Zinc in PDB 7y70: Rlgsgg-ATPRT6 Ubr Box (P4332)

All present enzymatic activity of Rlgsgg-ATPRT6 Ubr Box (P4332):
2.3.2.27;

The structure of Rlgsgg-ATPRT6 Ubr Box (P4332), PDB code: 7y70 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)	38.89 / 1.80
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	95.254, 95.254, 95.254, 90, 90, 90
R / Rfree (%)	21 / 22.3

The binding sites of Zinc atom in the Rlgsgg-ATPRT6 Ubr Box (P4332) (pdb code 7y70). 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 (P4332), PDB code: 7y70:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rlgsgg-ATPRT6 Ubr Box (P4332)


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 (P4332) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.1 occ:1.00 SG A:CYS149 2.3 31.1 1.0 SG A:CYS121 2.3 32.3 1.0 SG A:CYS170 2.3 25.2 1.0 SG A:CYS146 2.4 29.2 1.0 HB3 A:CYS121 3.1 44.1 1.0 CB A:CYS121 3.1 36.8 1.0 HB2 A:CYS121 3.1 44.1 1.0 HB3 A:CYS170 3.1 29.9 1.0 HB2 A:CYS170 3.1 29.9 1.0 CB A:CYS170 3.1 24.9 1.0 H A:CYS146 3.1 33.4 1.0 HB2 A:CYS149 3.2 37.6 1.0 HB3 A:CYS146 3.3 31.7 1.0 CB A:CYS149 3.4 31.3 1.0 CB A:CYS146 3.5 26.4 1.0 HB3 A:CYS172 3.5 37.7 1.0 HB2 A:SER123 3.5 64.4 1.0 HG A:SER123 3.7 70.7 1.0 HB2 A:CYS172 3.8 37.7 1.0 H A:CYS149 3.9 37.3 1.0 HB3 A:CYS149 3.9 37.6 1.0 N A:CYS146 3.9 27.8 1.0 HE1 A:HIS187 4.0 50.2 1.0 OG A:SER123 4.0 55.3 1.0 CB A:CYS172 4.1 31.4 1.0 HB2 A:CYS146 4.2 31.7 1.0 CB A:SER123 4.2 50.0 1.0 CA A:CYS146 4.3 25.4 1.0 H A:CYS172 4.3 35.2 1.0 HB A:ILE145 4.3 30.8 1.0 ZN A:ZN202 4.4 33.2 1.0 H A:SER123 4.4 54.0 1.0 CE1 A:HIS187 4.5 41.8 1.0 N A:CYS149 4.5 31.1 1.0 CA A:CYS121 4.6 37.3 1.0 CA A:CYS149 4.6 28.6 1.0 CA A:CYS170 4.6 24.4 1.0 HA A:ILE145 4.7 27.3 1.0 HB3 A:SER123 4.8 64.4 1.0 HA A:CYS121 4.8 44.7 1.0 ND1 A:HIS187 4.9 41.5 1.0 C A:CYS146 4.9 27.0 1.0 HA A:CYS149 4.9 34.4 1.0 HA A:CYS170 4.9 29.2 1.0 O A:CYS146 5.0 25.2 1.0

Zinc binding site 2 out of 3 in the Rlgsgg-ATPRT6 Ubr Box (P4332)


