Zinc in PDB 7y6w: Rrgsgg-ATPRT6 Ubr Box (I222)

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

The structure of Rrgsgg-ATPRT6 Ubr Box (I222), PDB code: 7y6w 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)	40.54 / 1.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	39.17, 45.769, 87.293, 90, 90, 90
R / Rfree (%)	19.2 / 23

The binding sites of Zinc atom in the Rrgsgg-ATPRT6 Ubr Box (I222) (pdb code 7y6w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Rrgsgg-ATPRT6 Ubr Box (I222), PDB code: 7y6w:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:26.5 occ:1.00 ND1 A:HIS187 2.0 28.7 1.0 SG A:CYS184 2.2 26.7 1.0 SG A:CYS172 2.3 26.3 1.0 SG A:CYS149 2.5 26.4 1.0 CE1 A:HIS187 2.8 34.5 1.0 HB3 A:CYS172 2.8 32.1 1.0 HB3 A:CYS149 2.9 30.7 1.0 HE1 A:HIS187 2.9 41.3 1.0 HB2 A:HIS187 3.0 36.5 1.0 HB3 A:CYS184 3.0 30.9 1.0 CG A:HIS187 3.1 30.2 1.0 CB A:CYS172 3.1 26.8 1.0 CB A:CYS149 3.2 25.6 1.0 CB A:CYS184 3.2 25.7 1.0 H A:CYS184 3.3 32.4 1.0 HB2 A:CYS121 3.4 37.1 1.0 HB2 A:CYS172 3.5 32.1 1.0 HA A:CYS149 3.5 29.6 1.0 CB A:HIS187 3.6 30.4 1.0 CA A:CYS149 4.0 24.7 1.0 NE2 A:HIS187 4.0 30.8 1.0 HB2 A:CYS184 4.0 30.9 1.0 HB2 A:CYS149 4.0 30.7 1.0 N A:CYS184 4.0 27.0 1.0 CD2 A:HIS187 4.1 33.1 1.0 HB3 A:HIS187 4.2 36.5 1.0 CA A:CYS184 4.2 26.2 1.0 H A:HIS187 4.3 40.2 1.0 CB A:CYS121 4.3 31.0 1.0 HB2 A:ASN186 4.4 41.3 1.0 ZN A:ZN202 4.4 25.9 1.0 CA A:CYS172 4.4 26.7 1.0 N A:HIS187 4.5 33.5 1.0 H A:ASN186 4.6 36.7 1.0 C A:CYS172 4.6 30.8 1.0 HB3 A:CYS121 4.7 37.1 1.0 CA A:HIS187 4.7 32.1 1.0 HE2 A:HIS187 4.7 37.0 1.0 C A:CYS184 4.7 30.7 1.0 O A:CYS172 4.8 28.5 1.0 HA A:CYS172 4.8 32.0 1.0 O A:CYS184 4.9 30.1 1.0 C A:CYS149 4.9 22.6 1.0 SG A:CYS121 5.0 27.5 1.0 HD2 A:HIS187 5.0 39.6 1.0 HA A:PHE183 5.0 34.9 1.0 O A:CYS149 5.0 25.6 1.0

