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

The structure of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna, PDB code: 6jni 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 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	71.090, 71.329, 98.797, 81.03, 83.52, 73.85
R / Rfree (%)	21.2 / 25.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna (pdb code 6jni). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna, PDB code: 6jni:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:91.2 occ:1.00 SG B:CYS119 2.3 87.2 1.0 SG A:CYS77 2.3 99.2 1.0 SG B:CYS112 2.4 0.7 1.0 CB A:CYS77 3.3 86.0 1.0 CA A:CYS77 3.5 73.5 1.0 CB B:CYS119 3.6 85.5 1.0 OD1 A:ASN81 3.8 63.5 1.0 CB B:CYS112 3.9 95.8 1.0 CG2 A:VAL80 4.1 73.5 1.0 O A:CYS77 4.3 81.4 1.0 C A:CYS77 4.4 68.2 1.0 CD1 B:ILE121 4.4 77.5 1.0 CA B:CYS119 4.4 87.4 1.0 ND2 A:ASN81 4.5 66.4 1.0 CG A:ASN81 4.5 62.1 1.0 N A:CYS77 4.6 77.1 1.0 CA B:CYS112 4.7 91.0 1.0 CG1 B:ILE121 4.8 73.4 1.0 CB B:ILE121 4.9 70.1 1.0 O B:ARG111 4.9 98.2 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:50.8 occ:1.00 OE1 A:GLU62 2.0 47.3 1.0 ND1 A:HIS90 2.0 54.1 1.0 ND1 A:HIS87 2.0 40.0 1.0 NE2 A:HIS140 2.0 46.6 1.0 CD A:GLU62 2.7 43.3 1.0 OE2 A:GLU62 2.9 41.0 1.0 CE1 A:HIS140 2.9 49.4 1.0 CG A:HIS87 3.0 41.2 1.0 CE1 A:HIS90 3.0 54.5 1.0 CE1 A:HIS87 3.0 37.9 1.0 CG A:HIS90 3.0 55.2 1.0 CD2 A:HIS140 3.1 47.3 1.0 CB A:HIS87 3.2 46.9 1.0 CB A:HIS90 3.4 52.8 1.0 CA A:HIS87 3.5 51.9 1.0 NE2 A:HIS90 4.1 54.1 1.0 CD2 A:HIS87 4.1 36.1 1.0 ND1 A:HIS140 4.1 44.8 1.0 NE2 A:HIS87 4.1 36.8 1.0 CD2 A:HIS90 4.1 56.2 1.0 CG A:GLU62 4.2 50.0 1.0 CG A:HIS140 4.2 46.7 1.0 O A:HIS87 4.4 50.7 1.0 N A:HIS87 4.5 56.8 1.0 C A:HIS87 4.5 51.9 1.0 O A:GLU86 4.8 76.2 1.0 CA A:HIS90 4.9 51.4 1.0 O A:ASP57 5.0 52.8 1.0 CG2 A:VAL141 5.0 43.9 1.0 C A:GLU86 5.0 65.2 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:59.5 occ:1.00 SG A:CYS112 2.2 55.8 1.0 SG B:CYS77 2.3 60.2 1.0 SG A:CYS119 2.4 54.0 1.0 CB B:CYS77 3.3 62.0 1.0 CB A:CYS112 3.4 57.3 1.0 CB A:CYS119 3.5 51.1 1.0 OD1 B:ASN81 3.7 47.1 1.0 CA B:CYS77 3.8 60.8 1.0 CA A:CYS112 4.1 55.2 1.0 ND2 B:ASN81 4.2 42.1 1.0 N A:ALA114 4.3 48.1 1.0 CG B:ASN81 4.4 43.0 1.0 N A:ASN113 4.4 52.3 1.0 O B:CYS77 4.5 61.0 1.0 CG2 B:VAL80 4.5 44.4 1.0 C B:CYS77 4.6 53.6 1.0 CA A:ALA114 4.6 49.1 1.0 C A:CYS112 4.6 52.2 1.0 CA A:CYS119 4.8 52.1 1.0 CD1 A:ILE121 4.9 39.0 1.0 N B:CYS77 5.0 63.9 