Magnesium in PDB 8dnf: Cryo-Em Structure of Nonmuscle Gamma-Actin

The binding sites of Magnesium atom in the Cryo-Em Structure of Nonmuscle Gamma-Actin (pdb code 8dnf). 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 Nonmuscle Gamma-Actin, PDB code: 8dnf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Nonmuscle Gamma-Actin


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 Nonmuscle Gamma-Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:116.5 occ:1.00 O1B A:ADP401 2.3 121.0 1.0 PB A:ADP401 3.6 132.1 1.0 O1A A:ADP401 3.8 118.9 1.0 CG2 A:VAL338 3.9 96.7 1.0 O2B A:ADP401 4.0 120.2 1.0 OD1 A:ASP153 4.2 116.2 1.0 OD2 A:ASP10 4.3 120.2 1.0 CB A:VAL338 4.5 90.7 1.0 CA A:GLY300 4.5 95.2 1.0 NZ A:LYS17 4.5 86.9 1.0 O3A A:ADP401 4.6 126.1 1.0 O3B A:ADP401 4.6 119.7 1.0 OD1 A:ASP10 4.7 107.2 1.0 CA A:GLY155 4.7 96.8 1.0 OD2 A:ASP153 4.8 120.8 1.0 PA A:ADP401 4.8 122.7 1.0 CG A:ASP10 4.9 118.5 1.0 CG A:ASP153 4.9 117.5 1.0 CG1 A:VAL338 5.0 92.7 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Nonmuscle Gamma-Actin


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 Nonmuscle Gamma-Actin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:160.3 occ:1.00 O1B B:ADP401 2.3 152.8 1.0 PB B:ADP401 3.2 164.4 1.0 O2B B:ADP401 3.3 149.5 1.0 O3A B:ADP401 3.6 152.3 1.0 OD1 B:ASP153 3.9 116.2 1.0 CG2 B:VAL338 4.1 96.7 1.0 OD2 B:ASP153 4.3 120.8 1.0 OE1 B:GLN136 4.3 104.7 1.0 CD B:GLN136 4.5 106.6 1.0 NE2 B:GLN136 4.5 108.6 1.0 OD2 B:ASP10 4.5 120.2 1.0 CG B:ASP153 4.5 117.5 1.0 O3B B:ADP401 4.6 150.5 1.0 OD1 B:ASP10 4.6 107.2 1.0 CA B:GLY155 4.6 96.8 1.0 CB B:VAL338 4.7 90.7 1.0 O1A B:ADP401 4.8 147.7 1.0 PA B:ADP401 4.9 138.4 1.0 CG1 B:VAL338 4.9 92.7 1.0 CA B:GLY300 5.0 95.2 1.0 CG B:ASP10 5.0 118.5 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Nonmuscle Gamma-Actin


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 Nonmuscle Gamma-Actin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:160.3 occ:1.00 O1B C:ADP401 2.8 152.8 1.0 PB C:ADP401 3.6 164.4 1.0 O2B C:ADP401 3.6 149.5 1.0 O3A C:ADP401 3.7 152.3 1.0 OD1 C:ASP153 4.0 116.2 1.0 CG2 C:VAL338 4.1 96.7 1.0 OD2 C:ASP10 4.4 120.2 1.0 OD2 C:ASP153 4.6 120.8 1.0 CA C:GLY155 4.6 96.8 1.0 O1A C:ADP401 4.6 147.7 1.0 OE1 C:GLN136 4.6 104.7 1.0 OD1 C:ASP10 4.7 107.2 1.0 CB C:VAL338 4.7 90.7 1.0 CG C:ASP153 4.7 117.5 1.0 CA C:GLY300 4.8 95.2 1.0 NE2 C:GLN136 4.8 108.6 1.0 CD C:GLN136 4.8 106.6 1.0 PA C:ADP401 4.8 138.4 1.0 NZ C:LYS17 4.9 86.9 1.0 CG C:ASP10 5.0 118.5 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Nonmuscle Gamma-Actin


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 Nonmuscle Gamma-Actin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:160.3 occ:1.00 O1B D:ADP401 2.5 152.8 1.0 O2B D:ADP401 3.2 149.5 1.0 PB D:ADP401 3.2 164.4 1.0 O3A D:ADP401 3.6 152.3 1.0 OD2 D:ASP10 4.0 120.2 1.0 CG2 D:VAL338 4.1 96.7 1.0 OD1 D:ASP153 4.4 116.2 1.0 CB D:VAL338 4.5 90.7 1.0 O1A D:ADP401 4.5 147.7 1.0 NZ D:LYS17 4.6 86.9 1.0 OD1 D:ASP10 4.6 107.2 1.0 CG D:ASP10 4.7 118.5 1.0 NE2 D:GLN136 4.7 108.6 1.0 O3B D:ADP401 4.7 150.5 1.0 OE1 D:GLN136 4.7 104.7 1.0 PA D:ADP401 4.7 138.4 1.0 OD2 D:ASP153 4.8 120.8 1.0 CD D:GLN136 4.8 106.6 1.0 CG1 D:VAL338 4.8 92.7 1.0 CA D:GLY155 4.8 96.8 1.0

A.S.Arora, H.L.Huang, R.Singh, Y.Narui, A.Suchenko, T.Hatano, S.M.Heissler, M.K.Balasubramanian, K.Chinthalapudi. Structural Insights Into Actin Isoforms. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 36790143
DOI: 10.7554/ELIFE.82015