Magnesium in PDB 8qxn: Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed

The structure of Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed (pdb code 8qxn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed, PDB code: 8qxn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


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 Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:21.0 occ:1.00 NE2 A:HIS233 2.3 32.4 1.0 OD1 A:ASP207 2.4 28.6 1.0 CD2 A:HIS233 3.1 32.4 1.0 CE1 A:HIS233 3.2 32.4 1.0 CG A:ASP207 3.6 28.6 1.0 NE2 A:HIS210 3.8 26.8 1.0 CE1 A:HIS210 4.1 26.8 1.0 OD2 A:ASP207 4.1 28.6 1.0 ND1 A:HIS233 4.2 32.4 1.0 CG A:HIS233 4.2 32.4 1.0 OH A:TYR315 4.2 35.6 1.0 CD2 A:HIS206 4.4 27.8 1.0 O A:HIS206 4.5 27.8 1.0 OE2 A:GLU234 4.6 35.5 1.0 FE A:FE702 4.6 31.9 1.0 OD2 A:ASP311 4.6 38.1 1.0 CB A:ASP207 4.8 28.6 1.0 CA A:ASP207 4.9 28.6 1.0 CD2 A:HIS210 4.9 26.8 1.0 NE2 A:HIS206 5.0 27.8 1.0

Magnesium binding site 2 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


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 Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:18.1 occ:1.00 NE2 B:HIS233 2.1 24.6 1.0 OD1 B:ASP207 2.9 21.2 1.0 CD2 B:HIS233 3.1 24.6 1.0 CE1 B:HIS233 3.1 24.6 1.0 O2B B:DCP705 3.3 26.2 1.0 O1A B:DCP705 4.1 26.2 1.0 CG B:ASP207 4.1 21.2 1.0 O3A B:DCP705 4.2 26.2 1.0 ND1 B:HIS233 4.2 24.6 1.0 CG B:HIS233 4.2 24.6 1.0 O2A B:DCP705 4.3 26.2 1.0 PB B:DCP705 4.4 26.2 1.0 PA B:DCP705 4.4 26.2 1.0 O B:HIS206 4.4 20.2 1.0 OE2 B:GLU234 4.5 26.4 1.0 CD B:GLU234 4.6 26.4 1.0 OD2 B:ASP207 4.6 21.2 1.0 CG B:GLU234 4.7 26.4 1.0 NE2 B:HIS210 4.7 23.1 1.0 CD2 B:HIS206 4.7 20.2 1.0 FE B:FE702 4.9 23.5 1.0 OD2 B:ASP311 4.9 21.1 1.0

Magnesium binding site 3 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


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 Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:56.6 occ:1.00 O1B A:DTP704 1.9 43.2 1.0 O2B B:GTP701 1.9 37.0 1.0 O1G A:DTP704 1.9 43.2 1.0 O1B B:GTP701 2.2 37.0 1.0 O3B A:DTP704 2.4 43.2 1.0 PB B:GTP701 2.5 37.0 1.0 PB A:DTP704 2.6 43.2 1.0 PG A:DTP704 2.6 43.2 1.0 O3A A:DTP704 3.6 43.2 1.0 O3G A:DTP704 3.6 43.2 1.0 O3B B:GTP701 3.7 37.0 1.0 O3A B:GTP701 3.7 37.0 1.0 O2G A:DTP704 3.8 43.2 1.0 O3' B:GTP701 3.9 37.0 1.0 O2B A:DTP704 3.9 43.2 1.0 O1G B:GTP701 4.5 37.0 1.0 NZ B:LYS116 4.7 35.5 1.0 PG B:GTP701 4.7 37.0 1.0 C5' B:GTP701 4.8 37.0 1.0 C3' B:GTP701 4.8 37.0 1.0 PA B:GTP701 5.0 37.0 1.0

Magnesium binding site 4 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


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 Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:19.5 occ:1.00 OD1 C:ASP207 2.8 26.4 1.0 OH C:TYR315 3.1 32.2 1.0 FE C:FE702 3.4 28.5 1.0 NE2 C:HIS233 3.4 35.4 1.0 CG C:ASP207 3.7 26.4 1.0 OD2 C:ASP207 3.9 26.4 1.0 NE2 C:HIS210 4.0 28.8 1.0 CE1 C:HIS233 4.1 35.4 1.0 CD2 C:HIS206 4.1 24.7 1.0 NE2 C:HIS206 4.2 24.7 1.0 CZ C:TYR315 4.4 32.2 1.0 CD2 C:HIS233 4.5 35.4 1.0 NH2 C:ARG164 4.5 25.6 1.0 O C:HIS206 4.6 24.7 1.0 OD1 C:ASP311 4.6 33.6 1.0 CE1 C:HIS215 4.6 36.2 1.0 CE1 C:HIS210 4.8 28.8 1.0 CD2 C:HIS210 4.8 28.8 1.0 CE2 C:TYR315 4.9 32.2 1.0

