Magnesium in PDB 6woy: Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp:
2.7.7.6;

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp, PDB code: 6woy was solved by Y.Shin, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	185.977, 102.465, 296.043, 90.00, 98.87, 90.00
R / Rfree (%)	20.6 / 21.9

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp (pdb code 6woy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp, PDB code: 6woy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:47.1 occ:1.00 OD1 D:ASP739 1.9 60.5 1.0 O3' I:A3 2.2 69.7 1.0 OD1 D:ASP741 2.3 58.9 1.0 OD2 D:ASP741 2.4 67.8 1.0 OD1 D:ASP743 2.4 48.6 1.0 CG D:ASP741 2.7 61.5 1.0 CG D:ASP739 2.9 59.4 1.0 OD2 D:ASP743 3.0 50.7 1.0 CG D:ASP743 3.1 50.7 1.0 OD2 D:ASP739 3.3 65.5 1.0 C3' I:A3 3.6 66.8 1.0 O2' I:A3 4.1 62.5 1.0 CB D:ASP739 4.2 55.6 1.0 CB D:ASP741 4.2 50.1 1.0 N D:ASP739 4.2 48.6 1.0 O5' I:CH1101 4.2 78.4 1.0 C4' I:A3 4.3 66.7 1.0 C2' I:A3 4.4 66.9 1.0 NH2 D:ARG704 4.4 61.1 1.0 C D:ASP739 4.5 48.3 1.0 H4' I:CH1101 4.5 84.6 1.0 CA D:ASP739 4.5 45.1 1.0 CB D:ASP743 4.6 49.2 1.0 N D:ASP741 4.6 49.4 1.0 O D:ASP739 4.7 52.5 1.0 C5' I:A3 4.8 65.4 1.0 O2B I:CH1101 4.9 74.9 1.0 O4' I:CH1101 4.9 65.4 1.0 CA D:ASP741 4.9 48.6 1.0 N D:PHE740 4.9 53.2 1.0 C4' I:CH1101 5.0 70.5 1.0

Magnesium binding site 2 out of 2 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2002 b:64.3 occ:1.00 O2G I:CH1101 2.0 75.5 1.0 OD2 D:ASP739 2.2 65.5 1.0 O2B I:CH1101 2.3 74.9 1.0 NH1 C:ARG879 2.8 70.7 1.0 PG I:CH1101 3.1 82.5 1.0 O3B I:CH1101 3.1 76.4 1.0 PB I:CH1101 3.3 83.4 1.0 O2A I:CH1101 3.3 79.4 1.0 CG D:ASP739 3.5 59.4 1.0 O3G I:CH1101 3.7 60.9 1.0 OD2 C:ASP686 4.0 58.0 1.0 CZ C:ARG879 4.1 59.0 1.0 CB D:ASP739 4.2 55.6 1.0 O3A I:CH1101 4.3 84.8 1.0 O1G I:CH1101 4.3 75.7 1.0 O1B I:CH1101 4.3 82.6 1.0 PA I:CH1101 4.4 83.4 1.0 OD1 D:ASP739 4.4 60.5 1.0 NH2 D:ARG1029 4.4 70.1 1.0 OD2 D:ASP741 4.6 67.8 1.0 NH2 C:ARG879 4.8 54.2 1.0 NH2 C:ARG557 5.0 58.1 1.0 O5' I:CH1101 5.0 78.4 1.0 NE C:ARG879 5.0 53.9 1.0

Y.Shin, K.S.Murakami. The Mechanism of Discrimination Against 2DNTPS By the Multisubunit Rna Polymerases To Be Published.