Zinc in PDB 7xwd: Apo-ATPRT6 Ubr Box

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

The structure of Apo-ATPRT6 Ubr Box, PDB code: 7xwd 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)	43.58 / 2.40
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.165, 87.165, 74.35, 90, 90, 90
R / Rfree (%)	21.9 / 26.9

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

Zinc binding site 1 out of 3 in the Apo-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 Apo-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:64.1 occ:1.00 ND1 A:HIS187 2.0 73.3 1.0 SG A:CYS172 2.2 63.0 1.0 SG A:CYS184 2.3 65.8 1.0 SG A:CYS149 2.5 61.6 1.0 CE1 A:HIS187 2.7 62.5 1.0 HE1 A:HIS187 2.7 75.0 1.0 HB3 A:CYS184 2.9 79.1 1.0 HB3 A:CYS149 2.9 64.6 1.0 HB3 A:CYS172 3.1 81.5 1.0 CB A:CYS184 3.2 65.9 1.0 H A:CYS184 3.2 74.9 1.0 CG A:HIS187 3.2 70.5 1.0 CB A:CYS149 3.2 53.8 1.0 HB2 A:HIS187 3.3 86.1 1.0 CB A:CYS172 3.3 68.0 1.0 HA A:CYS149 3.4 74.2 1.0 HB2 A:CYS121 3.7 75.3 1.0 HB2 A:CYS172 3.7 81.5 1.0 CB A:HIS187 3.8 71.8 1.0 CA A:CYS149 3.9 61.9 1.0 N A:CYS184 3.9 62.4 1.0 HB2 A:CYS184 3.9 79.1 1.0 NE2 A:HIS187 4.0 67.7 1.0 CA A:CYS184 4.1 66.2 1.0 HB2 A:CYS149 4.1 64.6 1.0 CD2 A:HIS187 4.2 63.9 1.0 H A:HIS187 4.3 86.5 1.0 HB2 A:ASN186 4.4 82.1 1.0 ZN A:ZN202 4.4 64.6 1.0 N A:HIS187 4.5 72.0 1.0 HB3 A:HIS187 4.5 86.1 1.0 CB A:CYS121 4.5 62.8 1.0 HB3 A:CYS121 4.6 75.3 1.0 CA A:CYS172 4.6 67.3 1.0 C A:CYS184 4.6 68.9 1.0 HE2 A:HIS187 4.7 81.2 1.0 H A:ASN186 4.7 86.2 1.0 C A:CYS172 4.8 60.5 1.0 CA A:HIS187 4.8 69.7 1.0 O A:CYS184 4.8 70.3 1.0 C A:CYS149 4.8 64.2 1.0 O A:CYS172 4.9 65.3 1.0 HA A:CYS184 4.9 79.5 1.0 HA A:PHE183 5.0 71.0 1.0 N A:CYS149 5.0 60.0 1.0 O A:CYS149 5.0 65.5 1.0

Zinc binding site 2 out of 3 in the Apo-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 Apo-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:64.6 occ:1.00 SG A:CYS149 2.2 61.6 1.0 SG A:CYS121 2.2 60.6 1.0 SG A:CYS170 2.2 62.5 1.0 SG A:CYS146 2.3 66.9 1.0 HB2 A:CYS149 3.0 64.6 1.0 HB3 A:CYS121 3.1 75.3 1.0 HB3 A:CYS170 3.1 77.4 1.0 CB A:CYS170 3.2 64.5 1.0 H A:CYS146 3.2 72.3 1.0 CB A:CYS121 3.2 62.8 1.0 HB2 A:CYS170 3.2 77.4 1.0 CB A:CYS149 3.3 53.8 1.0 HB2 A:CYS121 3.4 75.3 1.0 HB3 A:CYS146 3.5 65.7 1.0 CB A:CYS146 3.5 54.7 1.0 HB3 A:CYS172 3.6 81.5 1.0 H A:CYS149 3.7 72.0 1.0 HB3 A:CYS149 3.8 64.6 1.0 N A:CYS146 3.9 60.2 1.0 HE1 A:HIS187 3.9 75.0 1.0 OG A:SER123 4.0 74.4 1.0 HB A:ILE145 4.1 75.2 1.0 CA A:CYS146 4.3 57.6 1.0 HB2 A:CYS172 4.3 81.5 1.0 HB2 A:CYS146 4.3 65.7 1.0 CB A:CYS172 4.3 68.0 1.0 N A:CYS149 4.4 60.0 1.0 CA A:CYS149 4.4 61.9 1.0 ZN A:ZN201 4.4 64.1 1.0 CB A:SER123 4.5 64.8 1.0 H A:CYS172 4.6 75.9 1.0 CE1 A:HIS187 4.6 62.5 1.0 CA A:CYS170 4.6 66.1 1.0 CA A:CYS121 4.6 64.8 1.0 HA A:CYS149 4.7 74.2 1.0 HD2 A:PRO148 4.8 70.3 1.0 HA A:ILE145 4.8 71.7 1.0 N A:SER123 4.9 59.9 1.0 C A:CYS146 4.9 54.6 1.0 O A:CYS146 5.0 61.7 1.0 CB A:ILE145 5.0 62.7 1.0 HA A:CYS170 5.0 79.3 1.0

