Magnesium in PDB 7uqj: Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II

The binding sites of Magnesium atom in the Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II (pdb code 7uqj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II, PDB code: 7uqj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II


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 the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1402 b:20.4 occ:1.00 O1B C:AGS1401 2.1 27.5 1.0 O2G C:AGS1401 2.1 27.5 1.0 OG1 C:THR461 2.2 20.8 1.0 CB C:THR461 3.0 20.8 1.0 O B:ASP547 3.4 18.1 1.0 PB C:AGS1401 3.4 27.5 1.0 O2A C:AGS1401 3.4 27.5 1.0 PG C:AGS1401 3.6 27.5 1.0 CG2 C:THR461 3.8 20.8 1.0 NH2 B:ARG573 3.9 27.5 1.0 O3B C:AGS1401 3.9 27.5 1.0 O3A C:AGS1401 4.1 27.5 1.0 OD2 C:ASP518 4.1 14.0 1.0 CA C:THR461 4.2 20.8 1.0 NH1 B:ARG576 4.2 15.9 1.0 PA C:AGS1401 4.2 27.5 1.0 N C:THR461 4.2 20.8 1.0 OE2 C:GLU519 4.4 14.1 1.0 OD1 C:ASP518 4.5 14.0 1.0 O2B C:AGS1401 4.5 27.5 1.0 C B:ASP547 4.5 18.1 1.0 O1A C:AGS1401 4.5 27.5 1.0 O3G C:AGS1401 4.6 27.5 1.0 S1G C:AGS1401 4.7 27.5 1.0 CG C:ASP518 4.7 14.0 1.0 OD1 B:ASP547 4.9 18.1 1.0 CA B:GLY548 4.9 17.8 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II


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 the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1402 b:21.3 occ:1.00 O3G D:AGS1401 2.0 27.5 1.0 OG1 D:THR461 2.1 23.9 1.0 O1B D:AGS1401 2.1 27.5 1.0 CB D:THR461 3.4 23.9 1.0 PB D:AGS1401 3.4 27.5 1.0 PG D:AGS1401 3.4 27.5 1.0 OD1 D:ASP518 3.5 14.3 1.0 O3B D:AGS1401 3.8 27.5 1.0 OE2 D:GLU519 3.9 14.4 1.0 N D:THR461 4.0 23.9 1.0 O2G D:AGS1401 4.0 27.5 1.0 O2B D:AGS1401 4.2 27.5 1.0 OD2 D:ASP518 4.2 14.3 1.0 CG2 D:THR461 4.2 23.9 1.0 CA D:THR461 4.3 23.9 1.0 CG D:ASP518 4.3 14.3 1.0 O3A D:AGS1401 4.6 27.5 1.0 NH2 C:ARG576 4.6 16.7 1.0 O2A D:AGS1401 4.7 27.5 1.0 CB D:LYS460 4.7 27.5 1.0 CB D:ALA560 4.7 12.3 1.0 S1G D:AGS1401 4.8 27.5 1.0 CE D:LYS460 4.9 27.5 1.0 NH1 C:ARG573 4.9 27.5 1.0 O C:ASP547 4.9 17.5 1.0 C D:LYS460 5.0 27.5 1.0 CD D:GLU519 5.0 14.4 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II


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 the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1402 b:21.9 occ:1.00 O2G E:AGS1401 2.0 27.5 1.0 OG1 E:THR461 2.0 20.6 1.0 O1B E:AGS1401 2.3 27.5 1.0 CB E:THR461 3.3 20.6 1.0 PG E:AGS1401 3.5 27.5 1.0 PB E:AGS1401 3.6 27.5 1.0 O D:ASP547 3.8 19.1 1.0 CG2 E:THR461 3.9 20.6 1.0 OE2 E:GLU519 3.9 22.1 1.0 O3B E:AGS1401 4.0 27.5 1.0 OD2 E:ASP518 4.1 23.4 1.0 OD1 E:ASP518 4.2 23.4 1.0 O3A E:AGS1401 4.2 27.5 1.0 O3G E:AGS1401 4.3 27.5 1.0 N E:THR461 4.4 20.6 1.0 O2A E:AGS1401 4.4 27.5 1.0 CA E:THR461 4.4 20.6 1.0 NH1 D:ARG576 4.4 16.0 1.0 CG E:ASP518 4.5 23.4 1.0 NH2 D:ARG576 4.6 16.0 1.0 NH2 D:ARG573 4.6 12.4 1.0 S1G E:AGS1401 4.7 27.5 1.0 O2B E:AGS1401 4.8 27.5 1.0 PA E:AGS1401 4.9 27.5 1.0 CD E:GLU519 4.9 22.1 1.0 C D:ASP547 5.0 19.1 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the S. Cerevisiae Chromatin Remodeler YTA7 Hexamer Bound to Atpgs and Histone H3 Tail in State II within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1402 b:35.7 occ:1.00 O1B F:AGS1401 2.1 40.4 1.0 O3G F:AGS1401 2.2 40.4 1.0 OG1 F:THR461 2.2 42.2 1.0 OD2 F:ASP518 3.2 49.2 1.0 OD1 F:ASP518 3.4 49.2 1.0 PG F:AGS1401 3.5 40.4 1.0 PB F:AGS1401 3.5 40.4 1.0 CB F:THR461 3.6 42.2 1.0 OE1 F:GLU519 3.7 51.3 1.0 CG F:ASP518 3.7 49.2 1.0 O3B F:AGS1401 3.9 40.4 1.0 O2G F:AGS1401 4.0 40.4 1.0 CD F:GLU519 4.1 51.3 1.0 CG2 F:THR461 4.2 42.2 1.0 OE2 F:GLU519 4.3 51.3 1.0 O2B F:AGS1401 4.3 40.4 1.0 N F:THR461 4.3 42.2 1.0 O2A F:AGS1401 4.4 40.4 1.0 CA F:THR461 4.5 42.2 1.0 O3A F:AGS1401 4.6 40.4 1.0 PA F:AGS1401 4.9 40.4 1.0

F.Wang, X.Feng, Q.He, H.Li, H.Li. The S. Cerevisiae YTA7 Atpase Hexamer Contains A Unique Bromodomain Tier That Functions in Nucleosome Disassembly. J.Biol.Chem. 02852 2022.
ISSN: ESSN 1083-351X
PubMed: 36592926
DOI: 10.1016/J.JBC.2022.102852