Zinc in PDB 8red: Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex

All present enzymatic activity of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex:
2.7.7.6;

The structure of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex (pdb code 8red). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex, PDB code: 8red:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:55.5 occ:1.00 O D:LEU71 2.1 39.2 1.0 SG D:CYS88 2.3 36.4 1.0 SG D:CYS70 2.3 47.0 1.0 SG D:CYS72 3.1 42.5 1.0 C D:LEU71 3.1 39.2 1.0 CB D:LYS74 3.3 42.1 1.0 CB D:CYS85 3.4 36.7 1.0 N D:LEU71 3.7 39.2 1.0 CB D:CYS70 3.8 47.0 1.0 CA D:LEU71 3.9 39.2 1.0 N D:LYS74 3.9 42.1 1.0 CB D:CYS88 4.1 36.4 1.0 N D:CYS72 4.2 42.5 1.0 C D:CYS70 4.2 47.0 1.0 CA D:LYS74 4.2 42.1 1.0 CB D:LEU71 4.3 39.2 1.0 CB D:CYS72 4.4 42.5 1.0 N D:CYS88 4.5 36.4 1.0 N D:GLY73 4.5 40.3 1.0 CA D:CYS72 4.6 42.5 1.0 C D:CYS72 4.6 42.5 1.0 CA D:CYS70 4.7 47.0 1.0 O D:CYS70 4.8 47.0 1.0 N D:TYR75 4.8 50.7 1.0 O D:CYS88 4.8 36.4 1.0 CA D:CYS88 4.8 36.4 1.0 CA D:CYS85 4.9 36.7 1.0 CB D:LYS87 5.0 41.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1503 b:35.4 occ:1.00 SG D:CYS898 2.3 20.9 1.0 O D:CYS888 2.4 20.6 1.0 CB D:CYS895 2.4 18.5 1.0 CB D:CYS814 2.8 28.1 1.0 C D:CYS888 3.2 20.6 1.0 CA D:CYS888 3.4 20.6 1.0 CA D:CYS895 3.6 18.5 1.0 N D:CYS895 3.7 18.5 1.0 CB D:CYS888 3.8 20.6 1.0 N D:CYS814 3.8 28.1 1.0 CB D:CYS898 3.9 20.9 1.0 SG D:CYS814 3.9 28.1 1.0 CA D:CYS814 3.9 28.1 1.0 NH2 D:ARG883 4.1 28.0 1.0 N D:ASP889 4.5 28.3 1.0 CG2 D:THR816 4.5 33.8 1.0 C D:CYS895 4.5 18.5 1.0 N D:THR890 4.6 24.5 1.0 O D:SER887 4.7 21.9 1.0 N D:CYS898 4.7 20.9 1.0 N D:CYS888 4.7 20.6 1.0 CB D:THR890 4.7 24.5 1.0 O D:CYS895 4.7 18.5 1.0 CA D:CYS898 4.9 20.9 1.0 C D:CYS814 4.9 28.1 1.0 C D:VAL894 5.0 16.3 1.0

F.Gao, F.Ye, B.Zhang, N.Cronin, M.Buck, X.Zhang. Structural Basis of Sigma 54 Displacement and Promoter Escape in Bacterial Transcription. Proc.Natl.Acad.Sci.Usa V. 121 70120 2024.
ISSN: ESSN 1091-6490
PubMed: 38170755
DOI: 10.1073/PNAS.2309670120