Magnesium in PDB 5iyb: Human Core-Pic in the Open State

All present enzymatic activity of Human Core-Pic in the Open State:
2.7.7.48; 2.7.7.6; 3.6.4.12;

The structure of Human Core-Pic in the Open State also contains other interesting chemical elements:

Zinc

(Zn)

11 atoms

The binding sites of Magnesium atom in the Human Core-Pic in the Open State (pdb code 5iyb). 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 Open State, PDB code: 5iyb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:0.0 occ:1.00 OD2 A:ASP495 2.3 0.0 1.0 OD2 A:ASP499 2.7 0.0 1.0 CG A:ASP495 2.7 0.0 1.0 CB A:ASP495 3.1 0.0 1.0 O A:ASN493 3.3 0.0 1.0 N A:ASP495 3.4 0.0 1.0 OD1 A:ASP495 3.6 0.0 1.0 CG A:ASP499 3.6 0.0 1.0 CA A:ASP495 3.8 0.0 1.0 OD1 A:ASP499 3.8 0.0 1.0 OD1 A:ASP497 4.0 0.0 1.0 C A:ALA494 4.1 0.0 1.0 O A:ASP495 4.4 0.0 1.0 C A:ASN493 4.5 0.0 1.0 CA A:ALA494 4.5 0.0 1.0 C A:ASP495 4.6 0.0 1.0 O A:ALA494 4.9 0.0 1.0 CG A:ASP497 4.9 0.0 1.0 CB A:ASP499 5.0 0.0 1.0

Magnesium binding site 2 out of 2 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg401 b:0.0 occ:1.00 OD1 A:ASP495 2.5 0.0 1.0 O U:ALA281 2.6 0.0 1.0 CA U:ALA281 3.2 0.0 1.0 C U:ALA281 3.2 0.0 1.0 CG A:ASP495 3.4 0.0 1.0 OE1 B:GLU791 3.7 0.0 1.0 OE2 B:GLU791 3.7 0.0 1.0 OD2 A:ASP495 3.7 0.0 1.0 CB U:ALA281 3.8 0.0 1.0 CD B:GLU791 4.0 0.0 1.0 O U:SER280 4.1 0.0 1.0 N U:ALA281 4.4 0.0 1.0 N U:ASP282 4.5 0.0 1.0 OD1 U:ASP282 4.5 0.0 1.0 CB A:ASP495 4.6 0.0 1.0 C U:SER280 4.7 0.0 1.0 O A:ALA494 4.7 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