Zinc in PDB 5voi: X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex

All present enzymatic activity of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex:
2.7.7.6;

The structure of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex, PDB code: 5voi was solved by K.S.Murakami, Y.Shin, C.L.Turnbough Jr, V.Molodtsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.180, 103.474, 294.444, 90.00, 99.14, 90.00
R / Rfree (%)	19.2 / 23.6

The structure of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex (pdb code 5voi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex, PDB code: 5voi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:77.9 occ:1.00 SG D:CYS1112 2.0 53.1 1.0 SG D:CYS1201 2.0 42.3 1.0 SG D:CYS1194 2.2 44.5 1.0 SG D:CYS1204 2.5 34.4 1.0 CB D:CYS1194 3.1 47.2 1.0 CB D:CYS1204 3.3 30.9 1.0 CA D:CYS1194 3.4 38.9 1.0 CB D:CYS1112 3.4 34.2 1.0 CB D:CYS1201 3.5 43.0 1.0 N D:GLN1195 3.9 37.6 1.0 C D:CYS1194 4.1 36.4 1.0 NH2 D:ARG1189 4.1 34.2 1.0 N D:CYS1112 4.1 38.8 1.0 OG1 D:THR1196 4.2 41.6 1.0 CG2 D:THR1114 4.2 35.6 1.0 N D:CYS1201 4.2 37.8 1.0 CA D:CYS1112 4.3 34.6 1.0 N D:CYS1204 4.4 40.4 1.0 CA D:CYS1201 4.4 38.5 1.0 CA D:CYS1204 4.4 40.8 1.0 N D:CYS1194 4.6 33.7 1.0 N D:THR1196 4.7 33.5 1.0 C D:CYS1201 5.0 32.4 1.0

Zinc binding site 2 out of 2 in the X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Bacterial Rna Polymerase and Pyrg Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.9 occ:1.00 SG D:CYS76 1.9 0.6 1.0 SG D:CYS60 1.9 0.2 1.0 SG D:CYS73 2.0 0.8 1.0 SG D:CYS58 2.1 0.9 1.0 CB D:CYS76 2.7 0.2 1.0 CB D:CYS73 3.0 0.8 1.0 CB D:CYS58 3.2 0.7 1.0 CB D:CYS60 3.4 0.4 1.0 N D:CYS76 3.5 0.5 1.0 N D:CYS60 3.6 0.8 1.0 CA D:CYS76 3.7 0.6 1.0 N D:GLY61 3.9 93.1 1.0 CA D:CYS60 3.9 0.4 1.0 N D:LYS62 4.0 0.1 1.0 N D:ALA59 4.2 66.3 1.0 C D:CYS60 4.2 95.8 1.0 C D:CYS58 4.4 72.8 1.0 CB D:LYS62 4.4 70.0 1.0 CA D:CYS58 4.4 86.8 1.0 CA D:CYS73 4.5 96.5 1.0 C D:CYS76 4.6 95.7 1.0 C D:ARG75 4.6 93.6 1.0 C D:ALA59 4.6 82.7 1.0 CB D:ARG75 4.8 84.2 1.0 CA D:LYS62 4.8 90.3 1.0 CA D:GLY61 4.8 85.2 1.0 N D:GLY77 4.9 89.0 1.0 CD2 D:TYR63 4.9 84.8 1.0 C D:GLY61 4.9 97.5 1.0 CA D:ALA59 4.9 69.5 1.0

K.S.Murakami, Y.Shin, C.L.Turnbough, V.Molodtsov. X-Ray Crystal Structure of A Reiterative Transcription Complex Reveals An Atypical Rna Extension Pathway. Proc. Natl. Acad. Sci. V. 114 8211 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28652344
DOI: 10.1073/PNAS.1702741114