Zinc binding site 3 out of 3 in the Apo-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 Apo-ATPRT6 Ubr Box within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:63.4 occ:1.00 ND1 A:HIS158 2.0 68.8 1.0 ND1 A:HIS155 2.1 67.5 1.0 SG A:CYS137 2.3 63.2 1.0 SG A:CYS134 2.3 58.9 1.0 CE1 A:HIS158 2.9 62.6 1.0 CE1 A:HIS155 3.0 67.2 1.0 HE1 A:HIS158 3.0 75.1 1.0 CG A:HIS158 3.0 68.5 1.0 HB3 A:HIS155 3.1 80.2 1.0 HE1 A:HIS155 3.1 80.7 1.0 HB3 A:HIS158 3.2 83.5 1.0 CG A:HIS155 3.2 63.9 1.0 HB A:THR136 3.3 75.4 1.0 HB2 A:CYS137 3.4 73.6 1.0 HB2 A:HIS158 3.4 83.5 1.0 CB A:CYS134 3.4 58.6 1.0 CB A:HIS158 3.4 69.6 1.0 HB3 A:CYS134 3.5 70.3 1.0 H A:CYS137 3.5 76.9 1.0 CB A:CYS137 3.5 61.4 1.0 CB A:HIS155 3.6 66.8 1.0 HB2 A:CYS134 3.6 70.3 1.0 HA A:HIS155 3.7 82.2 1.0 N A:CYS137 3.9 64.1 1.0 NE2 A:HIS158 4.0 74.8 1.0 CD2 A:HIS158 4.1 72.6 1.0 NE2 A:HIS155 4.2 61.0 1.0 CA A:HIS155 4.2 68.5 1.0 HB3 A:CYS137 4.2 73.6 1.0 CD2 A:HIS155 4.3 66.7 1.0 CB A:THR136 4.3 62.8 1.0 CA A:CYS137 4.3 64.7 1.0 HZ2 A:TRP178 4.4 75.0 1.0 HB2 A:HIS155 4.4 80.2 1.0 H A:THR136 4.5 67.9 1.0 HB3 A:TYR160 4.7 65.3 1.0 HA3 A:GLY182 4.7 84.9 1.0 HA A:CYS137 4.7 77.6 1.0 HE1 A:PHE150 4.7 60.8 1.0 HA2 A:GLY182 4.7 84.9 1.0 C A:THR136 4.7 58.9 1.0 CA A:CYS134 4.7 62.7 1.0 HE2 A:HIS158 4.8 89.8 1.0 HG1 A:THR136 4.8 77.2 1.0 O A:ASP154 4.8 65.2 1.0 HG21 A:THR136 4.8 71.5 1.0 HE2 A:HIS155 4.9 73.2 1.0 CA A:THR136 4.9 60.2 1.0 CZ2 A:TRP178 4.9 62.5 1.0 HG22 A:THR136 4.9 71.5 1.0 CA A:HIS158 5.0 61.9 1.0 HD2 A:HIS158 5.0 87.2 1.0 HA A:CYS134 5.0 75.2 1.0 CG2 A:THR136 5.0 59.5 1.0 HE1 A:TRP178 5.0 74.9 1.0 OG1 A:THR136 5.0 64.3 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.