Magnesium in PDB 8jch: Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)

All present enzymatic activity of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1):
2.7.7.6;

The structure of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) (pdb code 8jch). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1), PDB code: 8jch:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:95.0 occ:1.00 OD1 A:ASP481 2.0 98.2 1.0 O3' P:U-1 2.1 104.9 1.0 OD1 A:ASP483 2.2 96.5 1.0 OD1 A:ASP485 2.6 89.0 1.0 OD2 A:ASP483 2.7 86.1 1.0 CG A:ASP481 2.8 95.5 1.0 CG A:ASP483 2.8 87.3 1.0 OD2 A:ASP481 2.9 98.0 1.0 C3' P:U-1 3.2 101.0 1.0 CG A:ASP485 3.5 85.0 1.0 C4' P:U-1 3.5 98.1 1.0 OD2 A:ASP485 3.6 83.9 1.0 C5' P:U-1 3.6 105.3 1.0 CB A:ASP481 4.2 84.6 1.0 CB A:ASP483 4.3 80.4 1.0 O2' P:U-1 4.4 113.7 1.0 C2' P:U-1 4.4 106.2 1.0 N A:ASP481 4.6 87.1 1.0 N A:ASP483 4.7 79.2 1.0 CA A:ASP481 4.8 78.9 1.0 O5' P:U-1 4.8 107.2 1.0 CB A:ASP485 4.9 83.4 1.0 C A:ASP481 4.9 81.3 1.0 CA A:ASP483 4.9 78.3 1.0 O4' P:U-1 4.9 98.5 1.0 O A:ASP481 5.0 88.5 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg2001 b:203.8 occ:1.00 OD2 M:ASP233 2.2 203.9 1.0 OP1 P:C-22 2.4 223.4 1.0 OD2 M:ASP333 2.7 197.7 1.0 CG M:ASP233 3.2 204.4 1.0 OE2 M:GLU205 3.4 176.8 1.0 OD1 M:ASP233 3.6 205.2 1.0 P P:C-22 3.7 224.3 1.0 OD2 M:ASP235 3.8 196.3 1.0 O3' P:A-23 3.9 224.1 1.0 CG M:ASP333 3.9 197.7 1.0 NZ M:LYS109 4.0 214.6 1.0 OD1 M:ASP235 4.2 197.7 1.0 C5' P:C-22 4.3 224.8 1.0 CG M:ASP235 4.3 196.6 1.0 O5' P:C-22 4.5 224.9 1.0 CD M:GLU205 4.5 177.7 1.0 CB M:ASP233 4.6 203.4 1.0 OD1 M:ASP333 4.7 197.6 1.0 CB M:ASP333 4.8 197.4 1.0 OP2 P:C-22 4.9 224.2 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg1001 b:205.2 occ:1.00 O O:LEU242 2.8 225.4 1.0 OE2 O:GLU241 3.4 228.6 1.0 CD2 O:LEU242 3.6 225.9 1.0 OD2 O:ASP223 3.8 231.4 1.0 C O:LEU242 3.9 226.2 1.0 CG O:LEU242 4.4 226.1 1.0 CD O:GLU241 4.4 229.5 1.0 CG O:LYS243 4.5 229.1 1.0 N O:LEU242 4.5 226.8 1.0 CG O:ASP223 4.7 231.5 1.0 OE1 O:GLU241 4.7 230.2 1.0 CA O:LEU242 4.7 226.6 1.0 CB O:ASP223 4.7 230.9 1.0 N O:LYS243 4.8 229.3 1.0 CA O:LYS243 4.9 229.3 1.0

Y.Zeng, H.Zhang, X.Wu, Y.Zhang. Structural Basis of Exoribonuclease-Mediated Mrna Transcription Termination To Be Published.