Zinc in PDB 7ubk: Transcription Antitermination Factor Qlambda, Type-II Crystal

The structure of Transcription Antitermination Factor Qlambda, Type-II Crystal, PDB code: 7ubk 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)	45.59 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.304, 64.317, 65.319, 90, 98.35, 90
R / Rfree (%)	18.4 / 22.8

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

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Transcription Antitermination Factor Qlambda, Type-II Crystal (pdb code 7ubk). 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-II Crystal, PDB code: 7ubk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Transcription Antitermination Factor Qlambda, Type-II 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-II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.2 occ:1.00 SG A:CYS121 2.3 23.4 1.0 SG A:CYS147 2.3 27.2 1.0 SG A:CYS118 2.3 32.7 1.0 SG A:CYS144 2.3 27.7 1.0 HB3 A:CYS118 2.9 25.3 1.0 HB3 A:CYS144 2.9 70.0 1.0 H A:CYS147 3.0 34.3 1.0 CB A:CYS118 3.0 21.3 1.0 CB A:CYS144 3.1 58.3 1.0 HB3 A:CYS147 3.1 35.5 1.0 H A:CYS121 3.2 29.1 1.0 HB3 A:CYS121 3.2 26.0 1.0 HB2 A:CYS118 3.2 25.3 1.0 CB A:CYS147 3.3 29.5 1.0 CB A:CYS121 3.3 21.6 1.0 HB2 A:CYS144 3.4 70.0 1.0 HB3 A:ARG146 3.6 48.5 1.0 HA2 A:GLY125 3.7 22.7 1.0 N A:CYS147 3.7 28.5 1.0 HB2 A:ASP120 3.8 46.9 1.0 N A:CYS121 3.8 24.2 1.0 HA2 A:GLY151 3.8 22.9 1.0 HB2 A:CYS147 4.1 35.5 1.0 HB2 A:CYS121 4.1 26.0 1.0 CA A:CYS147 4.1 29.3 1.0 H A:GLY125 4.1 23.7 1.0 CA A:CYS121 4.2 21.2 1.0 H A:ARG146 4.3 46.3 1.0 H A:GLY151 4.3 28.3 1.0 H A:ASP120 4.4 29.9 1.0 CA A:CYS118 4.5 21.9 1.0 CB A:ARG146 4.5 40.4 1.0 CA A:GLY125 4.5 19.2 1.0 CA A:CYS144 4.5 21.1 1.0 H A:GLY123 4.6 26.5 1.0 CA A:GLY151 4.7 19.1 1.0 CB A:ASP120 4.7 39.1 1.0 H A:GLY149 4.7 21.1 1.0 N A:GLY125 4.7 19.7 1.0 C A:ARG146 4.8 41.0 1.0 H A:LYS148 4.8 38.4 1.0 C A:ASP120 4.8 29.1 1.0 N A:ARG146 4.9 38.5 1.0 C A:CYS144 4.9 22.2 1.0 HA A:CYS147 4.9 35.2 1.0 N A:GLY151 4.9 23.5 1.0 HA A:CYS118 4.9 26.3 1.0 O A:HOH440 4.9 34.5 1.0 H A:HIS122 4.9 34.1 1.0 HA A:CYS121 4.9 25.5 1.0 C A:CYS118 4.9 21.2 1.0 C A:CYS147 5.0 25.5 1.0 CA A:ARG146 5.0 41.3 1.0 HB3 A:ASP120 5.0 46.9 1.0 N A:ASP120 5.0 24.9 1.0 HA A:CYS144 5.0 25.1 1.0 HD3 A:ARG146 5.0 66.6 1.0 C A:CYS121 5.0 34.2 1.0

Zinc binding site 2 out of 2 in the Transcription Antitermination Factor Qlambda, Type-II 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-II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.6 occ:1.00 SG B:CYS121 2.2 25.7 1.0 SG B:CYS118 2.3 27.1 1.0 SG B:CYS147 2.3 25.7 1.0 SG B:CYS144 2.4 41.7 1.0 HB3 B:CYS118 2.9 20.9 1.0 HB3 B:CYS144 3.0 70.8 1.0 HB3 B:CYS121 3.0 37.1 1.0 CB B:CYS118 3.0 17.6 1.0 H B:CYS147 3.0 63.8 1.0 H B:CYS121 3.1 33.3 1.0 CB B:CYS144 3.2 59.0 1.0 HB3 B:CYS147 3.2 34.1 1.0 CB B:CYS121 3.2 30.9 1.0 HB2 B:CYS118 3.2 20.9 1.0 HB2 B:CYS144 3.3 70.8 1.0 CB B:CYS147 3.4 28.4 1.0 HB3 B:ARG146 3.6 37.5 1.0 HA2 B:GLY125 3.7 47.8 1.0 N B:CYS121 3.7 28.0 1.0 N B:CYS147 3.8 53.1 1.0 HB2 B:ASP120 3.8 59.1 1.0 HB2 B:CYS121 4.0 37.1 1.0 HA2 B:GLY151 4.0 43.3 1.0 CA B:CYS121 4.1 28.9 1.0 H B:GLY125 4.1 30.3 1.0 HB2 B:CYS147 4.2 34.1 1.0 CA B:CYS147 4.2 27.6 1.0 H B:ASP120 4.3 48.7 1.0 H B:GLY151 4.3 26.3 1.0 H B:ARG146 4.3 47.0 1.0 CA B:CYS118 4.5 29.7 1.0 CA B:GLY125 4.5 39.8 1.0 CB B:ARG146 4.6 31.2 1.0 CA B:CYS144 4.6 105.6 1.0 H B:GLY123 4.6 26.3 1.0 CB B:ASP120 4.7 49.2 1.0 H B:GLY149 4.7 24.6 1.0 N B:GLY125 4.7 25.3 1.0 H B:LYS148 4.8 47.8 1.0 C B:ASP120 4.8 31.3 1.0 C B:ARG146 4.8 41.1 1.0 CA B:GLY151 4.8 36.0 1.0 HA B:CYS121 4.8 34.8 1.0 C B:CYS118 4.8 36.0 1.0 HD3 B:ARG146 4.9 66.2 1.0 HA B:CYS118 4.9 35.7 1.0 N B:ASP120 4.9 40.5 1.0 H B:HIS122 4.9 65.0 1.0 C B:CYS121 4.9 33.8 1.0 HA B:CYS147 4.9 33.2 1.0 N B:ARG146 5.0 39.1 1.0 N B:GLY151 5.0 21.9 1.0 C B:CYS144 5.0 90.8 1.0 C B:CYS147 5.0 37.0 1.0 HB3 B:ASP120 5.0 59.1 1.0 C B:GLY125 5.0 40.0 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