5 1.0 CB B:CYS265 3.0 69.0 1.0 CD2 B:HIS288 3.1 90.0 1.0 N B:CYS268 3.6 71.4 1.0 CB B:CYS268 3.6 69.5 1.0 CE1 B:HIS284 3.6 86.9 1.0 ND1 B:HIS288 4.1 88.6 1.0 CA B:CYS268 4.1 69.7 1.0 CG B:HIS288 4.2 91.6 1.0 CB B:MET267 4.3 77.3 1.0 CG B:HIS284 4.3 85.3 1.0 CA B:CYS265 4.4 67.6 1.0 ND1 B:HIS284 4.5 85.4 1.0 N B:SER269 4.6 74.6 1.0 C B:CYS268 4.6 70.3 1.0 C B:MET267 4.7 72.7 1.0 CB B:GLU270 4.7 74.6 1.0 N B:GLU270 4.7 70.3 1.0 N B:MET267 4.8 71.6 1.0 CA B:MET267 4.8 73.8 1.0 C B:CYS265 4.8 67.8 1.0 CG B:MET267 4.8 79.8 1.0 O B:HIS284 4.9 80.6 1.0

N.Suzuki, A.Rohaim, R.Kato, I.Dikic, S.Wakatsuki, M.Kawasaki. A Novel Mode of Ubiquitin Recognition By the Ubiquitin-Binding Zinc Finger Domain of WRNIP1. Febs J. V. 283 2004 2016.
ISSN: ISSN 1742-464X
PubMed: 27062441
DOI: 10.1111/FEBS.13734