Zinc in PDB 7xwg: Rsgsgg-ATPRT6 Ubr Box

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

The structure of Rsgsgg-ATPRT6 Ubr Box, PDB code: 7xwg 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)	33.15 / 1.83
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.915, 70.891, 93.719, 90, 90, 90
R / Rfree (%)	22.4 / 25.2

The binding sites of Zinc atom in the Rsgsgg-ATPRT6 Ubr Box (pdb code 7xwg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rsgsgg-ATPRT6 Ubr Box, PDB code: 7xwg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Rsgsgg-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 Rsgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:35.6 occ:1.00 ND1 A:HIS187 2.0 46.4 1.0 SG A:CYS172 2.2 34.9 1.0 SG A:CYS184 2.3 37.5 1.0 SG A:CYS149 2.4 33.5 1.0 CE1 A:HIS187 2.8 48.1 1.0 HB3 A:CYS184 2.8 42.0 1.0 HE1 A:HIS187 2.9 57.8 1.0 HB3 A:CYS172 2.9 45.6 1.0 CB A:CYS172 3.1 38.0 1.0 HB3 A:CYS149 3.1 41.7 1.0 CB A:CYS184 3.1 35.0 1.0 HB2 A:HIS187 3.1 58.4 1.0 CG A:HIS187 3.2 49.6 1.0 H A:CYS184 3.3 45.2 1.0 CB A:CYS149 3.3 34.8 1.0 HB2 A:CYS172 3.4 45.6 1.0 HA A:CYS149 3.5 41.1 1.0 HB2 A:CYS121 3.6 48.3 1.0 CB A:HIS187 3.7 48.7 1.0 HB2 A:CYS184 3.9 42.0 1.0 CA A:CYS149 4.0 34.3 1.0 N A:CYS184 4.0 37.7 1.0 NE2 A:HIS187 4.0 41.2 1.0 CA A:CYS184 4.1 37.8 1.0 HB2 A:CYS149 4.1 41.7 1.0 CD2 A:HIS187 4.2 44.9 1.0 H A:HIS187 4.3 52.4 1.0 HB3 A:HIS187 4.3 58.4 1.0 ZN A:ZN202 4.3 33.6 1.0 HB3 A:CYS121 4.4 48.3 1.0 CB A:CYS121 4.4 40.2 1.0 H A:ASN186 4.4 54.3 1.0 CA A:CYS172 4.4 29.3 1.0 HB2 A:ASN186 4.5 60.5 1.0 N A:HIS187 4.5 43.7 1.0 C A:CYS172 4.7 38.3 1.0 HE2 A:HIS187 4.7 49.5 1.0 C A:CYS184 4.7 41.5 1.0 CA A:HIS187 4.7 49.9 1.0 HA A:CYS172 4.8 35.2 1.0 C A:CYS149 4.9 30.9 1.0 O A:CYS172 4.9 35.0 1.0 O A:CYS149 4.9 38.7 1.0 HA A:CYS184 4.9 45.3 1.0 O A:CYS184 4.9 44.3 1.0 SG A:CYS121 5.0 35.1 1.0 HA A:PHE183 5.0 45.2 1.0

