Zinc in PDB 7xwf: Rlgsgg-ATPRT6 Ubr Box (Highest Resolution)

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

The structure of Rlgsgg-ATPRT6 Ubr Box (Highest Resolution), PDB code: 7xwf 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)	36.06 / 1.45
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	39.618, 45.795, 87.085, 90, 90, 90
R / Rfree (%)	18.9 / 21

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

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


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 (Highest Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:15.2 occ:1.00 ND1 A:HIS187 2.0 16.4 1.0 SG A:CYS172 2.2 15.2 1.0 SG A:CYS184 2.3 16.2 1.0 SG A:CYS149 2.4 13.6 1.0 HB3 A:CYS172 2.9 15.5 1.0 CE1 A:HIS187 2.9 19.2 1.0 HB2 A:HIS187 3.0 20.8 1.0 HB3 A:CYS149 3.0 17.0 1.0 HE1 A:HIS187 3.0 23.1 1.0 CG A:HIS187 3.1 19.1 1.0 CB A:CYS172 3.1 12.9 1.0 HB3 A:CYS184 3.2 19.6 1.0 CB A:CYS149 3.2 14.2 1.0 H A:CYS184 3.3 19.3 1.0 CB A:CYS184 3.4 16.3 1.0 HA A:CYS149 3.5 17.3 1.0 HB2 A:CYS172 3.5 15.5 1.0 CB A:HIS187 3.5 17.3 1.0 HB2 A:CYS121 3.6 21.0 1.0 CA A:CYS149 4.0 14.4 1.0 N A:CYS184 4.0 16.0 1.0 NE2 A:HIS187 4.1 20.8 1.0 HB2 A:CYS149 4.1 17.0 1.0 HB2 A:CYS184 4.1 19.6 1.0 HB3 A:HIS187 4.1 20.8 1.0 CD2 A:HIS187 4.2 21.3 1.0 CA A:CYS184 4.2 15.7 1.0 H A:HIS187 4.3 22.5 1.0 HB2 A:ASN186 4.3 24.6 1.0 O A:HOH314 4.3 21.4 1.0 ZN A:ZN202 4.4 14.5 1.0 CA A:CYS172 4.4 13.3 1.0 N A:HIS187 4.5 18.7 1.0 CB A:CYS121 4.5 17.5 1.0 H A:ASN186 4.5 21.5 1.0 C A:CYS172 4.6 14.7 1.0 CA A:HIS187 4.6 19.1 1.0 O A:CYS172 4.7 16.5 1.0 C A:CYS184 4.8 17.3 1.0 HB3 A:CYS121 4.8 21.0 1.0 HE2 A:HIS187 4.8 25.1 1.0 HA A:CYS172 4.8 16.0 1.0 O A:CYS184 4.9 16.2 1.0 C A:CYS149 4.9 14.6 1.0 O A:CYS149 5.0 15.3 1.0 HA A:PHE183 5.0 18.0 1.0

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


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 (Highest Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:14.5 occ:1.00 SG A:CYS170 2.3 13.2 1.0 SG A:CYS146 2.3 13.0 1.0 SG A:CYS121 2.3 16.8 1.0 SG A:CYS149 2.4 13.6 1.0 HB2 A:CYS149 3.0 17.0 1.0 HB3 A:CYS170 3.1 17.0 1.0 HB3 A:CYS121 3.1 21.0 1.0 CB A:CYS170 3.1 14.1 1.0 H A:CYS146 3.1 13.1 1.0 CB A:CYS121 3.2 17.5 1.0 HB2 A:CYS170 3.2 17.0 1.0 HB2 A:CYS121 3.2 21.0 1.0 CB A:CYS149 3.3 14.2 1.0 HB3 A:CYS146 3.3 16.4 1.0 HB3 A:CYS172 3.4 15.5 1.0 CB A:CYS146 3.4 13.6 1.0 HB2 A:SER123 3.7 31.3 1.0 HB3 A:CYS149 3.8 17.0 1.0 H A:CYS149 3.9 17.9 1.0 N A:CYS146 3.9 10.8 1.0 HB2 A:CYS172 4.0 15.5 1.0 HE1 A:HIS187 4.1 23.1 1.0 CB A:CYS172 4.1 12.9 1.0 HB2 A:CYS146 4.2 16.4 1.0 CA A:CYS146 4.2 13.6 1.0 H A:SER123 4.3 26.6 1.0 H A:CYS172 4.3 16.1 1.0 HB A:ILE145 4.3 15.7 1.0 ZN A:ZN201 4.4 15.2 1.0 CA A:CYS149 4.5 14.4 1.0 N A:CYS149 4.5 14.8 1.0 HG A:SER123 4.5 35.3 1.0 CB A:SER123 4.6 26.0 1.0 OG A:SER123 4.6 29.3 1.0 CE1 A:HIS187 4.6 19.2 1.0 CA A:CYS170 4.6 15.1 1.0 CA A:CYS121 4.6 21.1 1.0 HA A:ILE145 4.8 14.8 1.0 HA A:CYS149 4.8 17.3 1.0 O A:CYS146 4.9 13.6 1.0 C A:CYS146 4.9 13.3 1.0 HA A:CYS121 5.0 25.4 1.0 ND1 A:HIS187 5.0 16.4 1.0 HA A:CYS170 5.0 18.2 1.0

