Zinc in PDB 6iy8: Dmpr-Phenol Complex of Pseudomonas Putida

The structure of Dmpr-Phenol Complex of Pseudomonas Putida, PDB code: 6iy8 was solved by K.H.Park, E.J.Woo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.12 / 3.42
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.636, 129.998, 110.276, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.6

The binding sites of Zinc atom in the Dmpr-Phenol Complex of Pseudomonas Putida (pdb code 6iy8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dmpr-Phenol Complex of Pseudomonas Putida, PDB code: 6iy8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Dmpr-Phenol Complex of Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dmpr-Phenol Complex of Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:45.4 occ:1.00 OE2 A:GLU172 2.1 45.6 1.0 SG A:CYS149 2.4 67.0 1.0 SG A:CYS175 2.5 58.8 1.0 SG A:CYS183 2.5 96.2 1.0 CD A:GLU172 3.0 45.5 1.0 CB A:CYS183 3.2 91.6 1.0 CB A:CYS175 3.3 56.0 1.0 CB A:CYS149 3.5 72.3 1.0 OE1 A:GLU172 3.5 45.3 1.0 CA A:CYS175 3.6 53.0 1.0 N A:ARG176 3.9 62.6 1.0 CG1 A:VAL134 4.0 54.4 1.0 CA A:CYS183 4.1 88.7 1.0 CG A:GLU172 4.2 45.6 1.0 C A:CYS175 4.3 57.3 1.0 N A:CYS149 4.3 67.5 1.0 O A:SER174 4.5 77.4 1.0 CA A:CYS149 4.5 69.8 1.0 CE3 A:TRP128 4.7 46.5 1.0 N A:CYS175 4.9 45.0 1.0 CB A:SER131 4.9 51.5 1.0 N A:GLY177 5.0 74.0 1.0 CG1 A:VAL148 5.0 66.9 1.0

Zinc binding site 2 out of 4 in the Dmpr-Phenol Complex of Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dmpr-Phenol Complex of Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:90.0 occ:1.00 OE2 B:GLU172 2.1 84.2 1.0 SG B:CYS149 2.4 96.2 1.0 SG B:CYS175 2.4 0.9 1.0 SG B:CYS183 2.6 0.2 1.0 CD B:GLU172 3.2 84.1 1.0 CB B:CYS175 3.3 0.7 1.0 CB B:CYS183 3.6 0.8 1.0 CA B:CYS175 3.6 1.0 1.0 CB B:CYS149 3.7 98.3 1.0 OE1 B:GLU172 3.7 84.1 1.0 N B:ARG176 3.9 0.9 1.0 N B:CYS149 4.3 91.2 1.0 C B:CYS175 4.3 0.3 1.0 CG B:GLU172 4.4 87.9 1.0 CG1 B:VAL148 4.4 85.9 1.0 CA B:CYS149 4.6 99.4 1.0 CA B:CYS183 4.6 0.9 1.0 O B:SER174 4.6 0.1 1.0 CB B:SER131 4.8 0.1 1.0 OG B:SER131 4.8 0.4 1.0 N B:CYS175 4.9 0.3 1.0 CE3 B:TRP128 4.9 81.1 1.0 CB B:VAL134 4.9 0.6 1.0 N B:GLY177 5.0 77.1 1.0

Zinc binding site 3 out of 4 in the Dmpr-Phenol Complex of Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dmpr-Phenol Complex of Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:46.8 occ:1.00 OE2 C:GLU172 2.0 36.5 1.0 SG C:CYS175 2.3 36.1 1.0 SG C:CYS149 2.5 47.1 1.0 SG C:CYS183 2.5 73.7 1.0 CD C:GLU172 3.0 36.6 1.0 CB C:CYS175 3.2 36.0 1.0 CB C:CYS183 3.3 64.9 1.0 CB C:CYS149 3.5 39.2 1.0 OE1 C:GLU172 3.6 36.7 1.0 CA C:CYS175 3.7 43.5 1.0 N C:ARG176 4.1 57.3 1.0 CG C:GLU172 4.2 50.1 1.0 CA C:CYS183 4.3 50.5 1.0 N C:CYS149 4.4 47.8 1.0 CG1 C:VAL134 4.4 57.7 1.0 C C:CYS175 4.4 54.0 1.0 CA C:CYS149 4.6 43.3 1.0 O C:SER174 4.6 59.7 1.0 CE3 C:TRP128 4.7 46.7 1.0 N C:CYS175 4.9 41.9 1.0 CG1 C:VAL148 5.0 36.6 1.0

Zinc binding site 4 out of 4 in the Dmpr-Phenol Complex of Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dmpr-Phenol Complex of Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:85.8 occ:1.00 OE2 D:GLU172 2.0 85.6 1.0 SG D:CYS149 2.4 0.6 1.0 SG D:CYS183 2.4 89.9 1.0 SG D:CYS175 2.5 0.3 1.0 CD D:GLU172 2.9 88.8 1.0 OE1 D:GLU172 3.2 86.8 1.0 CB D:CYS183 3.2 89.6 1.0 CB D:CYS175 3.3 0.5 1.0 CB D:CYS149 3.5 97.6 1.0 CA D:CYS175 3.7 0.3 1.0 N D:ARG176 4.1 0.3 1.0 N D:CYS149 4.1 91.8 1.0 CG D:GLU172 4.2 91.6 1.0 CA D:CYS183 4.3 87.9 1.0 C D:CYS175 4.4 0.6 1.0 CA D:CYS149 4.4 93.0 1.0 O D:SER174 4.5 0.9 1.0 CG1 D:VAL148 4.7 0.4 1.0 N D:CYS175 4.8 0.1 1.0 N D:VAL148 5.0 0.6 1.0

K.H.Park, S.Kim, S.J.Lee, J.E.Cho, V.V.Patil, A.B.Dumbrepatil, H.N.Song, W.C.Ahn, C.Joo, S.G.Lee, V.Shingler, E.J.Woo. Tetrameric Architecture of An Active Phenol-Bound Form of the Aaa+ Transcriptional Regulator Dmpr Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-16562-5