Zinc in PDB 7y6z: Rlgsgg-ATPRT6 Ubr Box (I222)

All present enzymatic activity of Rlgsgg-ATPRT6 Ubr Box (I222):
2.3.2.27;

The structure of Rlgsgg-ATPRT6 Ubr Box (I222), PDB code: 7y6z was solved by L.Kim, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	38.986, 45.754, 86.824, 90, 90, 90
R / Rfree (%)	23.4 / 27.1

The binding sites of Zinc atom in the Rlgsgg-ATPRT6 Ubr Box (I222) (pdb code 7y6z). 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 (I222), PDB code: 7y6z:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rlgsgg-ATPRT6 Ubr Box (I222)


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 (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:32.2 occ:1.00 ND1 A:HIS187 1.9 28.5 1.0 SG A:CYS172 2.2 23.6 1.0 SG A:CYS184 2.2 26.3 1.0 SG A:CYS149 2.5 22.3 1.0 HB3 A:CYS149 2.7 26.0 1.0 CE1 A:HIS187 2.8 27.6 1.0 HB3 A:CYS172 2.8 23.1 1.0 HE1 A:HIS187 2.9 33.2 1.0 HB2 A:HIS187 3.0 34.5 1.0 CG A:HIS187 3.0 29.2 1.0 HB3 A:CYS184 3.1 33.0 1.0 CB A:CYS172 3.1 19.2 1.0 CB A:CYS149 3.1 21.6 1.0 CB A:CYS184 3.2 27.5 1.0 H A:CYS184 3.3 34.9 1.0 HB2 A:CYS121 3.5 30.5 1.0 CB A:HIS187 3.5 28.6 1.0 HB2 A:CYS172 3.5 23.1 1.0 HA A:CYS149 3.6 30.8 1.0 HB2 A:CYS149 3.9 26.0 1.0 NE2 A:HIS187 3.9 33.2 1.0 CA A:CYS149 4.0 25.6 1.0 N A:CYS184 4.0 29.0 1.0 HB2 A:CYS184 4.0 33.0 1.0 CD2 A:HIS187 4.0 32.6 1.0 HB3 A:HIS187 4.1 34.5 1.0 CA A:CYS184 4.1 27.9 1.0 ZN A:ZN202 4.3 31.6 1.0 H A:HIS187 4.4 37.3 1.0 CA A:CYS172 4.4 20.9 1.0 CB A:CYS121 4.4 25.3 1.0 HB2 A:ASN186 4.5 44.0 1.0 N A:HIS187 4.5 31.0 1.0 C A:CYS172 4.5 24.6 1.0 H A:ASN186 4.5 36.1 1.0 O A:CYS172 4.6 28.7 1.0 CA A:HIS187 4.6 26.7 1.0 HE2 A:HIS187 4.7 40.0 1.0 HB3 A:CYS121 4.7 30.5 1.0 C A:CYS184 4.8 28.2 1.0 HA A:CYS172 4.8 25.2 1.0 HD2 A:HIS187 4.9 39.2 1.0 C A:CYS149 4.9 23.1 1.0 HA A:PHE183 4.9 29.7 1.0 O A:CYS149 5.0 27.1 1.0 HA A:CYS184 5.0 33.6 1.0

Zinc binding site 2 out of 3 in the Rlgsgg-ATPRT6 Ubr Box (I222)


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 (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:31.6 occ:1.00 SG A:CYS149 2.2 22.3 1.0 SG A:CYS170 2.3 23.9 1.0 SG A:CYS146 2.3 23.8 1.0 SG A:CYS121 2.4 27.3 1.0 HB2 A:CYS149 3.0 26.0 1.0 HB3 A:CYS170 3.0 32.3 1.0 HB3 A:CYS121 3.1 30.5 1.0 HB2 A:CYS121 3.1 30.5 1.0 CB A:CYS121 3.1 25.3 1.0 CB A:CYS170 3.1 26.8 1.0 H A:CYS146 3.1 28.6 1.0 HB2 A:CYS170 3.2 32.3 1.0 CB A:CYS149 3.3 21.6 1.0 HB3 A:CYS146 3.4 27.9 1.0 HB3 A:CYS172 3.4 23.1 1.0 CB A:CYS146 3.5 23.2 1.0 HB2 A:SER123 3.8 44.9 1.0 H A:CYS149 3.8 30.9 1.0 HB3 A:CYS149 3.8 26.0 1.0 N A:CYS146 3.9 23.7 1.0 HB2 A:CYS172 4.1 23.1 1.0 HE1 A:HIS187 4.1 33.2 1.0 HG A:SER123 4.1 55.8 1.0 CB A:CYS172 4.2 19.2 1.0 CA A:CYS146 4.2 22.3 1.0 OG A:SER123 4.3 46.5 1.0 HB2 A:CYS146 4.3 27.9 1.0 HB A:ILE145 4.3 25.8 1.0 ZN A:ZN201 4.3 32.2 1.0 H A:CYS172 4.4 23.0 1.0 N A:CYS149 4.4 25.7 1.0 CA A:CYS149 4.5 25.6 1.0 CB A:SER123 4.5 37.3 1.0 CE1 A:HIS187 4.6 27.6 1.0 CA A:CYS121 4.6 29.4 1.0 CA A:CYS170 4.6 30.0 1.0 O A:CYS146 4.7 22.3 1.0 HA A:ILE145 4.8 23.2 1.0 C A:CYS146 4.8 22.1 1.0 HA A:CYS149 4.9 30.8 1.0 HA A:CYS121 4.9 35.4 1.0 HD2 A:PRO148 4.9 25.5 1.0 H A:SER123 4.9 48.5 1.0 HA A:CYS170 4.9 36.1 1.0 ND1 A:HIS187 5.0 28.5 1.0

