Magnesium in PDB 5i2d: Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo

All present enzymatic activity of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo:
2.7.7.6;

The structure of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo, PDB code: 5i2d was solved by Y.Feng, Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.31 / 4.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	171.487, 105.446, 374.585, 90.00, 102.39, 90.00
R / Rfree (%)	24.1 / 28.4

The structure of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo (pdb code 5i2d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo, PDB code: 5i2d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2003 b:18.5 occ:1.00 O3' K:A4 1.8 73.9 1.0 OD1 D:ASP739 2.0 36.8 1.0 OD1 D:ASP741 2.0 63.5 1.0 OD1 D:ASP743 2.1 62.8 1.0 OD2 D:ASP741 2.6 68.3 1.0 CG D:ASP741 2.7 64.5 1.0 CG D:ASP739 2.8 37.0 1.0 CG D:ASP743 2.9 58.5 1.0 OD2 D:ASP739 3.0 47.7 1.0 OD2 D:ASP743 3.0 61.9 1.0 C3' K:A4 3.2 72.8 1.0 C4' K:A4 3.9 72.7 1.0 O2' K:A4 4.1 73.8 1.0 C2' K:A4 4.1 74.5 1.0 CB D:ASP741 4.2 54.7 1.0 CB D:ASP739 4.3 27.5 1.0 C5' K:A4 4.3 74.6 1.0 CB D:ASP743 4.4 49.8 1.0 O D:ASP739 4.5 34.1 1.0 N D:ASP741 4.5 65.5 1.0 C D:ASP739 4.6 31.7 1.0 N D:ASP739 4.7 27.3 1.0 N D:ASP743 4.7 59.3 1.0 CA D:ASP739 4.7 24.6 1.0 CA D:ASP741 4.7 60.5 1.0 CA D:ASP743 4.9 50.6 1.0 C D:ASP741 4.9 61.0 1.0 NH2 D:ARG704 5.0 47.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg2003 b:13.7 occ:1.00 O3' V:A4 1.9 68.3 1.0 OD1 O:ASP739 2.0 69.9 1.0 OD1 O:ASP741 2.1 65.2 1.0 OD1 O:ASP743 2.1 71.4 1.0 OD2 O:ASP741 2.7 69.9 1.0 CG O:ASP741 2.7 66.2 1.0 CG O:ASP743 2.9 67.0 1.0 CG O:ASP739 2.9 70.1 1.0 OD2 O:ASP743 3.0 70.4 1.0 OD2 O:ASP739 3.1 80.8 1.0 C3' V:A4 3.2 67.2 1.0 C4' V:A4 4.0 67.2 1.0 CB O:ASP741 4.2 56.4 1.0 C5' V:A4 4.3 69.1 1.0 C2' V:A4 4.3 69.0 1.0 CB O:ASP743 4.3 58.4 1.0 CB O:ASP739 4.3 60.6 1.0 O O:ASP739 4.4 67.2 1.0 O2' V:A4 4.5 68.2 1.0 N O:ASP741 4.6 67.2 1.0 N O:ASP739 4.6 60.4 1.0 C O:ASP739 4.6 64.8 1.0 N O:ASP743 4.7 67.8 1.0 CA O:ASP739 4.8 57.7 1.0 CA O:ASP741 4.8 62.2 1.0 CA O:ASP743 4.9 59.2 1.0 O5' V:A4 4.9 78.9 1.0 NH2 O:ARG704 4.9 58.4 1.0 C O:ASP741 5.0 62.6 1.0

Y.Feng, Y.Zhang, R.H.Ebright. Structural Basis of Transcription Activation. Science V. 352 1330 2016.
ISSN: ESSN 1095-9203
PubMed: 27284196
DOI: 10.1126/SCIENCE.AAF4417