Zinc in PDB 5nbc: Structure of Prokaryotic Transcription Factors

The structure of Structure of Prokaryotic Transcription Factors, PDB code: 5nbc was solved by J.Perard, P.Carpentier, I.Michaud-Soret, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.08 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.150, 90.000, 63.950, 90.00, 93.48, 90.00
R / Rfree (%)	21.5 / 24.4

The structure of Structure of Prokaryotic Transcription Factors also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Zinc atom in the Structure of Prokaryotic Transcription Factors (pdb code 5nbc). 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 Prokaryotic Transcription Factors, PDB code: 5nbc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Prokaryotic Transcription Factors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Prokaryotic Transcription Factors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:24.5 occ:1.00 SG A:CYS96 2.2 25.1 1.0 SG A:CYS136 2.3 27.5 1.0 SG A:CYS133 2.3 27.0 1.0 SG A:CYS93 2.3 21.3 1.0 CB A:CYS93 3.2 19.9 1.0 CB A:CYS96 3.2 25.8 1.0 CB A:CYS136 3.3 28.4 1.0 CB A:CYS133 3.4 26.3 1.0 N A:CYS96 3.8 24.4 1.0 N A:CYS133 4.0 20.0 1.0 CA A:CYS96 4.1 22.1 1.0 N A:CYS136 4.2 32.3 1.0 CA A:CYS133 4.3 27.9 1.0 CA A:CYS136 4.3 35.0 1.0 CB A:MET98 4.6 20.9 1.0 CA A:CYS93 4.7 20.1 1.0 CB A:LYS95 4.8 20.3 1.0 C A:CYS96 4.8 25.3 1.0 C A:LYS95 4.8 20.0 1.0 C A:CYS133 4.9 30.6 1.0

Zinc binding site 2 out of 4 in the Structure of Prokaryotic Transcription Factors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Prokaryotic Transcription Factors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:26.2 occ:1.00 SG B:CYS96 2.2 29.8 1.0 SG B:CYS93 2.3 23.2 1.0 SG B:CYS136 2.3 29.0 1.0 SG B:CYS133 2.3 25.9 1.0 CB B:CYS93 3.2 20.5 1.0 CB B:CYS96 3.3 26.9 1.0 CB B:CYS136 3.3 31.5 1.0 CB B:CYS133 3.3 33.2 1.0 N B:CYS96 3.9 26.2 1.0 N B:CYS133 3.9 23.5 1.0 CA B:CYS96 4.1 28.0 1.0 N B:CYS136 4.2 33.7 1.0 CA B:CYS133 4.2 28.0 1.0 CA B:CYS136 4.4 34.6 1.0 CA B:CYS93 4.7 19.4 1.0 CB B:MET98 4.7 26.4 1.0 CB B:LYS95 4.7 24.7 1.0 C B:LYS95 4.8 23.8 1.0 C B:CYS96 4.8 27.2 1.0 C B:CYS133 4.8 33.5 1.0 O B:CYS133 5.0 25.8 1.0

Zinc binding site 3 out of 4 in the Structure of Prokaryotic Transcription Factors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Prokaryotic Transcription Factors within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:23.1 occ:1.00 SG C:CYS96 2.2 21.6 1.0 SG C:CYS133 2.3 20.4 1.0 SG C:CYS93 2.3 18.6 1.0 SG C:CYS136 2.4 24.3 1.0 CB C:CYS93 3.2 18.1 1.0 CB C:CYS96 3.3 19.8 1.0 CB C:CYS136 3.3 25.9 1.0 CB C:CYS133 3.4 17.8 1.0 N C:CYS96 3.7 16.5 1.0 N C:CYS133 4.0 18.4 1.0 CA C:CYS96 4.1 18.8 1.0 N C:CYS136 4.1 36.0 1.0 CA C:CYS133 4.2 21.7 1.0 CA C:CYS136 4.4 38.7 1.0 CB C:LYS95 4.4 19.0 1.0 CB C:MET98 4.5 22.2 1.0 CA C:CYS93 4.7 14.6 1.0 C C:LYS95 4.8 19.9 1.0 C C:CYS133 4.8 27.8 1.0 C C:CYS96 4.8 19.6 1.0 O C:CYS133 4.9 27.1 1.0 CA C:LYS95 5.0 19.3 1.0

Zinc binding site 4 out of 4 in the Structure of Prokaryotic Transcription Factors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Prokaryotic Transcription Factors within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:21.8 occ:1.00 SG D:CYS96 2.3 20.8 1.0 SG D:CYS133 2.3 22.7 1.0 SG D:CYS136 2.3 25.6 1.0 SG D:CYS93 2.4 18.4 1.0 CB D:CYS93 3.3 13.0 1.0 CB D:CYS96 3.3 19.9 1.0 CB D:CYS136 3.3 31.9 1.0 CB D:CYS133 3.4 18.1 1.0 N D:CYS96 3.7 17.2 1.0 O D:HOH407 4.0 38.9 1.0 N D:CYS133 4.0 20.4 1.0 CA D:CYS96 4.1 18.3 1.0 N D:CYS136 4.2 38.4 1.0 CA D:CYS133 4.3 18.9 1.0 CB D:LYS95 4.4 23.6 1.0 CA D:CYS136 4.4 33.8 1.0 O D:HOH402 4.4 40.7 1.0 CA D:CYS93 4.7 15.5 1.0 C D:LYS95 4.7 21.4 1.0 C D:CYS133 4.8 26.1 1.0 C D:CYS96 4.8 20.8 1.0 CB D:MET98 4.9 22.6 1.0 O D:CYS133 4.9 25.0 1.0 CA D:LYS95 5.0 18.8 1.0

J.Perard, S.Nader, M.Levert, L.Arnaud, P.Carpentier, C.Siebert, F.Blanquet, C.Cavazza, P.Renesto, D.Schneider, M.Maurin, J.Coves, S.Crouzy, I.Michaud-Soret. Structural and Functional Studies of the Metalloregulator Fur Identify A Promoter-Binding Mechanism and Its Role Infrancisella Tularensisvirulence. Commun Biol V. 1 93 2018.
ISSN: ESSN 2399-3642
PubMed: 30271974
DOI: 10.1038/S42003-018-0095-6