Zinc binding site 3 out of 3 in the Rlgsgg-ATPRT6 Ubr Box (I222)


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 (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:31.6 occ:1.00 ND1 A:HIS158 2.0 30.6 1.0 ND1 A:HIS155 2.1 20.0 1.0 SG A:CYS134 2.1 26.2 1.0 SG A:CYS137 2.4 23.5 1.0 CE1 A:HIS158 2.9 31.8 1.0 CE1 A:HIS155 2.9 22.3 1.0 HE1 A:HIS155 3.0 26.9 1.0 HE1 A:HIS158 3.0 38.3 1.0 CG A:HIS158 3.1 34.3 1.0 HB A:THR136 3.2 33.9 1.0 HB2 A:CYS137 3.2 26.1 1.0 HB3 A:HIS158 3.2 33.4 1.0 CG A:HIS155 3.2 25.9 1.0 HB3 A:HIS155 3.3 36.8 1.0 CB A:CYS134 3.3 26.2 1.0 HB3 A:CYS134 3.4 31.6 1.0 CB A:CYS137 3.4 21.6 1.0 HB2 A:CYS134 3.5 31.6 1.0 H A:CYS137 3.5 24.8 1.0 CB A:HIS158 3.6 27.8 1.0 HA A:HIS155 3.7 40.6 1.0 HB2 A:HIS158 3.7 33.4 1.0 CB A:HIS155 3.7 30.6 1.0 N A:CYS137 3.9 20.6 1.0 NE2 A:HIS158 4.0 33.7 1.0 NE2 A:HIS155 4.1 21.6 1.0 CB A:THR136 4.1 28.2 1.0 CD2 A:HIS158 4.2 34.2 1.0 HB3 A:CYS137 4.2 26.1 1.0 CA A:HIS155 4.2 33.7 1.0 CD2 A:HIS155 4.3 25.4 1.0 CA A:CYS137 4.3 25.5 1.0 HZ2 A:TRP178 4.4 25.0 1.0 H A:THR136 4.5 29.7 1.0 HB2 A:HIS155 4.6 36.8 1.0 HG21 A:THR136 4.6 34.2 1.0 HG22 A:THR136 4.6 34.2 1.0 C A:THR136 4.6 26.8 1.0 O A:ASP154 4.7 32.8 1.0 HB3 A:TYR160 4.7 32.8 1.0 HA3 A:GLY182 4.7 30.8 1.0 CA A:CYS134 4.7 22.7 1.0 HA A:CYS137 4.7 30.7 1.0 CG2 A:THR136 4.7 28.5 1.0 HE2 A:HIS158 4.8 40.5 1.0 HE1 A:PHE150 4.8 32.7 1.0 CA A:THR136 4.8 25.9 1.0 HE2 A:HIS155 4.8 26.0 1.0 HA2 A:GLY182 4.8 30.8 1.0 OG1 A:THR136 4.9 29.8 1.0 HA A:CYS134 4.9 27.4 1.0 N A:THR136 4.9 24.7 1.0 CZ2 A:TRP178 5.0 20.8 1.0 HG1 A:THR136 5.0 35.9 1.0

L.Kim, C.C.Lin, T.J.Lin, Y.C.Cao, M.C.Chen, M.Y.Chou, W.H.Lin, M.Kim, J.L.Wu, M.C.Shih, H.K.Song, M.C.Ho. Structural Analyses of Plant PRT6-Ubr Box For Cys-Arg/N-Degron Pathway and Insights Into the Plant Submergence Resistance To Be Published.