Magnesium in PDB 2a69: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin

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

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin, PDB code: 2a69 was solved by I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, D.G.Vassylyev, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.50
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 / 26.7

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

Zinc

(Zn)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 320; Page 33, Binding sites: 321 - 330; Page 34, Binding sites: 331 - 340; Page 35, Binding sites: 341 - 350; Page 36, Binding sites: 351 - 360; Page 37, Binding sites: 361 - 370; Page 38, Binding sites: 371 - 380; Page 39, Binding sites: 381 - 390; Page 40, Binding sites: 391 - 400; Page 41, Binding sites: 401 - 410; Page 42, Binding sites: 411 - 420; Page 43, Binding sites: 421 - 430; Page 44, Binding sites: 431 - 440; Page 45, Binding sites: 441 - 450; Page 46, Binding sites: 451 - 460; Page 47, Binding sites: 461 - 470; Page 48, Binding sites: 471 - 480; Page 49, Binding sites: 481 - 487;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin (pdb code 2a69). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 487 binding sites of Magnesium where determined in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin, PDB code: 2a69:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9002 b:31.5 occ:1.00 O A:HOH9608 2.5 43.0 1.0 O A:HOH9527 2.6 35.4 1.0 O A:VAL170 2.7 44.7 1.0 O A:HOH9478 3.1 27.6 1.0 O A:THR51 3.4 45.5 1.0 CB A:VAL170 3.5 45.2 1.0 O A:LYS83 3.6 61.2 1.0 CG2 A:VAL170 3.7 46.6 1.0 C A:VAL170 3.7 44.9 1.0 O A:HOH9702 3.8 64.1 1.0 CB A:ALA52 3.8 44.3 1.0 CA A:VAL170 4.2 43.8 1.0 CA A:ALA52 4.2 42.3 1.0 O A:LEU85 4.3 63.6 1.0 C A:THR51 4.5 44.7 1.0 CG1 A:VAL170 4.6 41.7 1.0 O A:HOH9589 4.7 74.4 1.0 C A:LYS83 4.7 61.7 1.0 N A:VAL170 4.8 43.4 1.0 N A:ALA52 4.8 41.6 1.0 N A:PHE171 4.9 45.2 1.0 OD1 A:ASP202 5.0 39.1 1.0

Magnesium binding site 2 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9010 b:30.8 occ:1.00 O A:HOH9481 2.6 34.5 1.0 OG A:SER204 3.6 38.6 1.0 CG2 A:THR51 4.2 47.4 1.0 CG A:ARG146 4.3 49.5 1.0 CD A:ARG146 4.4 51.8 1.0 CA A:GLY50 4.5 41.1 1.0 CG1 A:VAL205 4.5 34.8 1.0 CE2 A:PHE89 4.5 51.6 1.0 CD2 A:PHE89 4.7 51.3 1.0 O A:PHE89 4.7 51.9 1.0 C A:GLY50 4.7 41.6 1.0 O A:GLY50 4.8 41.2 1.0 O A:HOH9500 4.8 25.4 1.0 O A:PRO49 4.9 38.1 1.0 O A:SER204 4.9 42.4 1.0 CB A:SER204 5.0 41.0 1.0

Magnesium binding site 3 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9012 b:47.7 occ:1.00 O C:HOH9885 2.7 27.6 1.0 O A:HOH9624 2.8 55.9 1.0 O A:HIS156 2.9 89.4 1.0 N A:GLY157 2.9 89.8 1.0 C A:HIS156 2.9 89.6 1.0 O A:GLU154 3.0 83.0 1.0 O A:HOH9705 3.0 65.8 1.0 CA A:GLY157 3.0 90.2 1.0 O A:LYS155 3.4 86.4 1.0 C A:LYS155 3.7 86.0 1.0 CA A:HIS156 3.9 89.3 1.0 N A:HIS156 4.0 87.6 1.0 C A:GLU154 4.1 82.4 1.0 C A:GLY157 4.1 90.6 1.0 O A:GLY157 4.2 91.4 1.0 O C:HOH2419 4.4 48.4 1.0 O A:HOH9577 4.5 47.5 1.0 CA A:LYS155 4.6 84.5 1.0 O A:ALA153 4.8 80.5 1.0 N A:LYS155 4.8 83.2 1.0

Magnesium binding site 4 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9013 b:44.1 occ:1.00 O A:GLU29 2.6 73.3 1.0 O A:LEU28 2.6 65.1 1.0 C A:GLU29 2.9 72.5 1.0 O A:ASP191 3.0 69.8 1.0 CA A:GLU29 3.1 71.2 1.0 CA A:LEU192 3.2 62.9 1.0 C A:LEU28 3.5 64.1 1.0 CD2 A:LEU192 3.7 62.6 1.0 CB A:LEU192 3.7 62.8 1.0 C A:ASP191 3.8 69.6 1.0 N A:GLU29 3.8 67.4 1.0 N A:ASP193 3.9 55.7 1.0 N A:LEU192 3.9 66.5 1.0 N A:ARG30 3.9 74.2 1.0 O A:HOH9613 4.0 26.9 1.0 C A:LEU192 4.1 60.1 1.0 OD2 A:ASP191 4.1 73.3 1.0 OE2 A:GLU29 4.2 72.0 1.0 OD1 A:ASP193 4.3 50.8 1.0 CG A:LEU192 4.3 61.9 1.0 CB A:GLU29 4.5 70.6 1.0 CG A:ASP191 4.6 73.3 1.0 CA A:ARG30 4.6 73.9 1.0 CD A:GLU29 4.6 71.5 1.0 CA A:LEU28 4.9 61.5 1.0 OD1 A:ASP191 4.9 73.4 1.0 O A:HOH9526 4.9 33.5 1.0 N A:LEU28 4.9 57.9 1.0