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:38.3 occ:1.00 NE2 A:HIS145 2.0 44.5 1.0 OE1 B:GLU62 2.0 40.3 1.0 ND1 B:HIS90 2.1 44.2 1.0 ND1 B:HIS87 2.1 37.9 1.0 CD B:GLU62 2.8 40.4 1.0 OE2 B:GLU62 2.8 40.3 1.0 CE1 A:HIS145 2.8 49.5 1.0 CE1 B:HIS87 3.0 38.8 1.0 CE1 B:HIS90 3.0 43.0 1.0 CG B:HIS90 3.1 41.1 1.0 CG B:HIS87 3.1 38.9 1.0 CD2 A:HIS145 3.2 47.5 1.0 CB B:HIS90 3.4 39.3 1.0 CB B:HIS87 3.5 37.4 1.0 CA B:HIS87 3.8 37.9 1.0 ND1 A:HIS145 4.0 55.1 1.0 NE2 B:HIS87 4.1 42.7 1.0 NE2 B:HIS90 4.1 40.7 1.0 CD2 B:HIS90 4.2 37.4 1.0 CD2 B:HIS87 4.2 42.3 1.0 CG A:HIS145 4.2 52.5 1.0 CG B:GLU62 4.2 39.8 1.0 O B:HIS87 4.5 42.4 1.0 C B:HIS87 4.7 42.7 1.0 N B:HIS87 4.7 39.4 1.0 O B:ASP57 4.8 49.0 1.0 CA B:HIS90 4.9 36.7 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:41.9 occ:1.00 OE1 C:GLU62 2.0 39.4 1.0 ND1 C:HIS87 2.1 38.4 1.0 NE2 D:HIS145 2.1 52.9 1.0 ND1 C:HIS90 2.1 33.2 1.0 CD C:GLU62 2.8 33.9 1.0 OE2 C:GLU62 2.9 33.2 1.0 CE1 D:HIS145 3.0 55.3 1.0 CE1 C:HIS87 3.0 42.6 1.0 CE1 C:HIS90 3.0 31.4 1.0 CG C:HIS87 3.0 37.2 1.0 CG C:HIS90 3.0 31.8 1.0 CD2 D:HIS145 3.1 53.6 1.0 CB C:HIS90 3.4 33.9 1.0 CB C:HIS87 3.4 37.2 1.0 CA C:HIS87 3.7 39.5 1.0 NE2 C:HIS87 4.1 42.8 1.0 ND1 D:HIS145 4.1 56.0 1.0 NE2 C:HIS90 4.1 34.7 1.0 CD2 C:HIS87 4.2 41.5 1.0 CD2 C:HIS90 4.2 32.1 1.0 CG C:GLU62 4.2 35.0 1.0 CG D:HIS145 4.2 56.4 1.0 O C:HIS87 4.5 43.9 1.0 C C:HIS87 4.6 43.3 1.0 N C:HIS87 4.6 42.9 1.0 CA C:HIS90 4.9 34.6 1.0 O C:ASP57 4.9 48.9 1.0 O C:GLU86 4.9 47.3 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:59.2 occ:1.00 SG D:CYS119 2.3 59.0 1.0 SG C:CYS77 2.3 57.8 1.0 SG D:CYS112 2.3 55.5 1.0 CB D:CYS119 3.4 58.3 1.0 CB C:CYS77 3.4 52.8 1.0 CB D:CYS112 3.5 52.7 1.0 OD1 C:ASN81 3.8 41.7 1.0 CA C:CYS77 3.8 56.1 1.0 CA D:CYS112 4.1 52.2 1.0 CG2 C:VAL80 4.4 58.8 1.0 ND2 C:ASN81 4.4 48.1 1.0 N D:ALA114 4.4 56.9 1.0 CG C:ASN81 4.5 51.3 1.0 N D:ASN113 4.5 63.2 1.0 O C:CYS77 4.6 55.9 1.0 C C:CYS77 4.7 51.7 1.0 C D:CYS112 4.7 57.9 1.0 CA D:CYS119 4.7 56.2 1.0 CA D:ALA114 4.8 55.8 1.0 CD1 D:ILE121 4.8 41.0 1.0 N C:CYS77 4.9 61.0 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:0.6 occ:1.00 SG D:CYS77 2.3 0.8 1.0 SG C:CYS119 2.3 0.7 1.0 SG C:CYS112 2.3 0.2 1.0 CB D:CYS77 3.2 1.0 1.0 CA D:CYS77 3.4 0.4 1.0 CB C:CYS119 3.6 93.2 1.0 CB C:CYS112 3.8 92.9 1.0 OD1 D:ASN81 3.8 85.5 1.0 CG2 D:VAL80 3.9 73.0 1.0 O D:CYS77 4.2 0.5 1.0 C D:CYS77 4.3 97.6 1.0 N D:CYS77 4.4 0.1 1.0 ND2 D:ASN81 4.5 