Magnesium in PDB 5iyd: Human Core-Pic in the Initial Transcribing State (No Iis)

All present enzymatic activity of Human Core-Pic in the Initial Transcribing State (No Iis):
2.7.7.48; 2.7.7.6; 3.6.4.12;

The structure of Human Core-Pic in the Initial Transcribing State (No Iis) also contains other interesting chemical elements:

Zinc

(Zn)

11 atoms

The binding sites of Magnesium atom in the Human Core-Pic in the Initial Transcribing State (No Iis) (pdb code 5iyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Core-Pic in the Initial Transcribing State (No Iis), PDB code: 5iyd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:0.0 occ:1.00 N A:GLY498 2.4 0.0 1.0 CA A:GLY498 2.5 0.0 1.0 O A:ASP497 2.5 0.0 1.0 C A:ASP497 2.5 0.0 1.0 C A:GLY498 2.7 0.0 1.0 N A:ASP499 2.9 0.0 1.0 OD1 A:ASP497 2.9 0.0 1.0 C5' Z:C6 3.0 0.0 1.0 CG A:ASP497 3.1 0.0 1.0 OD1 A:ASP499 3.3 0.0 1.0 O A:GLY498 3.3 0.0 1.0 OD2 A:ASP497 3.4 0.0 1.0 C4' Z:C6 3.5 0.0 1.0 CA A:ASP497 3.7 0.0 1.0 CA A:ASP499 3.8 0.0 1.0 CB A:ASP497 3.9 0.0 1.0 O3' Z:C6 4.0 0.0 1.0 CG A:ASP499 4.0 0.0 1.0 O5' Z:C6 4.2 0.0 1.0 N A:ASP497 4.3 0.0 1.0 C3' Z:C6 4.3 0.0 1.0 CB A:ASP499 4.5 0.0 1.0 OP1 Z:C6 4.6 0.0 1.0 NZ B:LYS934 4.7 0.0 1.0 O4' Z:C6 4.7 0.0 1.0 OD2 A:ASP499 4.7 0.0 1.0 C A:PHE496 4.9 0.0 1.0 CE B:LYS934 4.9 0.0 1.0 P Z:C6 5.0 0.0 1.0

Magnesium binding site 2 out of 2 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:0.0 occ:1.00 CB A:ASP495 2.2 0.0 1.0 N A:ASP497 2.4 0.0 1.0 CB A:ASP497 2.5 0.0 1.0 OD2 B:ASP792 2.7 0.0 1.0 CB B:ASP792 2.8 0.0 1.0 CA A:ASP497 2.9 0.0 1.0 CG A:ASP495 2.9 0.0 1.0 CG A:ASP497 3.0 0.0 1.0 OD2 A:ASP495 3.0 0.0 1.0 OD1 A:ASP497 3.1 0.0 1.0 N A:PHE496 3.1 0.0 1.0 CG B:ASP792 3.1 0.0 1.0 O B:GLU791 3.3 0.0 1.0 C A:PHE496 3.5 0.0 1.0 CA A:ASP495 3.5 0.0 1.0 C A:ASP495 3.8 0.0 1.0 CA A:PHE496 4.0 0.0 1.0 OD2 A:ASP497 4.0 0.0 1.0 OD1 A:ASP495 4.0 0.0 1.0 O B:ASP792 4.0 0.0 1.0 C B:GLU791 4.0 0.0 1.0 CA B:ASP792 4.1 0.0 1.0 C A:ASP497 4.3 0.0 1.0 OD1 B:ASP792 4.3 0.0 1.0 N B:ASP792 4.4 0.0 1.0 O A:PHE496 4.4 0.0 1.0 C B:ASP792 4.5 0.0 1.0 N A:ASP495 4.6 0.0 1.0 NH2 B:ARG975 4.8 0.0 1.0 N A:GLY498 4.8 0.0 1.0 O A:ASP495 4.9 0.0 1.0 CB A:PHE496 4.9 0.0 1.0 OE1 B:GLU791 5.0 0.0 1.0

Y.He, C.Yan, J.Fang, C.Inouye, R.Tjian, I.Ivanov, E.Nogales. Near-Atomic Resolution Visualization of Human Transcription Promoter Opening. Nature V. 533 359 2016.
ISSN: ESSN 1476-4687
PubMed: 27193682
DOI: 10.1038/NATURE17970