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Magnesium in PDB 2be5: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin

Enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin, PDB code: 2be5 was solved by D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, I.Artsimovitch, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 239.500, 239.500, 253.100, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 27.4

Other elements in 2be5:

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin (pdb code 2be5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin, PDB code: 2be5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2be5

Go back to Magnesium Binding Sites List in 2be5
Magnesium binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin


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 the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg9004

b:17.5
occ:1.00
 OD1 D:ASP739 2.2 58.2 1.0
O8 D:TGT9001 2.2 50.7 1.0
OE2 C:GLU685 2.3 60.9 1.0
O D:HOH2099 2.5 38.9 1.0
OE1 C:GLU685 3.1 59.8 1.0
CD C:GLU685 3.1 58.8 1.0
CG D:ASP739 3.1 56.2 1.0
NH2 C:ARG879 3.2 34.4 1.0
CB D:ASP739 3.6 49.8 1.0
O4 D:TGT9001 3.6 45.6 1.0
NH2 D:ARG1029 3.7 46.1 1.0
P1 D:TGT9001 3.9 52.5 1.0
OD2 D:ASP739 4.2 61.0 1.0
OD1 C:ASP686 4.3 53.0 1.0
CZ C:ARG879 4.5 33.6 1.0
C1 D:TGT9001 4.5 47.1 1.0
O6 D:TGT9001 4.6 49.7 1.0
CA D:ASP739 4.6 43.9 1.0
O9 D:TGT9001 4.7 49.8 1.0
CG C:GLU685 4.7 56.0 1.0
O7 D:TGT9001 4.7 50.6 1.0
C9 D:TGT9001 4.7 44.5 1.0
CZ D:ARG1029 4.8 45.6 1.0
NH2 C:ARG557 4.8 39.8 1.0

Magnesium binding site 2 out of 4 in 2be5

Go back to Magnesium Binding Sites List in 2be5
Magnesium binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin


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 the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg9003

b:17.2
occ:1.00
 OD1 D:ASP741 2.2 34.2 1.0
OD2 D:ASP739 2.2 61.0 1.0
OD2 D:ASP743 2.3 34.2 1.0
OD2 D:ASP741 2.6 36.3 1.0
OD1 D:ASP743 2.7 31.9 1.0
CG D:ASP741 2.7 33.9 1.0
CG D:ASP743 2.9 31.9 1.0
CG D:ASP739 3.0 56.2 1.0
CB D:ASP739 3.2 49.8 1.0
O D:HOH2493 3.5 30.0 1.0
O D:HOH9398 4.0 11.3 1.0
CA D:ASP739 4.1 43.9 1.0
OD1 D:ASP739 4.1 58.2 1.0
N D:ASP739 4.1 43.0 1.0
CB D:ASP741 4.2 30.4 1.0
C D:ASP739 4.2 41.1 1.0
O D:ASP739 4.4 41.8 1.0
N D:ASP741 4.4 29.0 1.0
CB D:ASP743 4.4 29.5 1.0
O D:HOH9730 4.5 22.9 1.0
N D:PHE740 4.8 36.9 1.0
CA D:ASP741 4.8 27.9 1.0
O D:HOH2099 4.8 38.9 1.0
N D:ASP743 4.9 26.0 1.0

Magnesium binding site 3 out of 4 in 2be5

Go back to Magnesium Binding Sites List in 2be5
Magnesium binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg9005

b:13.3
occ:1.00
 OD1 N:ASP741 2.2 38.3 1.0
OD2 N:ASP739 2.3 43.1 1.0
OD2 N:ASP743 2.4 31.3 1.0
OD1 N:ASP743 2.7 33.4 1.0
CG N:ASP743 2.9 34.0 1.0
OD2 N:ASP741 2.9 36.1 1.0
CG N:ASP741 2.9 36.6 1.0
CG N:ASP739 3.1 42.1 1.0
CB N:ASP739 3.2 38.5 1.0
N N:ASP739 4.0 36.5 1.0
CA N:ASP739 4.0 38.1 1.0
C N:ASP739 4.3 37.7 1.0
OD1 N:ASP739 4.3 42.2 1.0
O N:ASP739 4.3 38.9 1.0
CB N:ASP741 4.4 35.0 1.0
CB N:ASP743 4.4 35.1 1.0
N N:ASP741 4.6 34.0 1.0
N N:ASP743 4.9 36.9 1.0
N N:PHE740 4.9 35.9 1.0
CA N:ASP741 5.0 34.0 1.0

Magnesium binding site 4 out of 4 in 2be5

Go back to Magnesium Binding Sites List in 2be5
Magnesium binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Inhibitor Tagetitoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg9006

b:4.2
occ:1.00
 OD1 N:ASP739 2.2 42.2 1.0
OE2 M:GLU685 2.3 34.9 1.0
O8 N:TGT9002 2.3 50.2 1.0
CG N:ASP739 2.7 42.1 1.0
NH2 M:ARG879 2.8 49.6 1.0
OD2 N:ASP739 3.4 43.1 1.0
CB N:ASP739 3.5 38.5 1.0
CD M:GLU685 3.5 33.3 1.0
NH2 N:ARG1029 3.8 32.6 1.0
OD1 M:ASP686 3.9 36.1 1.0
P1 N:TGT9002 4.0 51.9 1.0
CZ M:ARG879 4.0 49.5 1.0
O4 N:TGT9002 4.3 43.3 1.0
O N:HOH9933 4.3 32.9 1.0
OE1 M:GLU685 4.3 33.6 1.0
CG M:GLU685 4.5 31.9 1.0
CA N:ASP739 4.5 38.1 1.0
O7 N:TGT9002 4.6 49.6 1.0
NH1 M:ARG879 4.6 48.3 1.0
CG M:ASP686 4.8 35.8 1.0
O6 N:TGT9002 4.8 49.4 1.0
O9 N:TGT9002 4.8 48.0 1.0
NE M:ARG879 4.9 47.7 1.0
C1 N:TGT9002 4.9 47.8 1.0
CZ N:ARG1029 5.0 31.9 1.0
NH2 M:ARG557 5.0 59.0 1.0

Reference:

D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, I.Artsimovitch. Structural Basis For Transcription Inhibition By Tagetitoxin Nat.Struct.Mol.Biol. V. 12 1086 2005.
ISSN: ISSN 1545-9993
PubMed: 16273103
DOI: 10.1038/NSMB1015
Page generated: Sun Aug 10 09:59:00 2025

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