Magnesium in PDB 1zyr: Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin

All present enzymatic activity of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin:
2.7.7.6;

The structure of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin, PDB code: 1zyr was solved by S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	237.000, 237.000, 250.000, 90.00, 90.00, 120.00
R / Rfree (%)	26.1 / 28.1

The structure of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin (pdb code 1zyr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin, PDB code: 1zyr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg9901 b:20.0 occ:1.00 OD1 D:ASP739 2.6 31.0 1.0 OD2 D:ASP741 2.6 40.9 1.0 CG D:ASP739 3.2 33.4 1.0 OD2 D:ASP743 3.3 33.2 1.0 OD2 D:ASP739 3.4 34.5 1.0 OD1 D:ASP743 3.5 36.1 1.0 CG D:ASP741 3.5 39.0 1.0 CG D:ASP743 3.7 35.3 1.0 OD1 D:ASP741 3.8 37.8 1.0 CB D:ASP739 4.6 34.2 1.0 CB D:ASP741 4.8 38.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg9902 b:30.0 occ:1.00 OD1 N:ASP743 2.5 41.1 1.0 OD1 N:ASP741 2.7 39.0 1.0 OD1 N:ASP739 2.8 41.9 1.0 OD2 N:ASP743 2.9 39.0 1.0 CG N:ASP743 3.0 39.3 1.0 OD2 N:ASP739 3.4 39.4 1.0 CG N:ASP739 3.4 39.9 1.0 CG N:ASP741 3.8 38.8 1.0 OD2 N:ASP741 4.1 40.2 1.0 CB N:ASP743 4.4 37.5 1.0 O N:ASP739 4.5 34.1 1.0 NH1 N:ARG704 4.7 36.9 1.0 N N:ASP743 4.9 36.5 1.0 CB N:ASP739 4.9 36.7 1.0 CA N:ASP743 4.9 36.7 1.0

S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, E.Arnold. Inhibition of Bacterial Rna Polymerase By Streptolydigin: Stabilization of A Straight-Bridge-Helix Active-Center Conformation. Cell(Cambridge,Mass.) V. 122 541 2005.
ISSN: ISSN 0092-8674
PubMed: 16122422
DOI: 10.1016/J.CELL.2005.07.017