Zinc in PDB 6lhn: Rlgsgg-ATPRT6 Ubr Box

All present enzymatic activity of Rlgsgg-ATPRT6 Ubr Box:
2.3.2.27;

The structure of Rlgsgg-ATPRT6 Ubr Box, PDB code: 6lhn was solved by L.Kim, D.H.Kwon, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.95 / 2.50
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	95.414, 95.414, 95.414, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25

The binding sites of Zinc atom in the Rlgsgg-ATPRT6 Ubr Box (pdb code 6lhn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Rlgsgg-ATPRT6 Ubr Box, PDB code: 6lhn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rlgsgg-ATPRT6 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rlgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:47.2 occ:1.00 ND1 A:HIS187 2.1 62.8 1.0 SG A:CYS172 2.3 37.6 1.0 SG A:CYS149 2.4 34.5 1.0 SG A:CYS184 2.4 46.2 1.0 HB3 A:CYS172 2.7 53.1 1.0 CE1 A:HIS187 2.9 50.7 1.0 HE1 A:HIS187 3.0 60.9 1.0 HB3 A:CYS149 3.0 44.2 1.0 CB A:CYS172 3.0 44.2 1.0 HB2 A:HIS187 3.1 67.7 1.0 CG A:HIS187 3.2 46.0 1.0 CB A:CYS149 3.2 36.8 1.0 H A:CYS184 3.4 61.2 1.0 HB2 A:CYS172 3.4 53.1 1.0 HA A:CYS149 3.4 47.8 1.0 HB3 A:CYS184 3.4 56.8 1.0 HB2 A:CYS121 3.6 60.6 1.0 CB A:CYS184 3.6 47.3 1.0 CB A:HIS187 3.7 56.4 1.0 CA A:CYS149 3.9 39.8 1.0 NE2 A:HIS187 4.0 44.1 1.0 HB2 A:CYS149 4.1 44.2 1.0 N A:CYS184 4.1 51.0 1.0 CD2 A:HIS187 4.2 53.7 1.0 HB3 A:HIS187 4.2 67.7 1.0 ZN A:ZN202 4.3 45.3 1.0 HB2 A:CYS184 4.3 56.8 1.0 CA A:CYS184 4.4 48.4 1.0 CA A:CYS172 4.4 40.6 1.0 CB A:CYS121 4.4 50.5 1.0 HB3 A:CYS121 4.5 60.6 1.0 C A:CYS172 4.6 36.8 1.0 HE2 A:HIS187 4.8 53.0 1.0 O A:CYS172 4.8 47.6 1.0 N A:HIS187 4.8 52.1 1.0 HB2 A:ASN186 4.8 62.7 1.0 HA A:CYS172 4.8 48.8 1.0 H A:HIS187 4.8 62.5 1.0 HD22 A:ASN186 4.9 83.3 1.0 CA A:HIS187 4.9 61.6 1.0 C A:CYS149 4.9 40.6 1.0 N A:CYS149 4.9 45.5 1.0 C A:CYS184 4.9 58.2 1.0 O A:CYS149 4.9 39.9 1.0

