Zinc in PDB 7xwe: Rrgsgg-ATPRT6 Ubr Box

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

The structure of Rrgsgg-ATPRT6 Ubr Box, PDB code: 7xwe 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)	40.01 / 1.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.192, 55.859, 57.323, 90, 90, 90
R / Rfree (%)	17.7 / 20

The structure of Rrgsgg-ATPRT6 Ubr Box also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

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

Zinc binding site 1 out of 6 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:14.7 occ:1.00 ND1 A:HIS187 2.0 16.9 1.0 SG A:CYS172 2.2 14.0 1.0 SG A:CYS184 2.3 15.1 1.0 SG A:CYS149 2.4 13.8 1.0 HB2 A:HIS187 2.9 22.9 1.0 CE1 A:HIS187 2.9 22.6 1.0 HB3 A:CYS149 2.9 16.4 1.0 HB3 A:CYS172 2.9 14.8 1.0 HB3 A:CYS184 3.0 14.6 1.0 HE1 A:HIS187 3.1 27.2 1.0 CG A:HIS187 3.1 20.7 1.0 CB A:CYS172 3.1 12.3 1.0 CB A:CYS149 3.2 13.7 1.0 CB A:CYS184 3.3 12.2 1.0 H A:CYS184 3.3 18.7 1.0 HB2 A:CYS121 3.4 19.0 1.0 CB A:HIS187 3.5 19.1 1.0 HB2 A:CYS172 3.5 14.8 1.0 HA A:CYS149 3.6 16.7 1.0 HB2 A:CYS184 4.0 14.6 1.0 CA A:CYS149 4.0 13.9 1.0 HB2 A:CYS149 4.0 16.4 1.0 N A:CYS184 4.1 15.5 1.0 H A:HIS187 4.1 22.6 1.0 NE2 A:HIS187 4.1 23.2 1.0 HB3 A:HIS187 4.1 22.9 1.0 CD2 A:HIS187 4.2 20.5 1.0 CA A:CYS184 4.2 14.1 1.0 CB A:CYS121 4.3 15.8 1.0 ZN A:ZN503 4.3 13.9 1.0 N A:HIS187 4.4 18.8 1.0 HB2 A:ASN186 4.4 24.5 1.0 CA A:CYS172 4.5 13.6 1.0 CA A:HIS187 4.6 19.8 1.0 H A:ASN186 4.6 21.5 1.0 HB3 A:CYS121 4.7 19.0 1.0 C A:CYS172 4.7 14.8 1.0 C A:CYS184 4.8 14.3 1.0 HE2 A:HIS187 4.8 27.9 1.0 O A:CYS172 4.8 15.0 1.0 HA A:CYS172 4.9 16.3 1.0 O A:CYS184 4.9 15.3 1.0 C A:CYS149 4.9 13.6 1.0 SG A:CYS121 4.9 14.2 1.0

