Zinc in PDB 6za7: Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum

The structure of Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum, PDB code: 6za7 was solved by S.Morera, A.Vigouroux, P.Legrand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.38 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.110, 79.010, 140.610, 90.00, 95.08, 90.00
R / Rfree (%)	19.4 / 22.3

The binding sites of Zinc atom in the Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum (pdb code 6za7). 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 Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum, PDB code: 6za7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) 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 Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:46.2 occ:1.00 NE2 A:HIS214 2.1 43.4 1.0 OD1 A:ASN137 2.2 50.6 1.0 NE2 A:HIS141 2.3 37.1 1.0 NE2 A:HIS192 2.3 41.2 1.0 O3 A:GOL302 2.7 45.1 1.0 CE1 A:HIS214 2.9 43.8 1.0 CE1 A:HIS192 3.1 41.9 1.0 O2 A:GOL302 3.2 38.9 1.0 CE1 A:HIS141 3.2 36.1 1.0 CG A:ASN137 3.2 53.8 1.0 CD2 A:HIS214 3.3 43.0 1.0 CD2 A:HIS141 3.3 38.6 1.0 C3 A:GOL302 3.5 43.6 1.0 CD2 A:HIS192 3.5 40.6 1.0 ND2 A:ASN137 3.6 43.0 1.0 C2 A:GOL302 3.8 44.5 1.0 OH A:TYR133 4.0 51.0 1.0 ND1 A:HIS214 4.2 44.3 1.0 CG A:HIS214 4.3 41.6 1.0 ND1 A:HIS192 4.4 42.2 1.0 ND1 A:HIS141 4.4 36.8 1.0 CG A:HIS141 4.4 37.1 1.0 CG A:HIS192 4.5 40.0 1.0 CB A:ASN137 4.5 46.6 1.0 CZ A:TYR133 4.8 51.6 1.0 CE1 A:TYR133 4.8 48.5 1.0

Zinc binding site 2 out of 4 in the Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) 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 Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:63.2 occ:1.00 NE2 B:HIS141 2.1 51.9 1.0 OD1 B:ASN137 2.1 67.2 1.0 NE2 B:HIS192 2.2 56.6 1.0 NE2 B:HIS214 2.3 52.8 1.0 O3 B:GOL302 2.6 62.4 1.0 CE1 B:HIS141 3.0 50.3 1.0 O2 B:GOL302 3.0 67.0 1.0 CE1 B:HIS192 3.1 58.3 1.0 CD2 B:HIS141 3.1 52.9 1.0 CE1 B:HIS214 3.2 53.1 1.0 CG B:ASN137 3.2 70.4 1.0 CD2 B:HIS192 3.3 56.6 1.0 CD2 B:HIS214 3.4 51.9 1.0 ND2 B:ASN137 3.6 59.3 1.0 C3 B:GOL302 3.6 63.6 1.0 C2 B:GOL302 3.8 66.8 1.0 ND1 B:HIS141 4.2 50.6 1.0 CG B:HIS141 4.2 50.0 1.0 OH B:TYR133 4.3 79.2 1.0 ND1 B:HIS192 4.3 60.0 1.0 ND1 B:HIS214 4.4 53.0 1.0 CG B:HIS192 4.4 56.6 1.0 CG B:HIS214 4.5 50.1 1.0 CB B:ASN137 4.5 57.8 1.0 CD2 B:PHE140 4.7 51.1 1.0 O B:ASN137 4.8 57.7 1.0

Zinc binding site 3 out of 4 in the Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) 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 Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:69.3 occ:1.00 OD1 C:ASN137 2.1 66.4 1.0 NE2 C:HIS192 2.1 57.7 1.0 NE2 C:HIS214 2.2 55.1 1.0 NE2 C:HIS141 2.3 57.1 1.0 O2 C:GOL302 2.7 58.7 1.0 CE1 C:HIS192 3.0 59.6 1.0 O3 C:GOL302 3.0 61.1 1.0 CE1 C:HIS214 3.1 55.6 1.0 CD2 C:HIS141 3.2 58.0 1.0 CG C:ASN137 3.2 68.2 1.0 CD2 C:HIS192 3.3 57.2 1.0 CE1 C:HIS141 3.4 54.9 1.0 CD2 C:HIS214 3.4 53.5 1.0 ND2 C:ASN137 3.7 57.3 1.0 C2 C:GOL302 3.7 61.0 1.0 C3 C:GOL302 3.8 59.8 1.0 OH C:TYR133 4.2 79.7 1.0 ND1 C:HIS192 4.2 60.9 1.0 ND1 C:HIS214 4.3 55.3 1.0 CG C:HIS192 4.3 57.2 1.0 CG C:HIS141 4.4 54.7 1.0 CG C:HIS214 4.4 51.9 1.0 ND1 C:HIS141 4.4 54.7 1.0 CB C:ASN137 4.5 56.9 1.0 CD2 C:PHE140 4.7 53.1 1.0 O C:ASN137 4.8 67.2 1.0 CA C:ASN137 5.0 61.2 1.0

Zinc binding site 4 out of 4 in the Structure of the Apo Transcriptional Repressor ATU1419 (Vanr) 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 Apo Transcriptional Repressor ATU1419 (Vanr) From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:66.6 occ:1.00 NE2 D:HIS192 2.1 54.9 1.0 OD1 D:ASN137 2.1 60.0 1.0 NE2 D:HIS214 2.3 57.2 1.0 NE2 D:HIS141 2.3 57.2 1.0 O3 D:GOL302 2.7 55.7 1.0 O2 D:GOL302 2.8 52.1 1.0 CE1 D:HIS192 2.9 56.7 1.0 CE1 D:HIS214 3.1 57.3 1.0 CE1 D:HIS141 3.2 55.2 1.0 CG D:ASN137 3.2 69.0 1.0 CD2 D:HIS192 3.3 54.4 1.0 CD2 D:HIS141 3.3 58.6 1.0 CD2 D:HIS214 3.4 55.9 1.0 C3 D:GOL302 3.6 55.5 1.0 C2 D:GOL302 3.7 56.3 1.0 ND2 D:ASN137 3.7 58.6 1.0 OH D:TYR133 3.9 86.7 1.0 ND1 D:HIS192 4.2 58.4 1.0 ND1 D:HIS214 4.3 57.0 1.0 CG D:HIS192 4.3 54.8 1.0 ND1 D:HIS141 4.4 55.9 1.0 CG D:HIS214 4.4 53.8 1.0 CG D:HIS141 4.4 56.0 1.0 CB D:ASN137 4.5 60.5 1.0 CZ D:TYR133 4.8 90.8 1.0 CD2 D:PHE140 4.9 55.1 1.0 CE1 D:TYR133 4.9 85.3 1.0 O D:ASN137 5.0 65.9 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