Zinc in PDB 5yt6: Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin

The structure of Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin, PDB code: 5yt6 was solved by L.Pan, S.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.89 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.709, 72.938, 119.879, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.5

The binding sites of Zinc atom in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin (pdb code 5yt6). 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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin, PDB code: 5yt6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:10.3 occ:1.00 NE2 F:HIS60 2.1 9.6 1.0 NE2 F:HIS56 2.1 12.2 1.0 SG F:CYS37 2.3 9.6 1.0 SG F:CYS40 2.3 11.1 1.0 CD2 F:HIS60 3.0 9.6 1.0 CD2 F:HIS56 3.0 9.5 1.0 CE1 F:HIS56 3.1 13.2 1.0 CE1 F:HIS60 3.1 9.7 1.0 CB F:CYS37 3.1 9.4 1.0 CB F:CYS40 3.3 10.7 1.0 N F:CYS40 3.7 11.9 1.0 O F:HOH226 3.8 13.9 1.0 CA F:CYS40 4.1 10.9 1.0 ND1 F:HIS56 4.1 12.7 1.0 CG F:HIS56 4.1 8.1 1.0 CG F:HIS60 4.1 10.5 1.0 ND1 F:HIS60 4.2 10.2 1.0 CA F:CYS37 4.6 8.8 1.0 C F:MET39 4.7 12.8 1.0 CB F:MET39 4.7 12.5 1.0 C F:CYS40 4.7 10.9 1.0 N F:SER41 4.9 10.4 1.0 O F:HIS56 5.0 11.5 1.0 N F:MET39 5.0 9.9 1.0 CB F:GLU42 5.0 11.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:11.2 occ:1.00 NE2 B:HIS60 2.1 10.5 1.0 NE2 B:HIS56 2.1 11.8 1.0 SG B:CYS37 2.3 10.8 1.0 SG B:CYS40 2.3 12.2 1.0 CD2 B:HIS60 3.0 9.6 1.0 CD2 B:HIS56 3.0 10.7 1.0 CE1 B:HIS56 3.0 14.9 1.0 CE1 B:HIS60 3.1 9.9 1.0 CB B:CYS37 3.2 10.6 1.0 CB B:CYS40 3.3 12.9 1.0 N B:CYS40 3.7 10.3 1.0 CA B:CYS40 4.0 12.9 1.0 ND1 B:HIS56 4.1 16.2 1.0 CG B:HIS60 4.1 9.8 1.0 ND1 B:HIS60 4.2 9.9 1.0 CG B:HIS56 4.2 13.6 1.0 C B:MET39 4.5 13.8 1.0 CA B:CYS37 4.6 11.3 1.0 CB B:MET39 4.6 12.4 1.0 C B:CYS40 4.7 13.1 1.0 N B:MET39 4.8 10.7 1.0 ND2 B:ASN67 4.8 32.2 1.0 CB B:GLU42 4.9 15.1 1.0 CA B:MET39 4.9 11.5 1.0 N B:SER41 4.9 13.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:11.1 occ:1.00 NE2 D:HIS56 2.0 9.1 1.0 NE2 D:HIS60 2.1 11.8 1.0 SG D:CYS40 2.3 12.2 1.0 SG D:CYS37 2.3 9.0 1.0 CD2 D:HIS56 3.0 9.4 1.0 CE1 D:HIS56 3.0 12.1 1.0 CE1 D:HIS60 3.0 17.1 1.0 CD2 D:HIS60 3.0 9.9 1.0 CB D:CYS37 3.1 9.8 1.0 CB D:CYS40 3.4 12.9 1.0 N D:CYS40 3.7 11.6 1.0 ND1 D:HIS56 4.1 12.7 1.0 CA D:CYS40 4.1 12.4 1.0 CG D:HIS56 4.1 9.7 1.0 ND1 D:HIS60 4.1 14.6 1.0 CG D:HIS60 4.2 10.3 1.0 O D:HOH229 4.4 31.2 1.0 CA D:CYS37 4.6 9.0 1.0 CB D:MET39 4.7 13.0 1.0 C D:MET39 4.8 11.7 1.0 O D:HIS56 4.8 10.7 1.0 C D:CYS40 4.8 13.8 1.0 N D:SER41 5.0 12.5 1.0 CA D:VAL57 5.0 7.7 1.0 N D:MET39 5.0 11.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:11.2 occ:1.00 NE2 H:HIS60 2.1 12.7 1.0 NE2 H:HIS56 2.1 12.8 1.0 SG H:CYS40 2.3 12.2 1.0 SG H:CYS37 2.3 9.9 1.0 CE1 H:HIS56 3.0 13.7 1.0 CE1 H:HIS60 3.0 19.0 1.0 CD2 H:HIS56 3.1 11.6 1.0 CD2 H:HIS60 3.1 8.6 1.0 CB H:CYS37 3.1 9.2 1.0 CB H:CYS40 3.3 13.1 1.0 N H:CYS40 3.8 12.5 1.0 CA H:CYS40 4.1 12.7 1.0 ND1 H:HIS56 4.1 16.2 1.0 ND1 H:HIS60 4.1 18.5 1.0 CG H:HIS56 4.1 10.8 1.0 CG H:HIS60 4.2 10.6 1.0 CA H:CYS37 4.6 9.5 1.0 C H:CYS40 4.7 14.4 1.0 O H:HIS56 4.8 10.3 1.0 CB H:MET39 4.8 12.5 1.0 C H:MET39 4.8 16.9 1.0 CB H:GLU42 4.9 15.3 1.0 CA H:VAL57 4.9 8.1 1.0 N H:SER41 5.0 14.0 1.0

S.Hu, Y.Wang, Y.Gong, J.Liu, Y.Li, L.Pan. Mechanistic Insights Into Recognitions of Ubiquitin and Myosin VI By Autophagy Receptor TAX1BP1. J. Mol. Biol. V. 430 3283 2018.
ISSN: ESSN 1089-8638
PubMed: 29940186
DOI: 10.1016/J.JMB.2018.06.030