Zinc binding site 2 out of 6 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:13.9 occ:1.00 SG A:CYS121 2.3 14.2 1.0 SG A:CYS149 2.3 13.8 1.0 SG A:CYS146 2.3 13.7 1.0 SG A:CYS170 2.3 12.9 1.0 H A:CYS146 3.1 16.4 1.0 HB3 A:CYS170 3.1 17.0 1.0 CB A:CYS121 3.2 15.8 1.0 CB A:CYS170 3.2 14.1 1.0 HB2 A:CYS149 3.2 16.4 1.0 HB2 A:CYS121 3.2 19.0 1.0 HB2 A:CYS170 3.2 17.0 1.0 HB3 A:CYS121 3.2 19.0 1.0 HB3 A:CYS146 3.3 18.2 1.0 CB A:CYS149 3.4 13.7 1.0 HB3 A:CYS172 3.4 14.8 1.0 CB A:CYS146 3.4 15.2 1.0 HB2 A:SER123 3.6 31.1 1.0 HB2 A:CYS172 3.9 14.8 1.0 N A:CYS146 3.9 13.7 1.0 H A:CYS149 3.9 17.3 1.0 HB3 A:CYS149 3.9 16.4 1.0 HE1 A:HIS187 4.1 27.2 1.0 CB A:CYS172 4.1 12.3 1.0 HB2 A:CYS146 4.2 18.2 1.0 CA A:CYS146 4.2 13.8 1.0 ZN A:ZN502 4.3 14.7 1.0 H A:CYS172 4.3 16.5 1.0 H A:SER123 4.3 33.2 1.0 HB A:ILE145 4.4 16.7 1.0 HG A:SER123 4.5 42.1 1.0 CB A:SER123 4.5 25.9 1.0 N A:CYS149 4.5 14.4 1.0 CA A:CYS149 4.6 13.9 1.0 CE1 A:HIS187 4.6 22.6 1.0 CA A:CYS121 4.6 15.5 1.0 OG A:SER123 4.6 35.1 1.0 CA A:CYS170 4.7 15.0 1.0 HA A:ILE145 4.8 14.9 1.0 O A:CYS146 4.9 12.3 1.0 ND1 A:HIS187 4.9 16.9 1.0 C A:CYS146 4.9 13.3 1.0 HA A:CYS121 4.9 18.6 1.0 HA A:CYS149 4.9 16.7 1.0 HA A:CYS170 5.0 18.1 1.0

Zinc binding site 3 out of 6 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:13.1 occ:1.00 ND1 A:HIS155 2.1 12.4 1.0 ND1 A:HIS158 2.1 12.7 1.0 SG A:CYS137 2.3 13.9 1.0 SG A:CYS134 2.3 12.3 1.0 CE1 A:HIS155 2.9 12.6 1.0 CE1 A:HIS158 2.9 15.1 1.0 HE1 A:HIS155 2.9 15.2 1.0 HE1 A:HIS158 3.0 18.1 1.0 HB2 A:CYS137 3.1 16.2 1.0 CG A:HIS158 3.2 15.4 1.0 CG A:HIS155 3.2 11.9 1.0 HB3 A:HIS155 3.3 14.8 1.0 HB A:THR136 3.3 18.8 1.0 CB A:CYS137 3.3 13.5 1.0 HB3 A:HIS158 3.3 14.3 1.0 CB A:CYS134 3.4 10.7 1.0 HB3 A:CYS134 3.4 12.9 1.0 HB2 A:CYS134 3.6 12.9 1.0 HA A:HIS155 3.6 15.5 1.0 H A:CYS137 3.6 15.4 1.0 CB A:HIS158 3.6 11.9 1.0 HB2 A:HIS158 3.6 14.3 1.0 CB A:HIS155 3.7 12.3 1.0 N A:CYS137 3.9 12.8 1.0 HB3 A:CYS137 4.0 16.2 1.0 NE2 A:HIS155 4.1 13.2 1.0 NE2 A:HIS158 4.1 16.7 1.0 CA A:HIS155 4.2 12.9 1.0 CA A:CYS137 4.2 12.8 1.0 CD2 A:HIS158 4.2 15.5 1.0 CD2 A:HIS155 4.2 14.3 1.0 CB A:THR136 4.3 15.7 1.0 HZ2 A:TRP178 4.3 13.6 1.0 HA3 A:GLY182 4.5 18.5 1.0 H A:THR136 4.5 16.6 1.0 HB2 A:HIS155 4.6 14.8 1.0 HA A:CYS137 4.6 15.4 1.0 HG22 A:THR136 4.6 20.5 1.0 O A:ASP154 4.7 18.4 1.0 C A:THR136 4.7 14.3 1.0 CA A:CYS134 4.7 11.7 1.0 HB3 A:TYR160 4.8 15.8 1.0 HA2 A:GLY182 4.8 18.5 1.0 HE1 A:PHE150 4.8 17.9 1.0 HE2 A:HIS155 4.8 15.9 1.0 HE2 A:HIS158 4.8 20.0 1.0 CG2 A:THR136 4.9 17.1 1.0 CA A:THR136 4.9 13.1 1.0 CZ2 A:TRP178 4.9 11.3 1.0 HG21 A:THR136 4.9 20.5 1.0 HA A:CYS134 5.0 14.1 1.0