Zinc binding site 2 out of 6 in the Rsgsgg-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 Rsgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:33.6 occ:1.00 SG A:CYS170 2.3 29.0 1.0 SG A:CYS146 2.3 32.2 1.0 SG A:CYS149 2.3 33.5 1.0 SG A:CYS121 2.3 35.1 1.0 HB2 A:CYS149 2.9 41.7 1.0 H A:CYS146 3.1 37.0 1.0 CB A:CYS149 3.2 34.8 1.0 HB2 A:SER123 3.2 47.3 1.0 CB A:CYS170 3.2 30.1 1.0 HB3 A:CYS170 3.2 36.1 1.0 HB2 A:CYS170 3.2 36.1 1.0 HB3 A:CYS121 3.3 48.3 1.0 CB A:CYS121 3.4 40.2 1.0 HB3 A:CYS146 3.5 40.1 1.0 HB3 A:CYS172 3.5 45.6 1.0 CB A:CYS146 3.5 33.4 1.0 HB2 A:CYS121 3.6 48.3 1.0 HB3 A:CYS149 3.7 41.7 1.0 HB2 A:CYS172 3.8 45.6 1.0 H A:CYS149 3.9 36.9 1.0 N A:CYS146 3.9 30.8 1.0 CB A:SER123 4.1 39.5 1.0 CB A:CYS172 4.1 38.0 1.0 HE1 A:HIS187 4.1 57.8 1.0 HB A:ILE145 4.3 37.5 1.0 CA A:CYS146 4.3 28.9 1.0 HB2 A:CYS146 4.3 40.1 1.0 H A:SER123 4.3 51.2 1.0 HB3 A:SER123 4.3 47.3 1.0 ZN A:ZN201 4.3 35.6 1.0 H A:CYS172 4.4 40.6 1.0 CA A:CYS149 4.4 34.3 1.0 N A:CYS149 4.4 30.7 1.0 OG A:SER123 4.6 42.6 1.0 CE1 A:HIS187 4.6 48.1 1.0 CA A:CYS170 4.7 32.8 1.0 HA A:CYS149 4.7 41.1 1.0 HG A:SER123 4.7 51.1 1.0 HA A:ILE145 4.7 36.1 1.0 O A:CYS146 4.9 31.1 1.0 CA A:CYS121 4.9 38.3 1.0 C A:CYS146 4.9 29.5 1.0 HA A:CYS170 4.9 39.4 1.0 C A:ILE145 5.0 31.8 1.0

Zinc binding site 3 out of 6 in the Rsgsgg-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 Rsgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:31.5 occ:1.00 ND1 A:HIS155 2.0 26.6 1.0 ND1 A:HIS158 2.1 37.7 1.0 SG A:CYS134 2.2 32.2 1.0 SG A:CYS137 2.3 30.9 1.0 CE1 A:HIS155 2.8 37.3 1.0 HE1 A:HIS155 2.9 44.7 1.0 CE1 A:HIS158 3.0 37.3 1.0 HE1 A:HIS158 3.1 44.7 1.0 CG A:HIS155 3.1 36.6 1.0 HB3 A:HIS155 3.1 44.6 1.0 CG A:HIS158 3.2 37.0 1.0 HB2 A:CYS137 3.2 35.6 1.0 HB3 A:HIS158 3.3 44.6 1.0 HB A:THR136 3.3 40.8 1.0 CB A:CYS134 3.4 34.7 1.0 CB A:CYS137 3.4 29.7 1.0 HB3 A:CYS134 3.4 41.6 1.0 HB2 A:HIS158 3.5 44.6 1.0 CB A:HIS158 3.6 37.2 1.0 H A:CYS137 3.6 37.3 1.0 CB A:HIS155 3.6 37.1 1.0 HB2 A:CYS134 3.6 41.6 1.0 HA A:HIS155 3.8 47.7 1.0 N A:CYS137 4.0 31.1 1.0 NE2 A:HIS155 4.0 36.4 1.0 NE2 A:HIS158 4.1 35.1 1.0 HB3 A:CYS137 4.2 35.6 1.0 CD2 A:HIS155 4.2 34.2 1.0 CD2 A:HIS158 4.2 38.3 1.0 CA A:HIS155 4.3 39.8 1.0 CB A:THR136 4.3 34.0 1.0 HZ2 A:TRP178 4.3 42.4 1.0 CA A:CYS137 4.3 30.9 1.0 HB2 A:HIS155 4.4 44.6 1.0 HA3 A:GLY182 4.5 47.2 1.0 HG1 A:THR136 4.6 44.2 1.0 H A:THR136 4.6 41.8 1.0 HA2 A:GLY182 4.6 47.2 1.0 HA A:CYS137 4.7 37.0 1.0 HE2 A:HIS155 4.7 43.6 1.0 C A:THR136 4.8 37.7 1.0 CA A:CYS134 4.8 30.0 1.0 O A:HOH303 4.8 39.1 1.0 HG21 A:THR136 4.8 41.5 1.0 HB3 A:TYR160 4.8 42.2 1.0 HE1 A:PHE150 4.8 39.1 1.0 O A:ASP154 4.9 37.1 1.0 HE2 A:HIS158 4.9 42.1 1.0 CZ2 A:TRP178 4.9 35.3 1.0 HE1 A:TRP178 4.9 40.8 1.0 HG22 A:THR136 4.9 41.5 1.0 CG2 A:THR136 5.0 34.6 1.0 OG1 A:THR136 5.0 36.8 1.0 CA A:THR136 5.0 29.5 1.0

