Zinc in PDB 6kgi: Rlgs-YUBR1 Ubr Box

All present enzymatic activity of Rlgs-YUBR1 Ubr Box:
2.3.2.27;

The structure of Rlgs-YUBR1 Ubr Box, PDB code: 6kgi was solved by J.Heo, D.H.Kwon, L.Kim, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.25 / 1.04
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.630, 60.630, 69.811, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 20.2

The binding sites of Zinc atom in the Rlgs-YUBR1 Ubr Box (pdb code 6kgi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Rlgs-YUBR1 Ubr Box, PDB code: 6kgi:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rlgs-YUBR1 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rlgs-YUBR1 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:10.1 occ:1.00 SG B:CYS175 2.3 10.2 1.0 SG B:CYS148 2.3 10.0 1.0 SG B:CYS123 2.3 10.7 1.0 SG B:CYS151 2.4 9.6 1.0 HB2 B:CYS151 3.0 12.4 1.0 HB3 B:CYS175 3.1 13.2 1.0 HB2 B:CYS123 3.1 12.1 1.0 CB B:CYS123 3.1 10.1 1.0 CB B:CYS175 3.1 11.0 1.0 HB3 B:CYS123 3.2 12.1 1.0 HB2 B:CYS175 3.2 13.2 1.0 H B:CYS148 3.2 11.5 1.0 HB3 B:CYS148 3.2 12.3 1.0 CB B:CYS151 3.3 10.3 1.0 CB B:CYS148 3.4 10.2 1.0 HB3 B:CYS177 3.6 12.1 1.0 HB2 B:CYS177 3.8 12.1 1.0 HB3 B:CYS151 3.9 12.4 1.0 HB3 B:ARG125 3.9 16.8 1.0 N B:CYS148 4.0 9.6 1.0 H B:CYS151 4.1 11.2 1.0 CB B:CYS177 4.2 10.1 1.0 HB2 B:CYS148 4.2 12.3 1.0 CA B:CYS148 4.2 9.6 1.0 HB2 B:ARG125 4.2 16.8 1.0 H B:ARG125 4.3 16.3 1.0 H B:CYS177 4.3 12.4 1.0 ZN B:ZN203 4.3 9.7 1.0 N B:CYS151 4.4 9.3 1.0 HB2 B:HIS150 4.5 12.3 1.0 CA B:CYS151 4.5 8.9 1.0 O B:HOH311 4.5 13.8 1.0 CB B:ARG125 4.5 14.0 1.0 HD2 B:ARG125 4.6 25.5 1.0 CA B:CYS123 4.6 11.2 1.0 CA B:CYS175 4.6 12.2 1.0 HA B:LEU147 4.7 11.4 1.0 HD3 B:ARG125 4.8 25.5 1.0 C B:CYS148 4.8 9.3 1.0 NE2 B:HIS118 4.8 10.7 1.0 O B:CYS148 4.9 9.6 1.0 HA B:CYS151 4.9 10.7 1.0 HA B:CYS123 4.9 13.4 1.0 HD2 B:HIS118 4.9 12.0 1.0 HA B:CYS175 5.0 14.6 1.0 H B:HIS150 5.0 11.9 1.0