Zinc binding site 2 out of 3 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:25.9 occ:1.00 SG A:CYS121 2.2 27.5 1.0 SG A:CYS170 2.3 25.8 1.0 SG A:CYS149 2.3 26.4 1.0 SG A:CYS146 2.3 26.5 1.0 HB3 A:CYS170 3.0 33.7 1.0 H A:CYS146 3.0 29.0 1.0 HB3 A:CYS121 3.1 37.1 1.0 CB A:CYS121 3.1 31.0 1.0 HB2 A:CYS121 3.1 37.1 1.0 CB A:CYS170 3.1 28.1 1.0 HB2 A:CYS149 3.2 30.7 1.0 HB2 A:CYS170 3.2 33.7 1.0 HB3 A:CYS146 3.3 27.3 1.0 CB A:CYS149 3.4 25.6 1.0 CB A:CYS146 3.4 22.8 1.0 HB3 A:CYS172 3.5 32.1 1.0 HB3 A:SER123 3.5 43.8 1.0 N A:CYS146 3.8 24.2 1.0 H A:CYS149 3.9 32.3 1.0 HB3 A:CYS149 4.0 30.7 1.0 HB2 A:CYS172 4.1 32.1 1.0 CA A:CYS146 4.2 21.7 1.0 HE1 A:HIS187 4.2 41.3 1.0 HB2 A:CYS146 4.2 27.3 1.0 H A:SER123 4.2 46.6 1.0 CB A:CYS172 4.2 26.8 1.0 H A:CYS172 4.4 28.3 1.0 ZN A:ZN201 4.4 26.5 1.0 HB A:ILE145 4.4 29.2 1.0 CB A:SER123 4.5 36.5 1.0 CA A:CYS121 4.5 32.1 1.0 N A:CYS149 4.6 26.9 1.0 CA A:CYS149 4.6 24.7 1.0 CA A:CYS170 4.6 28.8 1.0 CE1 A:HIS187 4.7 34.5 1.0 HA A:ILE145 4.7 27.7 1.0 HB2 A:SER123 4.7 43.8 1.0 HD2 A:PRO148 4.8 32.8 1.0 HA A:CYS121 4.8 38.5 1.0 O A:CYS146 4.9 21.5 1.0 C A:CYS146 4.9 23.1 1.0 HA A:CYS149 5.0 29.6 1.0 C A:ILE145 5.0 24.5 1.0 C A:CYS121 5.0 32.7 1.0 HG A:SER123 5.0 61.3 1.0 HA A:CYS170 5.0 34.6 1.0 N A:SER123 5.0 38.9 1.0

Zinc binding site 3 out of 3 in the Rrgsgg-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 Rrgsgg-ATPRT6 Ubr Box (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:27.0 occ:1.00 ND1 A:HIS158 2.0 32.5 1.0 ND1 A:HIS155 2.0 25.8 1.0 SG A:CYS134 2.3 25.5 1.0 SG A:CYS137 2.3 29.0 1.0 CE1 A:HIS158 2.9 32.8 1.0 CE1 A:HIS155 2.9 31.0 1.0 HE1 A:HIS158 3.0 39.3 1.0 HE1 A:HIS155 3.0 37.2 1.0 HB3 A:HIS155 3.1 32.4 1.0 CG A:HIS155 3.1 25.3 1.0 CG A:HIS158 3.1 31.6 1.0 HB2 A:CYS137 3.2 28.8 1.0 HB3 A:HIS158 3.2 35.4 1.0 HB A:THR136 3.3 34.4 1.0 CB A:CYS137 3.4 24.0 1.0 CB A:CYS134 3.4 28.0 1.0 HB3 A:CYS134 3.4 33.6 1.0 H A:CYS137 3.5 27.7 1.0 CB A:HIS155 3.6 27.0 1.0 CB A:HIS158 3.6 29.5 1.0 HB2 A:HIS158 3.6 35.4 1.0 HB2 A:CYS134 3.6 33.6 1.0 HA A:HIS155 3.6 38.8 1.0 N A:CYS137 3.9 23.1 1.0 NE2 A:HIS158 4.0 30.7 1.0 NE2 A:HIS155 4.1 27.9 1.0 HB3 A:CYS137 4.1 28.8 1.0 CA A:HIS155 4.2 32.3 1.0 CD2 A:HIS158 4.2 33.8 1.0 CD2 A:HIS155 4.2 26.1 1.0 CB A:THR136 4.2 28.7 1.0 CA A:CYS137 4.3 26.4 1.0 HZ2 A:TRP178 4.3 29.2 1.0 HB2 A:HIS155 4.4 32.4 1.0 H A:THR136 4.5 29.0 1.0 HG22 A:THR136 4.5 40.5 1.0 HA A:CYS137 4.7 31.6 1.0 C A:THR136 4.7 27.7 1.0 CA A:CYS134 4.7 23.3 1.0 HE1 A:PHE150 4.7 32.9 1.0 HA2 A:GLY182 4.8 36.9 1.0 HA3 A:GLY182 4.8 36.9 1.0 HB3 A:TYR160 4.8 35.2 1.0 HE2 A:HIS158 4.8 36.8 1.0 O A:ASP154 4.8 30.3 1.0 HE2 A:HIS155 4.8 33.5 1.0 CG2 A:THR136 4.8 33.8 1.0 CA A:THR136 4.9 25.5 1.0 HG21 A:THR136 4.9 40.5 1.0 HG1 A:THR136 5.0 36.0 1.0 N A:THR136 5.0 24.2 1.0 HA A:CYS134 5.0 28.0 1.0 OG1 A:THR136 5.0 30.0 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.