Zinc in PDB 8reb: Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 6NT Complex

All present enzymatic activity of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 6NT Complex:
2.7.7.6;

The structure of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 6NT 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 - 6NT Complex (pdb code 8reb). 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 - 6NT Complex, PDB code: 8reb:
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 - 6NT 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 - 6NT Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:112.5 occ:1.00 SG D:CYS88 2.3 66.1 1.0 SG D:CYS70 2.3 66.6 1.0 O D:LEU71 2.4 63.6 1.0 CB D:CYS85 2.5 56.7 1.0 C D:LEU71 3.5 63.6 1.0 CB D:CYS70 3.7 66.6 1.0 N D:LEU71 3.9 63.6 1.0 CB D:CYS88 4.0 66.1 1.0 CA D:CYS85 4.0 56.7 1.0 O D:CYS88 4.1 66.1 1.0 C D:CYS70 4.1 66.6 1.0 CA D:LEU71 4.2 63.6 1.0 CB D:LYS74 4.3 64.8 1.0 N D:CYS88 4.3 66.1 1.0 N D:LYS74 4.5 64.8 1.0 N D:CYS85 4.6 56.7 1.0 CA D:CYS70 4.6 66.6 1.0 CB D:CYS72 4.6 75.6 1.0 O D:CYS70 4.6 66.6 1.0 CA D:CYS88 4.6 66.1 1.0 N D:CYS72 4.6 75.6 1.0 SG D:CYS72 4.6 75.6 1.0 CB D:LEU71 4.7 63.6 1.0 C D:CYS88 4.8 66.1 1.0 C D:CYS85 4.8 56.7 1.0 N D:GLY73 4.9 59.8 1.0 CA D:CYS72 5.0 75.6 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 6NT 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 - 6NT Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1503 b:56.1 occ:1.00 SG D:CYS898 2.3 25.7 1.0 SG D:CYS814 2.3 47.4 1.0 CB D:CYS888 2.4 29.1 1.0 CB D:CYS895 2.6 19.2 1.0 CB D:CYS898 2.8 25.7 1.0 CA D:CYS888 2.9 29.1 1.0 O D:CYS888 3.2 29.1 1.0 N D:CYS895 3.3 19.2 1.0 CB D:CYS814 3.4 47.4 1.0 C D:CYS888 3.5 29.1 1.0 CA D:CYS895 3.5 19.2 1.0 CA D:CYS898 4.1 25.7 1.0 N D:CYS888 4.2 29.1 1.0 N D:CYS898 4.2 25.7 1.0 C D:CYS895 4.4 19.2 1.0 N D:CYS814 4.4 47.4 1.0 O D:CYS895 4.5 19.2 1.0 C D:VAL894 4.5 18.6 1.0 CA D:CYS814 4.6 47.4 1.0 NH2 D:ARG883 4.7 28.2 1.0 N D:ASP889 4.8 43.3 1.0 CG1 D:VAL894 4.9 18.6 1.0 CB D:THR890 4.9 39.3 1.0 CA D:VAL894 5.0 18.6 1.0 CG2 D:THR890 5.0 39.3 1.0 O D:SER887 5.0 27.4 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