82.6 1.0 CD1 C:ILE121 4.5 78.2 1.0 CG D:ASN81 4.5 77.6 1.0 CA C:CYS119 4.5 86.9 1.0 CA C:CYS112 4.6 97.4 1.0 CB C:ILE121 4.9 76.3 1.0 CG1 C:ILE121 4.9 75.0 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:51.8 occ:1.00 OE1 D:GLU62 2.0 52.5 1.0 ND1 D:HIS87 2.0 47.0 1.0 ND1 D:HIS90 2.0 66.8 1.0 NE2 D:HIS140 2.1 50.2 1.0 CD D:GLU62 2.7 56.8 1.0 OE2 D:GLU62 2.9 60.0 1.0 CG D:HIS87 2.9 48.7 1.0 CE1 D:HIS140 2.9 56.5 1.0 CE1 D:HIS90 3.0 65.4 1.0 CE1 D:HIS87 3.0 52.0 1.0 CG D:HIS90 3.1 60.0 1.0 CD2 D:HIS140 3.1 51.3 1.0 CB D:HIS87 3.2 51.1 1.0 CB D:HIS90 3.4 52.0 1.0 CA D:HIS87 3.5 55.8 1.0 CD2 D:HIS87 4.1 48.1 1.0 NE2 D:HIS87 4.1 51.1 1.0 ND1 D:HIS140 4.1 55.9 1.0 NE2 D:HIS90 4.1 64.6 1.0 CD2 D:HIS90 4.2 62.9 1.0 CG D:GLU62 4.2 55.2 1.0 CG D:HIS140 4.2 57.8 1.0 O D:HIS87 4.4 54.0 1.0 N D:HIS87 4.4 63.0 1.0 C D:HIS87 4.5 48.6 1.0 O D:GLU86 4.8 66.0 1.0 CA D:HIS90 4.9 54.9 1.0 C D:GLU86 5.0 69.1 1.0 O D:ASP57 5.0 43.3 1.0 CG2 D:VAL141 5.0 48.9 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:50.5 occ:1.00 ND1 E:HIS87 2.0 55.4 1.0 OE1 E:GLU62 2.0 54.3 1.0 NE2 E:HIS140 2.0 56.7 1.0 ND1 E:HIS90 2.1 62.0 1.0 CD E:GLU62 2.8 52.4 1.0 OE2 E:GLU62 2.8 60.4 1.0 CE1 E:HIS140 2.9 62.3 1.0 CG E:HIS87 3.0 58.4 1.0 CE1 E:HIS87 3.0 59.4 1.0 CE1 E:HIS90 3.0 65.8 1.0 CG E:HIS90 3.1 56.5 1.0 CD2 E:HIS140 3.1 56.3 1.0 CB E:HIS87 3.3 57.0 1.0 CB E:HIS90 3.4 54.3 1.0 CA E:HIS87 3.6 59.0 1.0 ND1 E:HIS140 4.0 60.8 1.0 NE2 E:HIS87 4.1 58.1 1.0 CD2 E:HIS87 4.1 59.2 1.0 NE2 E:HIS90 4.1 67.8 1.0 CG E:HIS140 4.2 58.7 1.0 CD2 E:HIS90 4.2 59.1 1.0 CG E:GLU62 4.2 54.3 1.0 O E:HIS87 4.4 58.6 1.0 N E:HIS87 4.5 64.5 1.0 C E:HIS87 4.5 55.8 1.0 O E:GLU86 4.9 90.7 1.0 O E:ASP57 4.9 45.9 1.0 CA E:HIS90 4.9 51.6 1.0 CG2 E:VAL141 4.9 42.8 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Transcriptional Regulator Cadr From P. Putida in Complex with Zinc(II) and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:0.1 occ:1.00 SG E:CYS77 2.3 0.2 1.0 SG F:CYS112 2.4 0.8 1.0 SG F:CYS119 2.4 0.4 1.0 CB E:CYS77 3.1 84.2 1.0 CA E:CYS77 3.5 86.2 1.0 CB F:CYS119 3.6 88.2 1.0 CB F:CYS112 3.6 0.3 1.0 OD1 E:ASN81 4.1 1.0 1.0 CA F:CYS112 4.3 0.2 1.0 CG2 E:VAL80 4.3 76.5 1.0 C E:CYS77 4.4 95.0 1.0 O E:CYS77 4.4 99.8 1.0 CA F:CYS119 4.5 81.8 1.0 N E:CYS77 4.6 82.0 1.0 ND2 E:ASN81 4.6 87.5 1.0 CG E:ASN81 4.7 84.0 1.0 C F:CYS112 4.8 95.6 1.0 CD1 F:ILE121 4.9 77.2 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