Zinc binding site 4 out of 6 in the Rsgsgg-ATPRT6 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rsgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:35.0 occ:1.00 ND1 B:HIS187 2.1 47.0 1.0 SG B:CYS172 2.3 35.2 1.0 SG B:CYS184 2.4 36.6 1.0 SG B:CYS149 2.5 31.9 1.0 CE1 B:HIS187 2.9 48.0 1.0 HB3 B:CYS184 2.9 41.9 1.0 HB3 B:CYS172 2.9 44.5 1.0 HE1 B:HIS187 2.9 57.6 1.0 HB3 B:CYS149 3.0 38.4 1.0 CB B:CYS172 3.1 37.1 1.0 HB2 B:HIS187 3.1 53.0 1.0 CB B:CYS184 3.2 34.9 1.0 CG B:HIS187 3.2 47.3 1.0 H B:CYS184 3.3 42.0 1.0 CB B:CYS149 3.3 32.0 1.0 HB2 B:CYS172 3.5 44.5 1.0 HA B:CYS149 3.5 39.0 1.0 HB2 B:CYS121 3.6 45.7 1.0 CB B:HIS187 3.7 44.1 1.0 HB2 B:CYS184 3.9 41.9 1.0 N B:CYS184 3.9 35.0 1.0 CA B:CYS149 4.0 32.5 1.0 NE2 B:HIS187 4.0 41.0 1.0 CA B:CYS184 4.1 34.5 1.0 HB2 B:CYS149 4.1 38.4 1.0 CD2 B:HIS187 4.2 42.6 1.0 H B:HIS187 4.3 55.1 1.0 HB3 B:HIS187 4.3 53.0 1.0 ZN B:ZN202 4.4 31.0 1.0 HB2 B:ASN186 4.4 59.5 1.0 H B:ASN186 4.4 54.4 1.0 CA B:CYS172 4.5 32.5 1.0 CB B:CYS121 4.5 38.1 1.0 N B:HIS187 4.5 45.9 1.0 C B:CYS184 4.7 38.4 1.0 C B:CYS172 4.7 39.3 1.0 O B:CYS172 4.8 32.5 1.0 CA B:HIS187 4.8 47.1 1.0 HE2 B:HIS187 4.8 49.2 1.0 HB3 B:CYS121 4.8 45.7 1.0 O B:CYS184 4.8 38.7 1.0 HA B:CYS172 4.9 39.0 1.0 HA B:CYS184 4.9 41.4 1.0 C B:CYS149 4.9 30.5 1.0 SG B:CYS121 4.9 38.5 1.0 O B:CYS149 4.9 32.5 1.0

Zinc binding site 5 out of 6 in the Rsgsgg-ATPRT6 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rsgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:31.0 occ:1.00 SG B:CYS170 2.3 30.5 1.0 SG B:CYS146 2.3 29.5 1.0 SG B:CYS149 2.4 31.9 1.0 SG B:CYS121 2.4 38.5 1.0 HB2 B:CYS149 3.0 38.4 1.0 H B:CYS146 3.1 36.7 1.0 HB3 B:CYS121 3.1 45.7 1.0 CB B:CYS170 3.2 31.2 1.0 HB3 B:CYS170 3.2 37.4 1.0 HB2 B:CYS170 3.2 37.4 1.0 CB B:CYS121 3.2 38.1 1.0 CB B:CYS149 3.3 32.0 1.0 HB2 B:CYS121 3.3 45.7 1.0 HB2 B:SER123 3.3 42.0 1.0 HB3 B:CYS172 3.5 44.5 1.0 HB3 B:CYS146 3.5 37.9 1.0 CB B:CYS146 3.6 31.6 1.0 HB3 B:CYS149 3.8 38.4 1.0 HB2 B:CYS172 3.8 44.5 1.0 N B:CYS146 3.9 30.6 1.0 H B:CYS149 3.9 35.9 1.0 HE1 B:HIS187 4.1 57.6 1.0 CB B:CYS172 4.1 37.1 1.0 CB B:SER123 4.2 35.0 1.0 HB B:ILE145 4.3 36.8 1.0 CA B:CYS146 4.3 30.5 1.0 H B:SER123 4.3 48.6 1.0 HB2 B:CYS146 4.3 37.9 1.0 H B:CYS172 4.3 42.1 1.0 ZN B:ZN201 4.4 35.0 1.0 CA B:CYS149 4.5 32.5 1.0 HG B:SER123 4.5 46.0 1.0 N B:CYS149 4.5 29.9 1.0 OG B:SER123 4.5 38.3 1.0 HB3 B:SER123 4.6 42.0 1.0 CA B:CYS170 4.6 30.3 1.0 CE1 B:HIS187 4.7 48.0 1.0 HA B:ILE145 4.7 39.6 1.0 CA B:CYS121 4.7 36.2 1.0 O B:CYS146 4.8 29.0 1.0 HA B:CYS149 4.8 39.0 1.0 C B:CYS146 4.9 32.4 1.0 HA B:CYS170 4.9 36.3 1.0 C B:ILE145 5.0 29.4 1.0

