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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)

Protein crystallography data

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

Other elements in 1q08:

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

Zinc Binding Sites:

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 1q08

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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 1q08

Go back to Zinc Binding Sites List in 1q08
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 1q08

Go back to Zinc Binding Sites List in 1q08
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 1q08

Go back to Zinc Binding Sites List in 1q08
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

Reference:

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
Page generated: Wed Oct 16 17:58:43 2024

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