Magnesium binding site 5 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9016 b:36.0 occ:1.00 MG A:MG9345 3.6 41.9 1.0 O A:HOH9558 3.8 34.3 1.0 OG1 A:THR223 4.1 78.4 1.0 CG A:GLU220 4.2 75.5 1.0 CA A:GLU220 4.3 71.7 1.0 OE2 A:GLU216 4.3 61.0 1.0 CB A:GLU220 4.5 73.4 1.0 CG2 A:THR223 4.8 77.9 1.0 CB A:THR223 4.8 77.8 1.0 N A:GLU220 5.0 72.4 1.0 O A:HOH9709 5.0 59.4 1.0

Magnesium binding site 6 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9027 b:37.1 occ:1.00 O A:PHE114 2.5 78.5 1.0 O A:ARG112 2.7 77.0 1.0 O A:ALA111 2.9 74.7 1.0 C A:ARG112 3.0 75.7 1.0 O A:HOH9560 3.0 23.4 1.0 N A:PHE114 3.1 77.2 1.0 O A:HOH9644 3.2 41.8 1.0 CB A:PHE114 3.3 79.2 1.0 C A:PHE114 3.3 77.9 1.0 CA A:ARG112 3.4 75.5 1.0 CA A:PHE114 3.4 77.9 1.0 CD1 A:ILE122 3.7 60.8 1.0 N A:ASP113 3.8 75.2 1.0 C A:ALA111 3.9 74.0 1.0 C A:ASP113 4.0 77.0 1.0 N A:ARG112 4.1 75.1 1.0 CG A:PHE114 4.4 80.4 1.0 CA A:ASP113 4.4 76.2 1.0 CD1 A:PHE114 4.6 81.3 1.0 N A:LEU115 4.6 76.4 1.0 CB A:ARG112 4.6 73.6 1.0 CG1 A:ILE122 4.7 59.9 1.0 O A:HOH9540 4.8 47.6 1.0 O A:HOH9581 4.8 30.2 1.0 O A:ASP113 4.8 77.8 1.0 CB A:ILE122 4.9 61.2 1.0 O A:HOH9685 4.9 49.1 1.0 N A:PRO116 5.0 72.7 1.0

Magnesium binding site 7 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9043 b:37.7 occ:1.00 OE2 A:GLU59 2.5 73.8 1.0 CB A:GLU59 3.4 72.7 1.0 CD A:GLU59 3.5 74.6 1.0 ND2 A:ASN139 3.7 66.0 1.0 CG A:GLU59 3.9 74.2 1.0 OE1 A:GLU59 4.6 74.1 1.0 CA A:GLU59 4.8 71.2 1.0 CG A:ASN139 4.8 66.7 1.0

Magnesium binding site 8 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9066 b:47.1 occ:1.00 O A:HOH9618 3.3 47.3 1.0

Magnesium binding site 9 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9068 b:39.8 occ:1.00 O C:HOH9914 2.6 35.7 1.0 O C:HOH2003 3.1 46.3 1.0 O A:HOH9589 3.4 74.4 1.0 CG1 A:VAL170 3.5 41.7 1.0 CG2 A:VAL170 3.7 46.6 1.0 CB A:VAL170 4.1 45.2 1.0 O A:LYS83 4.2 61.2 1.0 O C:HOH9569 4.2 51.9 1.0 O C:LYS696 4.2 52.1 1.0 CB A:LYS83 4.5 61.2 1.0 C A:LYS83 4.7 61.7 1.0 C C:LYS696 4.8 50.5 1.0 CA C:ARG697 4.9 53.8 1.0

Magnesium binding site 10 out of 487 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9075 b:36.4 occ:1.00 O A:HOH9625 2.8 49.0 1.0 O A:HOH9488 2.8 49.7 1.0 CA A:ILE162 2.9 70.2 1.0 CB A:ILE162 3.1 70.3 1.0 CG2 A:ILE162 3.2 70.1 1.0 N A:ILE162 3.6 70.5 1.0 C A:ILE162 4.0 69.6 1.0 O A:ILE162 4.1 70.7 1.0 C A:ARG161 4.3 70.6 1.0 O A:ARG161 4.5 70.4 1.0 O C:HOH9862 4.6 35.0 1.0 CG1 A:ILE162 4.6 70.1 1.0 O C:HOH9581 4.7 24.5 1.0 O A:HOH9497 4.8 36.0 1.0 CB A:LYS159 4.8 74.9 1.0

I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, D.G.Vassylyev. Allosteric Modulation of the Rna Polymerase Catalytic Reaction Is An Essential Component of Transcription Control By Rifamycins. Cell(Cambridge,Mass.) V. 122 351 2005.
ISSN: ISSN 0092-8674
PubMed: 16096056
DOI: 10.1016/J.CELL.2005.07.014