Zinc in PDB 7mlb: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna:
2.7.7.6;

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna, PDB code: 7mlb was solved by Y.Liu, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.62 / 3.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	186.172, 104.266, 299.017, 90, 97.95, 90
R / Rfree (%)	23.3 / 27

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna (pdb code 7mlb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna, PDB code: 7mlb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:118.3 occ:1.00 SG D:CYS1194 2.3 166.1 1.0 SG D:CYS1112 2.3 108.8 1.0 SG D:CYS1201 2.3 104.5 1.0 SG D:CYS1204 2.3 86.9 1.0 CB D:CYS1204 3.0 122.5 1.0 CB D:CYS1194 3.2 121.1 1.0 CB D:CYS1112 3.5 125.7 1.0 CA D:CYS1194 3.6 99.8 1.0 CB D:CYS1201 3.6 110.5 1.0 OG1 D:THR1196 3.8 138.3 1.0 N D:GLN1195 4.0 117.7 1.0 N D:CYS1112 4.1 133.5 1.0 N D:CYS1204 4.2 104.2 1.0 CA D:CYS1204 4.2 97.2 1.0 N D:CYS1201 4.2 129.2 1.0 NH2 D:ARG1189 4.2 117.7 1.0 C D:CYS1194 4.3 107.4 1.0 CA D:CYS1112 4.4 128.4 1.0 CG2 D:THR1114 4.4 128.0 1.0 CA D:CYS1201 4.5 123.3 1.0 N D:THR1196 4.7 111.2 1.0 N D:CYS1194 4.8 102.9 1.0 CB D:THR1196 5.0 137.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:216.0 occ:1.00 SG D:CYS60 2.3 132.4 1.0 SG D:CYS76 2.3 166.5 1.0 SG D:CYS73 2.3 168.4 1.0 SG D:CYS58 2.3 186.0 1.0 CB D:CYS73 3.1 139.3 1.0 CB D:CYS58 3.2 175.8 1.0 CB D:CYS76 3.4 97.3 1.0 N D:CYS60 3.7 162.5 1.0 CB D:CYS60 3.7 147.7 1.0 N D:CYS76 3.9 158.0 1.0 N D:LYS62 4.1 180.5 1.0 N D:GLY61 4.1 181.9 1.0 CA D:CYS60 4.2 158.3 1.0 CB D:LYS62 4.2 186.4 1.0 N D:ALA59 4.2 145.4 1.0 CA D:CYS76 4.2 135.0 1.0 CA D:CYS58 4.4 156.6 1.0 C D:CYS58 4.5 145.3 1.0 C D:CYS60 4.5 171.0 1.0 CA D:CYS73 4.5 141.9 1.0 C D:ALA59 4.7 156.7 1.0 CB D:ARG75 4.7 137.9 1.0 CA D:LYS62 4.7 183.7 1.0 CD1 D:TYR63 4.8 150.7 1.0 CA D:ALA59 4.9 146.4 1.0 C D:ARG75 5.0 155.2 1.0 N D:GLY77 5.0 145.3 1.0 C D:CYS76 5.0 139.8 1.0

Y.Liu, L.Yu, C.Pukhrambam, J.T.Winkelman, E.Firlar, J.T.Kaelber, Y.Zhang, B.E.Nickels, R.H.Ebright. Structural and Mechanistic Basis of Reiterative Transcription Initiation. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35082149
DOI: 10.1073/PNAS.2115746119