Magnesium in PDB 8v6v: Cryo-Em Structure of Doubly-Bound SNF2H-Nucleosome Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of Doubly-Bound SNF2H-Nucleosome Complex (pdb code 8v6v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Doubly-Bound SNF2H-Nucleosome Complex, PDB code: 8v6v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Doubly-Bound SNF2H-Nucleosome Complex


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 Doubly-Bound SNF2H-Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ W:Mg1102 b:25.8 occ:1.00 O2B W:ADP1101 2.4 31.6 1.0 O3B W:ADP1101 2.7 27.5 1.0 PB W:ADP1101 3.0 25.1 1.0 HA2 W:GLY565 3.3 0.0 1.0 O2A W:ADP1101 3.7 17.6 1.0 HZ3 W:LYS211 3.7 0.0 1.0 OE2 W:GLU309 4.0 100.0 1.0 HG1 W:THR212 4.1 0.0 1.0 O1B W:ADP1101 4.1 23.5 1.0 O3A W:ADP1101 4.2 32.5 1.0 HH11 W:ARG592 4.3 0.0 1.0 HZ1 W:LYS211 4.3 0.0 1.0 OG1 W:THR212 4.4 100.0 1.0 NZ W:LYS211 4.4 100.0 1.0 HZ2 W:LYS211 4.4 0.0 1.0 CA W:GLY565 4.4 100.0 1.0 O W:GLY565 4.4 100.0 1.0 PA W:ADP1101 4.4 23.6 1.0 HB2 W:LYS211 4.5 0.0 1.0 HH22 W:ARG595 4.7 0.0 1.0 HH12 W:ARG595 4.7 0.0 1.0 HA3 W:GLY565 4.8 0.0 1.0 OD2 W:ASP308 4.9 100.0 1.0 O1A W:ADP1101 4.9 22.3 1.0 C W:GLY565 4.9 100.0 1.0 H W:GLY565 5.0 0.0 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Doubly-Bound SNF2H-Nucleosome Complex


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 Doubly-Bound SNF2H-Nucleosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1102 b:25.8 occ:1.00 O2B X:ADP1101 2.1 31.6 1.0 PB X:ADP1101 3.4 25.1 1.0 HG1 X:THR212 3.6 0.0 1.0 HA2 X:GLY565 3.6 0.0 1.0 O3B X:ADP1101 3.8 27.5 1.0 OE2 X:GLU309 3.9 100.0 1.0 OG1 X:THR212 4.0 100.0 1.0 O2A X:ADP1101 4.1 17.6 1.0 HZ3 X:LYS211 4.1 0.0 1.0 OD2 X:ASP308 4.2 100.0 1.0 O1B X:ADP1101 4.3 23.5 1.0 HZ2 X:LYS211 4.4 0.0 1.0 HB2 X:LYS211 4.4 0.0 1.0 O3A X:ADP1101 4.4 32.5 1.0 O1A X:ADP1101 4.5 22.3 1.0 PA X:ADP1101 4.5 23.6 1.0 HZ1 X:LYS211 4.6 0.0 1.0 NZ X:LYS211 4.6 100.0 1.0 OD1 X:ASP308 4.6 100.0 1.0 CA X:GLY565 4.6 100.0 1.0 O X:GLY565 4.6 100.0 1.0 H X:THR212 4.7 0.0 1.0 HA3 X:GLY565 4.9 0.0 1.0 HH12 X:ARG592 4.9 0.0 1.0 CG X:ASP308 4.9 100.0 1.0

U.S.Chio, E.Palovcak, A.A.A.Smith, H.Autzen, E.N.Munoz, Z.Yu, F.Wang, D.A.Agard, J.P.Armache, G.J.Narlikar, Y.Cheng. Functionalized Graphene-Oxide Grids Enable High-Resolution Cryo-Em Structures of the SNF2H-Nucleosome Complex Without Crosslinking. Nat Commun V. 15 2225 2024.
ISSN: ESSN 2041-1723
PubMed: 38472177
DOI: 10.1038/S41467-024-46178-Y