Zinc binding site 4 out of 6 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:15.1 occ:1.00 ND1 B:HIS187 2.1 16.2 1.0 SG B:CYS184 2.3 15.2 1.0 SG B:CYS172 2.3 14.4 1.0 SG B:CYS149 2.4 14.2 1.0 HB3 B:CYS172 2.8 17.7 1.0 HB2 B:HIS187 2.9 18.6 1.0 CE1 B:HIS187 2.9 16.4 1.0 HB3 B:CYS149 3.0 13.8 1.0 HE1 B:HIS187 3.1 19.7 1.0 CB B:CYS172 3.1 14.8 1.0 HB3 B:CYS184 3.1 17.5 1.0 CG B:HIS187 3.1 16.1 1.0 CB B:CYS149 3.2 11.4 1.0 H B:CYS184 3.3 19.1 1.0 CB B:CYS184 3.3 14.6 1.0 HB2 B:CYS172 3.5 17.7 1.0 CB B:HIS187 3.5 15.5 1.0 HA B:CYS149 3.6 16.6 1.0 HB2 B:CYS121 3.6 18.5 1.0 CA B:CYS149 4.0 13.8 1.0 N B:CYS184 4.0 15.9 1.0 HB2 B:CYS149 4.1 13.8 1.0 HB2 B:CYS184 4.1 17.5 1.0 H B:HIS187 4.1 22.3 1.0 NE2 B:HIS187 4.1 19.4 1.0 CA B:CYS184 4.2 16.0 1.0 HB3 B:HIS187 4.2 18.6 1.0 CD2 B:HIS187 4.2 17.1 1.0 HB2 B:ASN186 4.2 22.8 1.0 N B:HIS187 4.3 18.6 1.0 ZN B:ZN202 4.4 14.0 1.0 CA B:CYS172 4.4 13.2 1.0 H B:ASN186 4.5 22.4 1.0 CA B:HIS187 4.5 18.9 1.0 CB B:CYS121 4.6 15.4 1.0 C B:CYS172 4.6 14.9 1.0 C B:CYS184 4.8 16.6 1.0 O B:CYS172 4.8 15.9 1.0 HA B:CYS172 4.9 15.8 1.0 HE2 B:HIS187 4.9 23.3 1.0 C B:CYS149 4.9 14.2 1.0 C B:ASN186 4.9 23.0 1.0 HA B:PHE183 4.9 16.3 1.0 HB3 B:CYS121 4.9 18.5 1.0 O B:CYS184 4.9 16.8 1.0 O B:CYS149 5.0 13.8 1.0

Zinc binding site 5 out of 6 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:14.0 occ:1.00 SG B:CYS121 2.3 16.0 1.0 SG B:CYS170 2.3 14.0 1.0 SG B:CYS146 2.3 15.0 1.0 SG B:CYS149 2.4 14.2 1.0 HB2 B:CYS149 3.1 13.8 1.0 HB3 B:CYS121 3.1 18.5 1.0 CB B:CYS121 3.1 15.4 1.0 HB3 B:CYS170 3.1 15.5 1.0 HB2 B:CYS121 3.1 18.5 1.0 H B:CYS146 3.1 14.8 1.0 CB B:CYS170 3.2 12.9 1.0 HB2 B:CYS170 3.2 15.5 1.0 CB B:CYS149 3.4 11.4 1.0 HB3 B:CYS146 3.4 15.3 1.0 CB B:CYS146 3.5 12.8 1.0 HB3 B:CYS172 3.5 17.7 1.0 HB2 B:SER123 3.7 24.3 1.0 HB2 B:CYS172 3.9 17.7 1.0 H B:CYS149 3.9 17.5 1.0 HB3 B:CYS149 3.9 13.8 1.0 N B:CYS146 3.9 12.3 1.0 HE1 B:HIS187 4.0 19.7 1.0 HG B:SER123 4.0 37.8 1.0 CB B:CYS172 4.1 14.8 1.0 H B:SER123 4.2 26.0 1.0 HB2 B:CYS146 4.3 15.3 1.0 OG B:SER123 4.3 31.5 1.0 CA B:CYS146 4.3 13.5 1.0 H B:CYS172 4.3 18.7 1.0 HB B:ILE145 4.3 15.7 1.0 ZN B:ZN201 4.4 15.1 1.0 CB B:SER123 4.4 20.2 1.0 N B:CYS149 4.5 14.6 1.0 CA B:CYS149 4.5 13.8 1.0 CA B:CYS121 4.6 16.8 1.0 CE1 B:HIS187 4.6 16.4 1.0 CA B:CYS170 4.6 14.6 1.0 HA B:ILE145 4.7 15.0 1.0 HA B:CYS121 4.9 20.2 1.0 H B:GLY122 4.9 22.6 1.0 HA B:CYS149 4.9 16.6 1.0 O B:CYS146 4.9 13.2 1.0 ND1 B:HIS187 4.9 16.2 1.0 C B:CYS146 4.9 13.0 1.0 N B:SER123 5.0 21.7 1.0 HA B:CYS170 5.0 17.5 1.0

