Magnesium 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:

Zinc

(Zn)

2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of Re-Refinement of Thermus Thermophilus Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1604 b:0.2 occ:1.00 O D:LYS840 2.2 0.6 1.0 OD2 B:ASP168 3.1 0.4 1.0 C D:LYS840 3.4 0.6 1.0 OE2 B:GLU154 3.8 0.9 1.0 CG B:ASP168 4.0 0.9 1.0 OD1 B:ASP168 4.0 0.0 1.0 CG2 D:VAL842 4.2 0.0 1.0 N D:VAL842 4.2 0.7 1.0 N D:TYR841 4.3 0.4 1.0 CA D:TYR841 4.4 98.3 1.0 CA D:LYS840 4.4 0.6 1.0 O D:LEU839 4.5 0.9 1.0 CD B:GLU154 4.6 0.4 1.0 OE1 B:GLU154 4.6 0.0 1.0 CB D:VAL842 4.7 1.0 1.0 C D:TYR841 4.8 98.6 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of Re-Refinement of Thermus Thermophilus Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1605 b:98.0 occ:1.00 OD1 D:ASP741 2.6 82.5 1.0 OD1 D:ASP743 2.6 97.2 1.0 OD1 D:ASP739 2.7 90.4 1.0 OD2 D:ASP741 3.0 95.3 1.0 CG D:ASP741 3.1 90.0 1.0 CG D:ASP743 3.4 86.7 1.0 OD2 D:ASP743 3.5 92.4 1.0 CG D:ASP739 3.8 79.5 1.0 OD2 D:ASP739 4.2 80.9 1.0 NH2 D:ARG704 4.6 93.5 1.0 CB D:ASP741 4.7 79.9 1.0 O D:ASP739 4.8 65.6 1.0 CB D:ASP743 4.9 71.3 1.0

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