Zinc binding site 2 out of 3 in the Rlgsgg-ATPRT6 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rlgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:45.3 occ:1.00 SG A:CYS149 2.3 34.5 1.0 SG A:CYS170 2.4 35.7 1.0 SG A:CYS121 2.4 47.2 1.0 SG A:CYS146 2.4 46.9 1.0 H A:CYS146 3.0 39.1 1.0 HB2 A:CYS149 3.1 44.2 1.0 HB3 A:CYS121 3.1 60.6 1.0 HB3 A:CYS170 3.1 35.8 1.0 CB A:CYS170 3.1 29.9 1.0 HB2 A:CYS170 3.1 35.8 1.0 CB A:CYS121 3.2 50.5 1.0 HB2 A:CYS121 3.2 60.6 1.0 CB A:CYS149 3.3 36.8 1.0 HB3 A:CYS146 3.4 46.1 1.0 CB A:CYS146 3.5 38.4 1.0 HB3 A:CYS172 3.6 53.1 1.0 HB2 A:SER123 3.6 60.3 1.0 HB2 A:CYS172 3.7 53.1 1.0 HG A:SER123 3.8 86.7 1.0 N A:CYS146 3.8 32.5 1.0 HB3 A:CYS149 3.8 44.2 1.0 H A:CYS149 3.9 54.7 1.0 CB A:CYS172 4.1 44.2 1.0 OG A:SER123 4.1 72.2 1.0 CA A:CYS146 4.2 36.2 1.0 HE1 A:HIS187 4.2 60.9 1.0 HB A:ILE145 4.3 46.9 1.0 H A:CYS172 4.3 49.7 1.0 ZN A:ZN201 4.3 47.2 1.0 HB2 A:CYS146 4.3 46.1 1.0 CB A:SER123 4.4 50.3 1.0 CA A:CYS149 4.5 39.8 1.0 N A:CYS149 4.5 45.5 1.0 H A:SER123 4.6 63.3 1.0 CA A:CYS170 4.6 42.2 1.0 CA A:CYS121 4.6 54.6 1.0 HA A:ILE145 4.7 46.3 1.0 CE1 A:HIS187 4.8 50.7 1.0 C A:CYS146 4.8 36.5 1.0 O A:CYS146 4.8 42.0 1.0 HA A:CYS149 4.8 47.8 1.0 HB3 A:SER123 4.9 60.3 1.0 HA A:CYS170 4.9 50.7 1.0 C A:ILE145 4.9 41.7 1.0

Zinc binding site 3 out of 3 in the Rlgsgg-ATPRT6 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rlgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:43.7 occ:1.00 ND1 A:HIS155 2.0 33.6 1.0 ND1 A:HIS158 2.0 57.0 1.0 SG A:CYS137 2.3 43.8 1.0 SG A:CYS134 2.4 38.9 1.0 CE1 A:HIS155 2.8 40.3 1.0 HE1 A:HIS155 2.9 48.4 1.0 CE1 A:HIS158 2.9 53.7 1.0 HE1 A:HIS158 3.1 64.5 1.0 CG A:HIS158 3.1 53.0 1.0 CG A:HIS155 3.1 44.5 1.0 HB3 A:HIS155 3.2 69.4 1.0 HB3 A:HIS158 3.2 66.0 1.0 HB A:THR136 3.3 50.2 1.0 H A:CYS137 3.3 59.5 1.0 HB2 A:HIS158 3.4 66.0 1.0 CB A:CYS134 3.4 46.3 1.0 HB3 A:CYS134 3.4 55.6 1.0 CB A:HIS158 3.5 55.0 1.0 HB2 A:CYS137 3.5 54.4 1.0 CB A:CYS137 3.5 45.3 1.0 HB2 A:CYS134 3.6 55.6 1.0 CB A:HIS155 3.7 57.8 1.0 HA A:HIS155 3.7 71.9 1.0 N A:CYS137 3.8 49.5 1.0 NE2 A:HIS155 4.0 40.9 1.0 NE2 A:HIS158 4.1 49.9 1.0 CD2 A:HIS155 4.2 41.7 1.0 CD2 A:HIS158 4.2 41.8 1.0 CA A:HIS155 4.2 59.9 1.0 CB A:THR136 4.3 41.9 1.0 HB3 A:CYS137 4.3 54.4 1.0 HZ2 A:TRP178 4.3 46.6 1.0 CA A:CYS137 4.3 47.2 1.0 H A:THR136 4.5 56.2 1.0 HB2 A:HIS155 4.5 69.4 1.0 O A:ASP154 4.7 57.9 1.0 HA3 A:GLY182 4.7 54.6 1.0 C A:THR136 4.7 46.2 1.0 HG21 A:THR136 4.7 47.7 1.0 HA A:CYS137 4.7 56.7 1.0 HE2 A:HIS155 4.7 49.1 1.0 CA A:CYS134 4.8 45.5 1.0 HE2 A:HIS158 4.8 59.9 1.0 HE1 A:PHE150 4.8 58.6 1.0 HB3 A:TYR160 4.8 52.2 1.0 HA2 A:GLY182 4.9 54.6 1.0 CZ2 A:TRP178 4.9 38.8 1.0 CA A:THR136 4.9 35.2 1.0 CG2 A:THR136 5.0 39.8 1.0 CA A:HIS158 5.0 58.4 1.0 HE1 A:TRP178 5.0 54.7 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