Zinc in PDB 5tmf: Re-Refinement of Thermus Thermophilus Rna Polymerase

All present enzymatic activity of Re-Refinement of Thermus Thermophilus Rna Polymerase:
2.7.7.6;

The structure of Re-Refinement of Thermus Thermophilus Rna Polymerase, PDB code: 5tmf was solved by J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 3.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	235.090, 235.090, 250.880, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.4

The structure of Re-Refinement of Thermus Thermophilus Rna Polymerase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Re-Refinement of Thermus Thermophilus Rna Polymerase (pdb code 5tmf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Re-Refinement of Thermus Thermophilus Rna Polymerase, PDB code: 5tmf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Re-Refinement of Thermus Thermophilus Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Re-Refinement of Thermus Thermophilus Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1601 b:0.8 occ:1.00 SG D:CYS76 2.4 0.9 1.0 SG D:CYS60 2.4 0.7 1.0 SG D:CYS58 2.4 0.5 1.0 SG D:CYS73 2.4 0.6 1.0 CB D:CYS58 2.9 0.8 1.0 CB D:CYS76 3.1 0.1 1.0 CB D:CYS73 3.2 1.0 1.0 CB D:CYS60 3.6 0.0 1.0 N D:CYS60 3.8 0.4 1.0 N D:CYS76 3.9 0.0 1.0 N D:GLY61 4.0 0.7 1.0 N D:LYS62 4.1 0.6 1.0 CA D:CYS76 4.1 0.1 1.0 CB D:LYS62 4.1 0.6 1.0 CA D:CYS60 4.2 0.8 1.0 CA D:CYS58 4.2 0.2 1.0 N D:ALA59 4.2 1.0 1.0 C D:CYS58 4.3 1.0 1.0 CD1 D:TYR63 4.6 0.8 1.0 C D:CYS60 4.6 0.9 1.0 CA D:LYS62 4.7 0.8 1.0 CA D:CYS73 4.7 0.1 1.0 C D:ALA59 4.8 0.4 1.0 CB D:ARG75 4.9 0.4 1.0 C D:CYS76 4.9 0.4 1.0 N D:TYR63 4.9 0.7 1.0 C D:ARG75 5.0 0.3 1.0 C D:GLY61 5.0 0.9 1.0 CA D:GLY61 5.0 0.9 1.0 CA D:ALA59 5.0 0.2 1.0 O D:CYS58 5.0 0.5 1.0

Zinc binding site 2 out of 2 in the Re-Refinement of Thermus Thermophilus Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Re-Refinement of Thermus Thermophilus Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1602 b:84.5 occ:1.00 SG D:CYS1194 2.4 0.8 1.0 SG D:CYS1201 2.4 77.5 1.0 SG D:CYS1112 2.4 0.5 1.0 SG D:CYS1204 2.4 92.2 1.0 CB D:CYS1194 3.1 83.2 1.0 CB D:CYS1201 3.2 84.5 1.0 CB D:CYS1204 3.2 83.3 1.0 CB D:CYS1112 3.4 0.4 1.0 CA D:CYS1194 3.5 88.4 1.0 N D:GLN1195 3.6 97.2 1.0 N D:CYS1201 3.8 84.0 1.0 CA D:CYS1201 4.0 85.0 1.0 C D:CYS1194 4.0 93.2 1.0 OG1 D:THR1196 4.1 0.1 1.0 NH1 D:ARG1189 4.2 0.6 1.0 N D:CYS1112 4.2 99.7 1.0 N D:CYS1204 4.4 83.4 1.0 CG2 D:THR1114 4.4 0.6 1.0 CA D:CYS1112 4.4 0.8 1.0 CA D:CYS1204 4.4 82.4 1.0 N D:THR1196 4.5 0.4 1.0 C D:CYS1201 4.6 84.0 1.0 O D:CYS1201 4.7 85.8 1.0 N D:CYS1194 4.8 85.9 1.0 CA D:GLN1195 4.8 0.5 1.0 C D:VAL1200 5.0 84.5 1.0

J.Wang, J.Wang. N/A N/A.
ISSN: ESSN 1469-896X
PubMed: 25352397
DOI: 10.1002/PRO.2595