Zinc in PDB 6z74: Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum

The structure of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum, PDB code: 6z74 was solved by S.Morera, V.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.170, 113.660, 130.520, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.5

The structure of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum (pdb code 6z74). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum, PDB code: 6z74:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:35.0 occ:1.00 NE2 A:HIS192 2.0 33.2 1.0 NE2 A:HIS141 2.1 33.4 1.0 O1 A:CIT302 2.1 33.6 1.0 NE2 A:HIS214 2.2 33.0 1.0 OD1 A:ASN137 2.4 36.5 1.0 O2 A:CIT302 2.6 35.4 1.0 C1 A:CIT302 2.7 36.0 1.0 CE1 A:HIS192 2.9 34.4 1.0 CE1 A:HIS141 3.0 33.5 1.0 CD2 A:HIS192 3.1 33.9 1.0 CE1 A:HIS214 3.1 32.5 1.0 CD2 A:HIS141 3.1 33.5 1.0 CD2 A:HIS214 3.3 32.9 1.0 CG A:ASN137 3.4 34.3 1.0 ND2 A:ASN137 3.6 27.6 1.0 ND1 A:HIS192 4.1 36.0 1.0 CG A:HIS192 4.2 33.5 1.0 C2 A:CIT302 4.2 38.7 1.0 ND1 A:HIS141 4.2 34.3 1.0 CG A:HIS141 4.2 32.6 1.0 ND1 A:HIS214 4.3 33.4 1.0 CG A:HIS214 4.4 32.5 1.0 CD2 A:PHE140 4.5 28.2 1.0 OH A:TYR133 4.6 38.3 1.0 CB A:ASN137 4.7 30.7 1.0 C6 A:CIT302 4.9 53.8 1.0 O7 A:CIT302 4.9 49.7 1.0 CE2 A:PHE140 4.9 29.0 1.0 C3 A:CIT302 4.9 46.4 1.0 O6 A:CIT302 4.9 57.6 1.0

Zinc binding site 2 out of 4 in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:41.4 occ:1.00 NE2 B:HIS141 2.1 39.3 1.0 NE2 B:HIS192 2.1 42.0 1.0 NE2 B:HIS214 2.2 36.7 1.0 OD1 B:ASN137 2.2 37.3 1.0 O5 B:CIT302 2.3 42.1 1.0 O7 B:CIT302 2.3 44.7 1.0 CE1 B:HIS192 3.0 43.0 1.0 CE1 B:HIS141 3.1 39.0 1.0 CE1 B:HIS214 3.1 36.3 1.0 CD2 B:HIS141 3.2 40.1 1.0 CG B:ASN137 3.2 46.0 1.0 CD2 B:HIS214 3.2 36.2 1.0 CD2 B:HIS192 3.2 41.4 1.0 C6 B:CIT302 3.2 44.8 1.0 C3 B:CIT302 3.3 44.0 1.0 ND2 B:ASN137 3.6 34.6 1.0 C2 B:CIT302 4.0 43.4 1.0 O1 B:CIT302 4.2 37.2 1.0 ND1 B:HIS192 4.2 44.5 1.0 ND1 B:HIS141 4.2 39.3 1.0 ND1 B:HIS214 4.3 37.2 1.0 CG B:HIS141 4.3 38.0 1.0 CG B:HIS192 4.3 41.0 1.0 CG B:HIS214 4.3 35.2 1.0 OH B:TYR133 4.4 46.8 1.0 O6 B:CIT302 4.4 48.0 1.0 C1 B:CIT302 4.6 41.3 1.0 C4 B:CIT302 4.6 47.0 1.0 CB B:ASN137 4.6 41.3 1.0 CD2 B:PHE140 4.8 40.3 1.0

Zinc binding site 3 out of 4 in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:39.7 occ:1.00 NE2 C:HIS141 2.1 34.2 1.0 NE2 C:HIS192 2.1 39.1 1.0 NE2 C:HIS214 2.1 33.6 1.0 OD1 C:ASN137 2.3 36.6 1.0 O5 C:CIT302 2.3 38.3 1.0 O7 C:CIT302 2.3 40.0 1.0 CE1 C:HIS192 3.0 40.2 1.0 CE1 C:HIS141 3.0 33.7 1.0 CE1 C:HIS214 3.1 33.8 1.0 C6 C:CIT302 3.2 44.3 1.0 CD2 C:HIS141 3.2 35.1 1.0 CD2 C:HIS214 3.2 32.4 1.0 CD2 C:HIS192 3.2 38.5 1.0 C3 C:CIT302 3.3 44.1 1.0 CG C:ASN137 3.3 37.2 1.0 ND2 C:ASN137 3.6 29.1 1.0 C2 C:CIT302 4.0 40.0 1.0 ND1 C:HIS192 4.2 41.6 1.0 ND1 C:HIS141 4.2 34.4 1.0 ND1 C:HIS214 4.2 33.7 1.0 O2 C:CIT302 4.2 43.5 1.0 CG C:HIS141 4.3 34.0 1.0 CG C:HIS192 4.3 38.6 1.0 CG C:HIS214 4.3 32.3 1.0 O6 C:CIT302 4.3 50.3 1.0 OH C:TYR133 4.4 45.9 1.0 C4 C:CIT302 4.5 45.0 1.0 CB C:ASN137 4.6 36.4 1.0 C1 C:CIT302 4.6 43.2 1.0 CD2 C:PHE140 4.7 33.8 1.0

Zinc binding site 4 out of 4 in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:45.2 occ:1.00 NE2 D:HIS141 2.1 43.4 1.0 NE2 D:HIS214 2.2 38.6 1.0 NE2 D:HIS192 2.2 46.9 1.0 OD1 D:ASN137 2.2 45.4 1.0 O7 D:CIT302 2.3 45.2 1.0 O6 D:CIT302 2.3 46.5 1.0 CE1 D:HIS141 3.0 42.6 1.0 CE1 D:HIS192 3.1 48.0 1.0 CE1 D:HIS214 3.1 38.4 1.0 CD2 D:HIS141 3.2 44.2 1.0 CD2 D:HIS214 3.2 37.9 1.0 CG D:ASN137 3.2 52.8 1.0 C6 D:CIT302 3.2 46.6 1.0 CD2 D:HIS192 3.3 46.5 1.0 C3 D:CIT302 3.3 45.7 1.0 ND2 D:ASN137 3.6 39.3 1.0 C2 D:CIT302 4.0 41.6 1.0 O2 D:CIT302 4.2 41.4 1.0 ND1 D:HIS141 4.2 43.0 1.0 ND1 D:HIS192 4.2 49.0 1.0 ND1 D:HIS214 4.2 38.7 1.0 CG D:HIS141 4.3 41.7 1.0 CG D:HIS214 4.3 37.6 1.0 CG D:HIS192 4.3 45.6 1.0 OH D:TYR133 4.4 48.3 1.0 O5 D:CIT302 4.4 51.0 1.0 C1 D:CIT302 4.5 42.6 1.0 C4 D:CIT302 4.6 46.6 1.0 CB D:ASN137 4.6 46.9 1.0 CD2 D:PHE140 4.8 39.9 1.0

A.Vigouroux, T.Meyer, A.Naretto, P.Legrand, M.Aumont-Nicaise, A.Di Cicco, S.Renoud, J.Dore, D.Levy, L.Vial, C.Lavire, S.Morera. Characterization of the First Tetrameric Transcription Factor of the Gntr Superfamily with Allosteric Regulation From the Bacterial Pathogen Agrobacterium Fabrum Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962