Magnesium in PDB 8k5p: Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2)

All present enzymatic activity of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2):
2.7.7.6;

The structure of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2) 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 2 (Pol II RAT1-PTTC2) (pdb code 8k5p). 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 2 (Pol II RAT1-PTTC2), PDB code: 8k5p:
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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:100.1 occ:1.00 OD1 A:ASP481 2.1 101.5 1.0 OD1 A:ASP483 2.1 96.9 1.0 OD2 A:ASP481 2.5 102.4 1.0 OD1 A:ASP485 2.5 94.1 1.0 OD2 A:ASP483 2.5 95.7 1.0 CG A:ASP481 2.5 101.6 1.0 CG A:ASP483 2.6 92.1 1.0 O3' P:A-1 2.7 100.4 1.0 CG A:ASP485 3.4 88.4 1.0 OD2 A:ASP485 3.5 90.0 1.0 C3' P:A-1 3.8 98.1 1.0 C4' P:A-1 3.8 92.0 1.0 C5' P:A-1 3.8 98.1 1.0 CB A:ASP481 4.0 89.8 1.0 CB A:ASP483 4.1 84.3 1.0 N A:ASP481 4.5 89.9 1.0 N A:ASP483 4.6 82.3 1.0 CA A:ASP481 4.6 84.6 1.0 O5' P:A-1 4.7 104.6 1.0 CB A:ASP485 4.7 82.8 1.0 C A:ASP481 4.8 86.8 1.0 CA A:ASP483 4.8 83.0 1.0 O2' P:A-1 4.9 108.3 1.0 O A:ASP481 4.9 95.4 1.0 OD2 B:ASP837 5.0 106.4 1.0 C2' P:A-1 5.0 102.5 1.0 N A:ASP485 5.0 82.7 1.0 C A:ASP483 5.0 90.1 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg2001 b:165.9 occ:1.00 OD2 M:ASP233 2.4 193.5 1.0 OE2 M:GLU205 3.0 171.2 1.0 CG M:ASP233 3.6 194.8 1.0 OD2 M:ASP235 3.8 182.3 1.0 OD1 M:ASP235 3.8 182.5 1.0 CD M:GLU205 4.0 171.8 1.0 NZ M:LYS109 4.0 187.2 1.0 OP1 P:C-19 4.2 225.2 1.0 OD1 M:ASP233 4.2 195.8 1.0 CG M:ASP235 4.2 182.5 1.0 O3' P:A-20 4.3 219.3 1.0 OE1 M:GLU205 4.4 171.9 1.0 OD2 M:ASP333 4.5 199.6 1.0 O2' P:A-20 4.5 215.6 1.0 CB M:ASP233 4.7 194.6 1.0 CB M:ASP333 4.8 198.7 1.0 P P:C-19 5.0 228.1 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg1001 b:208.1 occ:1.00 OE2 O:GLU241 2.1 224.4 1.0 OD2 O:ASP223 2.8 223.8 1.0 O O:LEU242 3.0 220.6 1.0 CD O:GLU241 3.3 223.8 1.0 OE1 O:GLU172 3.7 214.7 1.0 OE1 O:GLU241 3.9 223.4 1.0 CG O:ASP223 3.9 223.8 1.0 CG O:LYS243 4.0 221.8 1.0 C O:LEU242 4.2 220.8 1.0 OD1 O:ASP223 4.4 223.8 1.0 CG O:GLU241 4.5 223.0 1.0 CE O:LYS243 4.5 222.3 1.0 CD O:GLU172 4.7 214.7 1.0 N O:LEU242 4.8 220.2 1.0 CD O:LYS243 4.9 222.1 1.0 CA O:LYS243 5.0 222.3 1.0

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