Zinc in PDB 1q08: Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121)

The structure of Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121), PDB code: 1q08 was solved by A.Changela, K.Chen, Y.Xue, J.Holschen, C.E.Outten, T.V.O'halloran, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.83 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.989, 46.681, 118.927, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.4

The structure of Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121) (pdb code 1q08). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121), PDB code: 1q08:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121)


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 Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.2 occ:1.00 O4 A:PO4301 2.1 15.2 1.0 SG A:CYS114 2.3 15.8 1.0 SG A:CYS124 2.4 15.1 1.0 SG B:CYS79 2.4 16.0 1.0 CB B:CYS79 3.1 16.7 1.0 P A:PO4301 3.2 16.0 1.0 CB A:CYS124 3.3 17.5 1.0 CB A:CYS114 3.4 14.7 1.0 CA A:CYS124 3.4 17.8 1.0 O2 A:PO4301 3.4 13.8 1.0 O3 A:PO4301 3.6 14.9 1.0 ZN A:ZN402 3.6 17.7 1.0 N A:SER125 3.7 17.1 1.0 CA B:CYS79 3.8 18.2 1.0 CA A:CYS114 3.9 13.8 1.0 C A:CYS124 4.0 18.1 1.0 OG B:SER82 4.2 20.3 1.0 OG A:SER125 4.2 16.0 1.0 N A:CYS115 4.3 13.8 1.0 O1 A:PO4301 4.4 15.2 1.0 N A:CYS124 4.5 18.2 1.0 C A:CYS114 4.5 14.2 1.0 N A:ILE126 4.6 15.9 1.0 O B:CYS79 4.6 18.6 1.0 C B:CYS79 4.7 18.7 1.0 CG1 A:ILE126 4.7 11.9 1.0 CD1 A:ILE126 4.9 14.7 1.0 CA A:SER125 4.9 16.2 1.0 N A:GLY116 4.9 15.9 1.0 N B:CYS79 4.9 19.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121)


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 Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.7 occ:1.00 O2 A:PO4301 2.1 13.8 1.0 ND1 A:HIS119 2.2 16.6 1.0 SG A:CYS115 2.4 17.2 1.0 SG B:CYS79 2.4 16.0 1.0 O3 A:PO4301 2.9 14.9 1.0 P A:PO4301 3.0 16.0 1.0 CG A:HIS119 3.1 16.9 1.0 CB A:HIS119 3.2 16.4 1.0 CB B:CYS79 3.3 16.7 1.0 CE1 A:HIS119 3.3 17.2 1.0 CB A:CYS115 3.4 15.8 1.0 ZN A:ZN401 3.6 17.2 1.0 O4 A:PO4301 3.7 15.2 1.0 N A:CYS115 3.8 13.8 1.0 CA A:CYS115 4.1 15.1 1.0 O1 A:PO4301 4.2 15.2 1.0 CD2 A:HIS119 4.3 16.2 1.0 NE2 A:HIS119 4.4 17.0 1.0 N A:GLY116 4.5 15.9 1.0 CA A:HIS119 4.6 17.1 1.0 SG A:CYS114 4.6 15.8 1.0 C A:CYS115 4.8 15.5 1.0 CA B:CYS79 4.8 18.2 1.0 O A:HIS119 4.9 17.9 1.0 OG1 A:THR117 4.9 17.0 1.0 C A:CYS114 4.9 14.2 1.0 C A:HIS119 5.0 18.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121)


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 Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:16.5 occ:1.00 O3 B:PO4302 2.1 14.2 1.0 SG B:CYS114 2.3 14.1 1.0 SG A:CYS79 2.4 14.8 1.0 SG B:CYS124 2.5 16.4 1.0 CB A:CYS79 3.1 18.6 1.0 P B:PO4302 3.2 15.9 1.0 CB B:CYS114 3.3 13.9 1.0 CB B:CYS124 3.3 15.3 1.0 O2 B:PO4302 3.4 13.9 1.0 CA B:CYS124 3.4 15.9 1.0 ZN B:ZN404 3.6 17.2 1.0 O1 B:PO4302 3.6 16.1 1.0 N B:SER125 3.8 15.9 1.0 CA B:CYS114 3.8 14.8 1.0 CA A:CYS79 3.8 18.2 1.0 C B:CYS124 4.1 16.2 1.0 OG A:SER82 4.1 18.3 1.0 N B:CYS115 4.3 13.9 1.0 OG B:SER125 4.3 20.0 1.0 O4 B:PO4302 4.5 14.4 1.0 C B:CYS114 4.5 15.8 1.0 N B:CYS124 4.6 17.1 1.0 O A:CYS79 4.6 18.2 1.0 N B:ILE126 4.7 16.9 1.0 CG1 B:ILE126 4.7 13.4 1.0 C A:CYS79 4.7 18.8 1.0 CD1 B:ILE126 4.8 12.8 1.0 N B:GLY116 4.8 16.0 1.0 CA B:SER125 4.9 17.6 1.0 N A:CYS79 4.9 18.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121)


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 Zn(II) Form of E. Coli Zntr, A Zinc-Sensing Transcriptional Regulator, at 1.9 A Resolution (Space Group P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:17.2 occ:1.00 O2 B:PO4302 2.2 13.9 1.0 ND1 B:HIS119 2.3 15.6 1.0 SG B:CYS115 2.3 15.6 1.0 SG A:CYS79 2.4 14.8 1.0 O1 B:PO4302 2.9 16.1 1.0 P B:PO4302 3.0 15.9 1.0 CG B:HIS119 3.1 16.6 1.0 CB B:HIS119 3.2 15.1 1.0 CB A:CYS79 3.3 18.6 1.0 CB B:CYS115 3.3 15.3 1.0 CE1 B:HIS119 3.4 15.6 1.0 ZN B:ZN403 3.6 16.5 1.0 O3 B:PO4302 3.7 14.2 1.0 N B:CYS115 3.8 13.9 1.0 CA B:CYS115 4.1 15.8 1.0 O4 B:PO4302 4.3 14.4 1.0 CD2 B:HIS119 4.3 14.3 1.0 NE2 B:HIS119 4.4 15.2 1.0 N B:GLY116 4.5 16.0 1.0 SG B:CYS114 4.6 14.1 1.0 CA B:HIS119 4.6 15.9 1.0 C B:CYS115 4.7 16.4 1.0 CA A:CYS79 4.7 18.2 1.0 O B:HIS119 4.8 14.7 1.0 C B:CYS114 4.9 15.8 1.0 OG1 B:THR117 4.9 14.2 1.0 C B:HIS119 5.0 17.0 1.0

A.Changela, K.Chen, Y.Xue, J.Holschen, C.E.Outten, T.V.O'halloran, A.Mondragon. Molecular Basis of Metal-Ion Selectivity and Zeptomolar Sensitivity By Cuer Science V. 301 1383 2003.
ISSN: ISSN 0036-8075
PubMed: 12958362
DOI: 10.1126/SCIENCE.1085950