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 (P4332) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:33.2 occ:1.00 ND1 A:HIS187 2.1 41.5 1.0 SG A:CYS172 2.3 30.0 1.0 SG A:CYS184 2.3 32.8 1.0 SG A:CYS149 2.5 31.1 1.0 HB3 A:CYS172 2.8 37.7 1.0 HB2 A:HIS187 2.8 49.4 1.0 HB3 A:CYS149 2.9 37.6 1.0 CE1 A:HIS187 3.0 41.8 1.0 CB A:CYS172 3.1 31.4 1.0 CG A:HIS187 3.1 39.8 1.0 HE1 A:HIS187 3.1 50.2 1.0 HB3 A:CYS184 3.2 39.4 1.0 CB A:CYS149 3.2 31.3 1.0 H A:CYS184 3.3 41.5 1.0 CB A:CYS184 3.4 32.9 1.0 HB2 A:CYS172 3.4 37.7 1.0 CB A:HIS187 3.5 41.1 1.0 HA A:CYS149 3.5 34.4 1.0 HB2 A:CYS121 3.6 44.1 1.0 CA A:CYS149 3.9 28.6 1.0 HB3 A:HIS187 4.0 49.4 1.0 HB2 A:CYS149 4.0 37.6 1.0 N A:CYS184 4.1 34.6 1.0 NE2 A:HIS187 4.1 45.4 1.0 HB2 A:CYS184 4.1 39.4 1.0 CD2 A:HIS187 4.2 44.4 1.0 CA A:CYS184 4.3 39.2 1.0 ZN A:ZN201 4.4 30.1 1.0 H A:HIS187 4.4 53.5 1.0 CA A:CYS172 4.4 28.5 1.0 HB2 A:ASN186 4.5 52.2 1.0 N A:HIS187 4.5 44.6 1.0 CB A:CYS121 4.5 36.8 1.0 H A:ASN186 4.6 51.4 1.0 CA A:HIS187 4.6 44.6 1.0 C A:CYS172 4.6 28.5 1.0 HB3 A:CYS121 4.8 44.1 1.0 C A:CYS184 4.8 43.3 1.0 O A:CYS172 4.8 33.9 1.0 HA A:CYS172 4.9 34.2 1.0 HE2 A:HIS187 4.9 54.5 1.0 C A:CYS149 4.9 26.7 1.0 N A:CYS149 4.9 31.1 1.0 O A:CYS184 5.0 39.9 1.0 O A:CYS149 5.0 30.8 1.0

Zinc binding site 3 out of 3 in the Rlgsgg-ATPRT6 Ubr Box (P4332)


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 (P4332) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:30.8 occ:1.00 ND1 A:HIS155 2.0 26.0 1.0 ND1 A:HIS158 2.1 32.7 1.0 SG A:CYS134 2.3 28.1 1.0 SG A:CYS137 2.3 31.1 1.0 CE1 A:HIS155 2.8 28.4 1.0 HE1 A:HIS155 2.9 34.0 1.0 CE1 A:HIS158 3.0 43.1 1.0 CG A:HIS155 3.1 29.4 1.0 HE1 A:HIS158 3.1 51.7 1.0 CG A:HIS158 3.2 43.1 1.0 HB3 A:HIS155 3.2 43.8 1.0 HB2 A:CYS137 3.2 32.9 1.0 HB3 A:HIS158 3.2 48.6 1.0 HB A:THR136 3.2 41.1 1.0 CB A:CYS134 3.4 29.9 1.0 HB3 A:CYS134 3.4 35.9 1.0 CB A:CYS137 3.4 27.4 1.0 H A:CYS137 3.5 35.8 1.0 CB A:HIS158 3.6 40.5 1.0 HB2 A:HIS158 3.6 48.6 1.0 HB2 A:CYS134 3.6 35.9 1.0 CB A:HIS155 3.6 36.5 1.0 HA A:HIS155 3.6 52.9 1.0 N A:CYS137 3.9 29.8 1.0 NE2 A:HIS155 4.0 30.0 1.0 HB3 A:CYS137 4.1 32.9 1.0 CD2 A:HIS155 4.1 32.0 1.0 NE2 A:HIS158 4.2 39.6 1.0 CA A:HIS155 4.2 44.1 1.0 CB A:THR136 4.2 34.2 1.0 CD2 A:HIS158 4.3 40.6 1.0 HZ2 A:TRP178 4.3 28.0 1.0 CA A:CYS137 4.3 29.1 1.0 HB2 A:HIS155 4.5 43.8 1.0 H A:THR136 4.6 36.4 1.0 HA3 A:GLY182 4.6 40.9 1.0 HA A:CYS137 4.7 35.0 1.0 HG22 A:THR136 4.7 43.8 1.0 C A:THR136 4.7 32.7 1.0 CA A:CYS134 4.7 23.0 1.0 HE2 A:HIS155 4.7 36.0 1.0 HG1 A:THR136 4.8 43.5 1.0 HE1 A:PHE150 4.8 42.5 1.0 O A:ASP154 4.8 43.1 1.0 CZ2 A:TRP178 4.9 23.3 1.0 CG2 A:THR136 4.9 36.5 1.0 HB3 A:TYR160 4.9 31.3 1.0 HG21 A:THR136 4.9 43.8 1.0 CA A:THR136 4.9 31.7 1.0 HE2 A:HIS158 4.9 47.5 1.0 HA A:CYS134 4.9 27.6 1.0 OG1 A:THR136 5.0 36.3 1.0 HA2 A:GLY182 5.0 40.9 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.