Zinc binding site 6 out of 6 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:13.2 occ:1.00 ND1 B:HIS155 2.1 11.6 1.0 ND1 B:HIS158 2.1 12.5 1.0 SG B:CYS134 2.3 12.3 1.0 SG B:CYS137 2.3 14.2 1.0 CE1 B:HIS155 2.9 13.4 1.0 CE1 B:HIS158 3.0 14.7 1.0 HE1 B:HIS155 3.0 16.2 1.0 HE1 B:HIS158 3.1 17.6 1.0 CG B:HIS158 3.2 15.1 1.0 CG B:HIS155 3.2 12.6 1.0 HB2 B:CYS137 3.2 13.9 1.0 HB B:THR136 3.2 18.4 1.0 HB3 B:HIS155 3.3 14.0 1.0 HB3 B:HIS158 3.3 12.8 1.0 CB B:CYS134 3.4 11.6 1.0 CB B:CYS137 3.4 11.6 1.0 HB3 B:CYS134 3.4 14.0 1.0 H B:CYS137 3.5 13.5 1.0 HB2 B:CYS134 3.6 14.0 1.0 CB B:HIS158 3.6 10.7 1.0 HB2 B:HIS158 3.6 12.8 1.0 HA B:HIS155 3.6 14.7 1.0 CB B:HIS155 3.7 11.7 1.0 N B:CYS137 3.9 11.2 1.0 NE2 B:HIS155 4.1 12.1 1.0 NE2 B:HIS158 4.1 16.5 1.0 HB3 B:CYS137 4.2 13.9 1.0 CB B:THR136 4.2 15.3 1.0 CA B:HIS155 4.2 12.2 1.0 CD2 B:HIS158 4.2 16.3 1.0 CD2 B:HIS155 4.3 13.1 1.0 CA B:CYS137 4.3 11.9 1.0 HZ2 B:TRP178 4.4 13.6 1.0 HG21 B:THR136 4.4 18.3 1.0 HA3 B:GLY182 4.5 19.6 1.0 HB2 B:HIS155 4.6 14.0 1.0 H B:THR136 4.6 16.9 1.0 C B:THR136 4.6 14.9 1.0 HA B:CYS137 4.7 14.3 1.0 O B:ASP154 4.7 17.1 1.0 CG2 B:THR136 4.7 15.2 1.0 CA B:CYS134 4.7 12.0 1.0 HA2 B:GLY182 4.8 19.6 1.0 HB3 B:TYR160 4.8 15.5 1.0 HG23 B:THR136 4.8 18.3 1.0 HE1 B:PHE150 4.8 16.3 1.0 HE2 B:HIS155 4.8 14.6 1.0 CA B:THR136 4.9 13.0 1.0 HE2 B:HIS158 4.9 19.8 1.0 CZ2 B:TRP178 4.9 11.3 1.0 HA B:CYS134 5.0 14.4 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.