Magnesium binding site 5 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:17.9 occ:1.00 O1G D:DTP701 1.9 21.9 1.0 O1B D:DTP701 1.9 21.9 1.0 O3B D:DTP701 2.3 21.9 1.0 PG D:DTP701 2.3 21.9 1.0 PB D:DTP701 2.3 21.9 1.0 O3A D:DTP701 2.8 21.9 1.0 O3G D:DTP701 2.8 21.9 1.0 O1B A:GTP701 2.8 22.9 1.0 O3' A:GTP701 3.4 22.9 1.0 O5' A:GTP701 3.7 22.9 1.0 O2G D:DTP701 3.8 21.9 1.0 O2B D:DTP701 3.8 21.9 1.0 PA D:DTP701 4.3 21.9 1.0 PB A:GTP701 4.3 22.9 1.0 C3' A:GTP701 4.4 22.9 1.0 O2A A:GTP701 4.5 22.9 1.0 C4' A:GTP701 4.5 22.9 1.0 C5' A:GTP701 4.6 22.9 1.0 PA A:GTP701 4.6 22.9 1.0 O1A D:DTP701 4.7 21.9 1.0 O3G A:GTP701 4.7 22.9 1.0 NZ D:LYS523 4.8 31.1 1.0 O3A A:GTP701 5.0 22.9 1.0

Magnesium binding site 6 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:23.6 occ:1.00 O1B C:GTP701 1.9 19.4 1.0 O1B B:DTP706 1.9 33.0 1.0 O1G B:DTP706 1.9 33.0 1.0 O3B B:DTP706 1.9 33.0 1.0 PG B:DTP706 2.2 33.0 1.0 PB B:DTP706 2.3 33.0 1.0 O2G B:DTP706 3.0 33.0 1.0 PB C:GTP701 3.3 19.4 1.0 O2B B:DTP706 3.4 33.0 1.0 O3A B:DTP706 3.5 33.0 1.0 O3G B:DTP706 3.6 33.0 1.0 O3G C:GTP701 3.7 19.4 1.0 O5' C:GTP701 3.8 19.4 1.0 O2B C:GTP701 3.9 19.4 1.0 O3B C:GTP701 4.2 19.4 1.0 O3A C:GTP701 4.3 19.4 1.0 O2A C:GTP701 4.4 19.4 1.0 PA C:GTP701 4.4 19.4 1.0 O3' C:GTP701 4.4 19.4 1.0 PG C:GTP701 4.6 19.4 1.0 C5' C:GTP701 4.8 19.4 1.0

Magnesium binding site 7 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg706 b:19.3 occ:1.00 OD1 D:ASP207 2.0 23.9 1.0 NE2 D:HIS233 2.1 25.1 1.0 O1A D:DCP708 2.7 28.2 1.0 CD2 D:HIS233 2.9 25.1 1.0 CG D:ASP207 3.0 23.9 1.0 CE1 D:HIS233 3.1 25.1 1.0 OD2 D:ASP207 3.4 23.9 1.0 NE2 D:HIS210 3.8 23.8 1.0 PA D:DCP708 3.9 28.2 1.0 O2A D:DCP708 3.9 28.2 1.0 O D:HIS206 4.0 21.1 1.0 CG D:HIS233 4.0 25.1 1.0 FE D:FE705 4.1 33.1 1.0 ND1 D:HIS233 4.1 25.1 1.0 O2B D:DCP708 4.3 28.2 1.0 CB D:ASP207 4.3 23.9 1.0 CD2 D:HIS210 4.4 23.8 1.0 CD2 D:HIS206 4.5 21.1 1.0 CA D:ASP207 4.6 23.9 1.0 CE1 D:HIS210 4.8 23.8 1.0 O3A D:DCP708 4.8 28.2 1.0 C D:HIS206 4.9 21.1 1.0 PB D:DCP708 5.0 28.2 1.0 O3B D:DCP708 5.0 28.2 1.0

Magnesium binding site 8 out of 8 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Tetrameric Human SAMHD1 State IV - Depleted Relaxed within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg707 b:63.3 occ:1.00 O3G D:GTP704 2.0 37.5 1.0 O1G A:DTP705 2.0 46.0 1.0 O1B D:GTP704 2.0 37.5 1.0 PB D:GTP704 2.9 37.5 1.0 PG D:GTP704 2.9 37.5 1.0 O1G D:GTP704 3.2 37.5 1.0 O2B D:GTP704 3.2 37.5 1.0 O3B D:GTP704 3.3 37.5 1.0 PG A:DTP705 3.4 46.0 1.0 O2G A:DTP705 3.9 46.0 1.0 O3B A:DTP705 4.2 46.0 1.0 O2G D:GTP704 4.3 37.5 1.0 O3A D:GTP704 4.4 37.5 1.0 O1B A:DTP705 4.4 46.0 1.0 O2A D:GTP704 4.5 37.5 1.0 O3G A:DTP705 4.5 46.0 1.0 NZ D:LYS116 4.6 32.4 1.0 PB A:DTP705 5.0 46.0 1.0

O.J.Acton, D.Sheppard, E.R.Morris, S.Kunzelmann, S.J.Caswell, A.Nans, A.Burgess, G.Kelly, P.B.Rosenthal, I.A.Taylor. Platform-Directed Allostery and Quaternary Structure Dynamics of SAMHD1 Catalysis To Be Published.