Zinc binding site 6 out of 6 in the Rsgsgg-ATPRT6 Ubr Box


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rsgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:31.8 occ:1.00 ND1 B:HIS155 1.9 29.1 1.0 ND1 B:HIS158 2.1 37.1 1.0 SG B:CYS134 2.3 31.6 1.0 SG B:CYS137 2.3 30.8 1.0 CE1 B:HIS155 2.7 33.4 1.0 HE1 B:HIS155 2.7 40.1 1.0 CE1 B:HIS158 3.0 39.4 1.0 HE1 B:HIS158 3.1 47.3 1.0 CG B:HIS155 3.1 31.5 1.0 CG B:HIS158 3.1 39.3 1.0 HB B:THR136 3.2 40.2 1.0 HB3 B:HIS158 3.3 41.0 1.0 HB3 B:HIS155 3.3 42.0 1.0 HB2 B:CYS137 3.3 38.5 1.0 HB3 B:CYS134 3.4 35.6 1.0 CB B:CYS134 3.4 29.7 1.0 CB B:CYS137 3.4 32.1 1.0 H B:CYS137 3.5 38.5 1.0 HB2 B:HIS158 3.5 41.0 1.0 CB B:HIS158 3.5 34.1 1.0 HB2 B:CYS134 3.6 35.6 1.0 CB B:HIS155 3.7 35.0 1.0 HA B:HIS155 3.8 47.0 1.0 N B:CYS137 3.9 32.0 1.0 NE2 B:HIS155 3.9 29.4 1.0 CD2 B:HIS155 4.1 32.2 1.0 NE2 B:HIS158 4.1 35.3 1.0 HB3 B:CYS137 4.2 38.5 1.0 CB B:THR136 4.2 33.5 1.0 CD2 B:HIS158 4.2 40.1 1.0 HZ2 B:TRP178 4.2 38.5 1.0 CA B:CYS137 4.3 33.6 1.0 CA B:HIS155 4.3 39.2 1.0 HG1 B:THR136 4.5 48.7 1.0 H B:THR136 4.5 41.2 1.0 HB2 B:HIS155 4.5 42.0 1.0 HE2 B:HIS155 4.6 35.3 1.0 C B:THR136 4.7 38.6 1.0 HA3 B:GLY182 4.7 43.9 1.0 HA B:CYS137 4.7 40.3 1.0 HE1 B:PHE150 4.7 35.4 1.0 CA B:CYS134 4.7 28.2 1.0 HG21 B:THR136 4.8 43.6 1.0 CZ2 B:TRP178 4.8 32.1 1.0 OG1 B:THR136 4.9 40.6 1.0 CA B:THR136 4.9 35.3 1.0 HB3 B:TYR160 4.9 40.7 1.0 HE1 B:TRP178 4.9 36.2 1.0 HE2 B:HIS158 4.9 42.3 1.0 HA2 B:GLY182 4.9 43.9 1.0 CG2 B:THR136 5.0 36.3 1.0 N B:THR136 5.0 34.3 1.0 O B:ASP154 5.0 40.0 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.