Zinc binding site 2 out of 3 in the Rlgs-YUBR1 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rlgs-YUBR1 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:11.0 occ:1.00 ND1 B:HIS160 2.1 11.2 1.0 ND1 B:HIS157 2.1 11.7 1.0 SG B:CYS136 2.3 10.6 1.0 SG B:CYS139 2.3 12.4 1.0 CE1 B:HIS160 2.9 11.5 1.0 CE1 B:HIS157 2.9 10.3 1.0 HE1 B:HIS160 3.0 13.8 1.0 HE1 B:HIS157 3.0 12.4 1.0 HB2 B:CYS139 3.0 14.5 1.0 CG B:HIS160 3.1 10.6 1.0 CG B:HIS157 3.2 9.9 1.0 CB B:CYS139 3.3 12.1 1.0 HB3 B:HIS157 3.3 12.5 1.0 CB B:CYS136 3.3 10.6 1.0 HA B:HIS157 3.3 12.1 1.0 H B:CYS139 3.4 13.6 1.0 HB3 B:HIS160 3.4 13.1 1.0 HB3 B:CYS136 3.4 12.8 1.0 HB2 B:CYS136 3.4 12.8 1.0 HB2 B:HIS160 3.5 13.1 1.0 CB B:HIS160 3.6 10.9 1.0 CB B:HIS157 3.6 10.4 1.0 HB2 B:GLU138 3.8 15.3 1.0 N B:CYS139 3.9 11.3 1.0 CA B:HIS157 4.0 10.1 1.0 HB3 B:CYS139 4.0 14.5 1.0 O B:ASP156 4.0 10.8 1.0 NE2 B:HIS160 4.0 12.7 1.0 NE2 B:HIS157 4.1 11.4 1.0 CA B:CYS139 4.1 11.9 1.0 CD2 B:HIS160 4.2 11.6 1.0 CD2 B:HIS157 4.2 10.3 1.0 O B:HOH309 4.4 16.2 1.0 HA B:CYS139 4.5 14.3 1.0 HB2 B:HIS157 4.5 12.5 1.0 H B:GLU138 4.6 14.2 1.0 CB B:GLU138 4.7 12.8 1.0 C B:ASP156 4.7 9.9 1.0 CA B:CYS136 4.7 10.4 1.0 C B:GLU138 4.8 11.5 1.0 HE2 B:HIS160 4.8 15.2 1.0 N B:HIS157 4.8 9.9 1.0 HG22 B:VAL162 4.8 16.1 1.0 HB3 B:GLU138 4.8 15.3 1.0 HE2 B:HIS157 4.9 13.7 1.0 HB3 B:ASP156 4.9 13.0 1.0 HA B:CYS136 5.0 12.5 1.0

Zinc binding site 3 out of 3 in the Rlgs-YUBR1 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rlgs-YUBR1 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:9.7 occ:1.00 NE2 B:HIS118 2.0 10.7 1.0 SG B:CYS189 2.3 10.0 1.0 SG B:CYS177 2.3 9.9 1.0 SG B:CYS151 2.3 9.6 1.0 HB3 B:CYS151 2.8 12.4 1.0 HB3 B:CYS177 2.8 12.1 1.0 HB2 B:CYS189 2.9 12.2 1.0 CD2 B:HIS118 3.0 10.0 1.0 CE1 B:HIS118 3.0 9.7 1.0 CB B:CYS177 3.1 10.1 1.0 CB B:CYS151 3.1 10.3 1.0 CB B:CYS189 3.2 10.2 1.0 HD2 B:HIS118 3.2 12.0 1.0 HE1 B:HIS118 3.2 11.6 1.0 HA B:CYS151 3.4 10.7 1.0 HB2 B:CYS177 3.4 12.1 1.0 HB2 B:CYS123 3.5 12.1 1.0 CA B:CYS151 3.8 8.9 1.0 HA B:CYS189 3.9 11.8 1.0 HB3 B:CYS189 3.9 12.2 1.0 HB2 B:CYS151 3.9 12.4 1.0 ND1 B:HIS118 4.1 10.6 1.0 CA B:CYS189 4.1 9.9 1.0 CG B:HIS118 4.2 10.4 1.0 O B:HOH318 4.2 11.8 1.0 ZN B:ZN201 4.3 10.1 1.0 CA B:CYS177 4.4 10.2 1.0 CB B:CYS123 4.4 10.1 1.0 HB3 B:ALA191 4.5 14.6 1.0 H B:ALA191 4.7 12.2 1.0 C B:CYS177 4.7 10.7 1.0 C B:CYS151 4.7 8.7 1.0 O B:CYS151 4.7 9.3 1.0 O B:HOH323 4.8 11.2 1.0 HB3 B:CYS123 4.8 12.1 1.0 HA B:CYS177 4.8 12.3 1.0 H B:LYS190 4.8 11.8 1.0 N B:CYS151 4.9 9.3 1.0 O B:CYS177 4.9 11.5 1.0 HD1 B:HIS118 4.9 12.7 1.0

L.Kim, D.H.Kwon, J.Heo, M.R.Park, H.K.Song. Use of the LC3B-Fusion Technique For Biochemical and Structural Studies of Proteins Involved in the N-Degron Pathway. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 31919097
DOI: 10.1074/JBC.RA119.010912