Cadmium in PDB 6jgx: Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna

The structure of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna, PDB code: 6jgx was solved by X.C.Liu, J.H.Gan, H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.71
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	131.490, 131.490, 85.118, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 23.3

The binding sites of Cadmium atom in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna (pdb code 6jgx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna, PDB code: 6jgx:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:0.8 occ:1.00 OD1 A:ASN81 2.3 0.3 1.0 SG B:CYS112 2.4 93.9 1.0 SG B:CYS119 2.5 0.7 1.0 SG A:CYS77 2.5 0.7 1.0 O A:CYS77 3.1 84.7 1.0 CG A:ASN81 3.1 0.5 1.0 ND2 A:ASN81 3.3 1.0 1.0 CB B:CYS119 3.6 0.7 1.0 CB A:CYS77 3.6 97.4 1.0 C A:CYS77 3.7 95.8 1.0 CA A:CYS77 3.8 94.7 1.0 CB B:CYS112 4.0 0.7 1.0 CA B:CYS119 4.0 0.3 1.0 CG2 A:VAL80 4.4 87.0 1.0 N B:ALA120 4.5 95.1 1.0 CB A:ASN81 4.5 0.2 1.0 CD1 B:ILE121 4.6 0.1 1.0 C B:CYS119 4.6 0.6 1.0 N A:ASN81 4.8 95.3 1.0 CB B:ILE121 4.8 0.0 1.0 N B:ILE121 4.9 96.4 1.0 N A:GLY78 4.9 0.1 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:83.0 occ:1.00 NE2 A:HIS140 2.2 89.9 1.0 OE1 A:GLU62 2.2 67.1 1.0 ND1 A:HIS87 2.3 73.4 1.0 OE2 A:GLU62 2.3 88.0 1.0 ND1 A:HIS90 2.5 92.9 1.0 CD A:GLU62 2.6 74.9 1.0 CE1 A:HIS87 3.1 72.3 1.0 CD2 A:HIS140 3.1 97.0 1.0 CE1 A:HIS140 3.2 93.2 1.0 CG A:HIS87 3.4 79.9 1.0 CG A:HIS90 3.4 76.8 1.0 CE1 A:HIS90 3.4 85.2 1.0 CB A:HIS90 3.6 73.0 1.0 CB A:HIS87 3.8 85.5 1.0 CA A:HIS87 3.9 85.0 1.0 CG A:GLU62 4.1 77.1 1.0 ND1 A:HIS140 4.2 94.8 1.0 CG A:HIS140 4.3 0.2 1.0 NE2 A:HIS87 4.3 72.1 1.0 CD2 A:HIS87 4.4 75.5 1.0 NE2 A:HIS90 4.5 87.3 1.0 CD2 A:HIS90 4.5 84.0 1.0 O A:HIS87 4.7 73.9 1.0 N A:HIS87 4.8 90.2 1.0 CG2 A:THR59 4.8 69.0 1.0 C A:HIS87 4.8 77.0 1.0 CA A:MET58 4.9 76.4 1.0 N A:THR59 4.9 71.9 1.0 O A:ASP57 4.9 81.2 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:0.1 occ:1.00 OD1 B:ASN81 2.3 1.0 1.0 SG A:CYS112 2.4 89.7 1.0 SG A:CYS119 2.5 0.1 1.0 SG B:CYS77 2.6 0.8 1.0 O B:CYS77 3.1 86.3 1.0 CG B:ASN81 3.1 0.2 1.0 ND2 B:ASN81 3.3 0.6 1.0 CB A:CYS119 3.6 0.0 1.0 CB B:CYS77 3.7 95.7 1.0 C B:CYS77 3.8 97.2 1.0 CA B:CYS77 3.8 96.3 1.0 CB A:CYS112 4.0 0.2 1.0 CA A:CYS119 4.0 0.1 1.0 CG2 B:VAL80 4.4 86.1 1.0 N A:ALA120 4.5 95.6 1.0 CD1 A:ILE121 4.5 0.3 1.0 CB B:ASN81 4.6 0.5 1.0 C A:CYS119 4.6 99.1 1.0 CB A:ILE121 4.8 96.8 1.0 N A:ILE121 4.8 92.6 1.0 N B:ASN81 4.8 95.7 1.0 N B:GLY78 4.9 0.9 1.0 CG1 A:ILE121 5.0 98.9 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Cadmium(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:83.9 occ:1.00 OE1 B:GLU62 2.2 66.8 1.0 ND1 B:HIS87 2.3 75.8 1.0 NE2 A:HIS145 2.3 98.6 1.0 OE2 B:GLU62 2.4 92.5 1.0 ND1 B:HIS90 2.5 91.0 1.0 CD B:GLU62 2.6 76.6 1.0 CE1 B:HIS87 3.1 74.2 1.0 CE1 A:HIS145 3.2 0.6 1.0 CD2 A:HIS145 3.3 0.6 1.0 CG B:HIS87 3.4 82.6 1.0 CG B:HIS90 3.4 73.1 1.0 CE1 B:HIS90 3.4 83.6 1.0 CB B:HIS90 3.6 69.9 1.0 CB B:HIS87 3.8 87.2 1.0 CA B:HIS87 3.9 84.5 1.0 CG B:GLU62 4.1 78.1 1.0 NE2 B:HIS87 4.3 71.9 1.0 ND1 A:HIS145 4.4 0.1 1.0 CD2 B:HIS87 4.4 75.4 1.0 CG A:HIS145 4.4 0.4 1.0 NE2 B:HIS90 4.5 86.5 1.0 CD2 B:HIS90 4.5 82.0 1.0 O B:HIS87 4.7 73.4 1.0 N B:HIS87 4.8 91.0 1.0 CG2 B:THR59 4.8 67.7 1.0 C B:HIS87 4.8 76.4 1.0 CA B:MET58 4.9 77.2 1.0 N B:THR59 4.9 72.4 1.0 O B:ASP57 4.9 78.3 1.0

X.Liu, Q.Hu, J.Yang, S.Huang, T.Wei, W.Chen, Y.He, D.Wang, Z.Liu, K.Wang, J.Gan, H.Chen. Selective Cadmium Regulation Mediated By A Cooperative Binding Mechanism in Cadr. Proc.Natl.Acad.Sci.Usa V. 116 20398 2019.
ISSN: ESSN 1091-6490
PubMed: 31548408
DOI: 10.1073/PNAS.1908610116