Zinc in PDB 7ubj: Transcription Antitermination Factor Qlambda, Type-I Crystal

The structure of Transcription Antitermination Factor Qlambda, Type-I Crystal, PDB code: 7ubj was solved by Z.Yin, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.27 / 1.46
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	54.341, 54.341, 110.09, 90, 90, 120
R / Rfree (%)	17.8 / 20.3

The structure of Transcription Antitermination Factor Qlambda, Type-I Crystal also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Transcription Antitermination Factor Qlambda, Type-I Crystal (pdb code 7ubj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Transcription Antitermination Factor Qlambda, Type-I Crystal, PDB code: 7ubj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Transcription Antitermination Factor Qlambda, Type-I Crystal


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Transcription Antitermination Factor Qlambda, Type-I Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.4 occ:1.00 SG A:CYS144 2.2 20.7 1.0 SG A:CYS121 2.3 13.9 1.0 SG A:CYS118 2.3 16.6 1.0 SG A:CYS147 2.4 17.8 1.0 HB3 A:CYS118 2.9 18.6 1.0 HB3 A:CYS121 3.0 19.7 1.0 HB3 A:CYS144 3.0 21.7 1.0 H A:CYS147 3.0 23.1 1.0 H A:CYS121 3.0 18.9 1.0 CB A:CYS118 3.1 15.4 1.0 HB3 A:CYS147 3.1 19.1 1.0 CB A:CYS144 3.1 18.0 1.0 CB A:CYS121 3.2 16.4 1.0 HB2 A:CYS118 3.3 18.6 1.0 CB A:CYS147 3.4 15.8 1.0 HB2 A:CYS144 3.4 21.7 1.0 N A:CYS121 3.7 15.7 1.0 HB3 A:ARG146 3.7 32.5 1.0 N A:CYS147 3.7 19.2 1.0 HA2 A:GLY125 3.8 19.8 1.0 HB2 A:ASP120 3.8 36.4 1.0 HA2 A:GLY151 3.9 19.0 1.0 HB2 A:CYS121 4.0 19.7 1.0 CA A:CYS121 4.1 16.3 1.0 HB2 A:CYS147 4.1 19.1 1.0 CA A:CYS147 4.2 20.8 1.0 H A:GLY125 4.2 14.7 1.0 H A:ASP120 4.2 24.1 1.0 H A:GLY151 4.4 19.6 1.0 CA A:CYS118 4.5 11.5 1.0 CA A:CYS144 4.6 19.1 1.0 CA A:GLY125 4.6 16.4 1.0 H A:ARG146 4.6 31.0 1.0 H A:GLY149 4.6 25.8 1.0 CB A:ASP120 4.6 30.3 1.0 CB A:ARG146 4.7 27.1 1.0 H A:GLY123 4.7 11.9 1.0 N A:GLY125 4.8 12.2 1.0 C A:ASP120 4.8 18.0 1.0 HB3 A:ASP120 4.8 36.4 1.0 HA A:CYS121 4.8 19.6 1.0 C A:ARG146 4.8 29.5 1.0 CA A:GLY151 4.8 15.8 1.0 O A:HOH549 4.8 27.5 1.0 C A:CYS144 4.9 18.9 1.0 O A:CYS144 4.9 20.8 1.0 HA A:CYS147 4.9 25.0 1.0 N A:ASP120 4.9 20.0 1.0 H A:HIS122 4.9 14.1 1.0 C A:GLY125 4.9 14.5 1.0 C A:CYS118 4.9 15.4 1.0 C A:CYS121 4.9 15.8 1.0 HD3 A:ARG146 5.0 48.5 1.0 HA A:CYS144 5.0 22.9 1.0 O A:HOH571 5.0 29.0 1.0 N A:GLY151 5.0 16.3 1.0 HA A:CYS118 5.0 13.8 1.0

Zinc binding site 2 out of 2 in the Transcription Antitermination Factor Qlambda, Type-I Crystal


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Transcription Antitermination Factor Qlambda, Type-I Crystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:12.4 occ:1.00 SG B:CYS144 2.3 14.4 1.0 SG B:CYS121 2.3 9.8 1.0 SG B:CYS118 2.3 13.1 1.0 SG B:CYS147 2.4 13.4 1.0 HB3 B:CYS118 2.9 13.1 1.0 HB3 B:CYS144 2.9 16.2 1.0 HB3 B:CYS121 3.0 17.1 1.0 HB3 B:CYS147 3.0 16.3 1.0 CB B:CYS118 3.1 10.9 1.0 H B:CYS121 3.1 13.0 1.0 CB B:CYS144 3.1 13.5 1.0 HB2 B:CYS118 3.2 13.1 1.0 H B:CYS147 3.2 20.6 1.0 CB B:CYS121 3.2 14.2 1.0 CB B:CYS147 3.3 13.6 1.0 HB2 B:CYS144 3.4 16.2 1.0 N B:CYS121 3.7 10.8 1.0 HA2 B:GLY151 3.7 16.1 1.0 HB3 B:ARG146 3.8 29.3 1.0 HA2 B:GLY125 3.8 16.2 1.0 HB2 B:ASP120 3.8 21.7 1.0 N B:CYS147 3.8 17.2 1.0 HB2 B:CYS121 4.0 17.1 1.0 HB2 B:CYS147 4.0 16.3 1.0 CA B:CYS121 4.1 12.2 1.0 CA B:CYS147 4.2 19.7 1.0 H B:GLY125 4.3 12.6 1.0 H B:ASP120 4.3 20.3 1.0 H B:GLY151 4.3 21.1 1.0 CA B:CYS118 4.5 9.7 1.0 CA B:CYS144 4.5 18.4 1.0 H B:ARG146 4.6 29.8 1.0 CA B:GLY125 4.6 13.4 1.0 CA B:GLY151 4.6 13.4 1.0 CB B:ASP120 4.7 18.0 1.0 H B:GLY149 4.7 19.4 1.0 CB B:ARG146 4.7 24.4 1.0 C B:ASP120 4.8 12.9 1.0 O B:HOH562 4.8 28.6 1.0 HA B:CYS121 4.8 14.6 1.0 HB3 B:ASP120 4.8 21.7 1.0 H B:HIS122 4.8 11.1 1.0 C B:ARG146 4.8 22.0 1.0 C B:CYS144 4.9 13.9 1.0 N B:GLY125 4.9 10.4 1.0 H B:GLY123 4.9 10.8 1.0 HA B:CYS147 4.9 23.7 1.0 O B:CYS144 4.9 17.6 1.0 N B:GLY151 4.9 17.5 1.0 C B:CYS121 4.9 9.8 1.0 HA B:CYS118 5.0 11.7 1.0 O B:HOH458 5.0 19.9 1.0 C B:CYS118 5.0 9.4 1.0 N B:ASP120 5.0 16.9 1.0 HA B:CYS144 5.0 22.2 1.0 N B:ARG146 5.0 24.8 1.0 C B:GLY125 5.0 11.4 1.0

Z.Yin, J.G.Bird, J.T.Kaelber, B.E.Nickels, R.H.Ebright. In Transcription Antitermination By Q Lambda , Nusa Induces Refolding of Q Lambda to Form A Nozzle That Extends the Rna Polymerase Rna-Exit Channel. Proc.Natl.Acad.Sci.Usa V. 119 78119 2022.
ISSN: ESSN 1091-6490
PubMed: 35951650
DOI: 10.1073/PNAS.2205278119