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


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 (Highest Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:15.4 occ:1.00 ND1 A:HIS158 2.0 17.8 1.0 ND1 A:HIS155 2.1 12.1 1.0 SG A:CYS134 2.3 14.6 1.0 SG A:CYS137 2.3 14.9 1.0 CE1 A:HIS155 2.9 15.2 1.0 CE1 A:HIS158 2.9 17.2 1.0 HE1 A:HIS155 3.0 18.2 1.0 HE1 A:HIS158 3.0 20.7 1.0 HB2 A:CYS137 3.1 14.0 1.0 CG A:HIS158 3.2 20.0 1.0 CG A:HIS155 3.2 15.8 1.0 HB3 A:HIS155 3.2 18.9 1.0 HB3 A:HIS158 3.3 20.3 1.0 HB A:THR136 3.3 20.5 1.0 CB A:CYS137 3.3 11.6 1.0 CB A:CYS134 3.4 14.0 1.0 HB3 A:CYS134 3.4 16.8 1.0 HB2 A:CYS134 3.6 16.8 1.0 CB A:HIS158 3.6 16.9 1.0 HA A:HIS155 3.6 24.0 1.0 CB A:HIS155 3.7 15.7 1.0 HB2 A:HIS158 3.7 20.3 1.0 H A:CYS137 3.7 14.2 1.0 N A:CYS137 4.0 11.8 1.0 NE2 A:HIS155 4.1 16.6 1.0 NE2 A:HIS158 4.1 20.7 1.0 HB3 A:CYS137 4.1 14.0 1.0 CD2 A:HIS158 4.2 21.0 1.0 CB A:THR136 4.2 17.1 1.0 CD2 A:HIS155 4.2 15.9 1.0 CA A:HIS155 4.2 20.0 1.0 CA A:CYS137 4.3 12.2 1.0 HZ2 A:TRP178 4.4 15.6 1.0 HB2 A:HIS155 4.5 18.9 1.0 H A:THR136 4.6 16.1 1.0 HA A:CYS137 4.6 14.7 1.0 HA3 A:GLY182 4.6 18.8 1.0 C A:THR136 4.7 16.1 1.0 HA2 A:GLY182 4.7 18.8 1.0 CA A:CYS134 4.7 13.1 1.0 O A:ASP154 4.7 22.4 1.0 HG21 A:THR136 4.7 22.7 1.0 HB3 A:TYR160 4.7 18.2 1.0 HE1 A:PHE150 4.8 19.3 1.0 HG22 A:THR136 4.8 22.7 1.0 HE2 A:HIS155 4.8 20.0 1.0 HE2 A:HIS158 4.8 24.9 1.0 CG2 A:THR136 4.9 18.9 1.0 CA A:THR136 4.9 16.2 1.0 HA A:CYS134 4.9 15.7 1.0 HG1 A:THR136 4.9 23.9 1.0 CZ2 A:TRP178 5.0 12.9 1.0 OG1 A:THR136 5.0 19.9 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.