Magnesium in PDB 8qxk: Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense

The structure of Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense (pdb code 8qxk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense, PDB code: 8qxk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:4.9 occ:1.00 OD1 A:ASP207 2.5 1.0 1.0 NE2 A:HIS233 2.6 2.0 1.0 O2A A:DCP706 2.8 4.8 1.0 CE1 A:HIS233 3.4 2.0 1.0 CG A:ASP207 3.5 1.0 1.0 CD2 A:HIS233 3.7 2.0 1.0 OD2 A:ASP207 3.8 1.0 1.0 PA A:DCP706 3.8 4.8 1.0 O2B A:DCP706 3.8 4.8 1.0 O1A A:DCP706 3.9 4.8 1.0 OE2 A:GLU234 3.9 2.2 1.0 CD2 A:HIS206 4.1 0.9 1.0 O A:HIS206 4.3 0.9 1.0 O3A A:DCP706 4.3 4.8 1.0 FE A:FE702 4.4 3.2 1.0 CD A:GLU234 4.4 2.2 1.0 PB A:DCP706 4.4 4.8 1.0 NE2 A:HIS210 4.5 1.3 1.0 OD2 A:ASP311 4.5 1.3 1.0 O1B A:DCP706 4.5 4.8 1.0 ND1 A:HIS233 4.6 2.0 1.0 NE2 A:HIS206 4.6 0.9 1.0 CG A:GLU234 4.7 2.2 1.0 CG A:HIS233 4.8 2.0 1.0 CB A:ASP207 4.8 1.0 1.0

Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:8.8 occ:1.00 OG A:SER302 3.7 4.3 1.0 O2G A:DCP706 3.8 4.8 1.0 OD2 A:ASP309 3.9 2.4 1.0 O2B A:DCP706 3.9 4.8 1.0 CB A:SER302 4.4 4.3 1.0 O1B A:DCP706 4.5 4.8 1.0 CA A:SER302 4.6 4.3 1.0 OD2 A:ASP311 4.7 1.3 1.0 PB A:DCP706 4.8 4.8 1.0 PG A:DCP706 4.9 4.8 1.0 O3G A:DCP706 4.9 4.8 1.0 CG A:ASP309 4.9 2.4 1.0

Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:1.9 occ:1.00 O1B A:GTP701 2.0 1.2 1.0 O1B D:DTP701 2.1 4.1 1.0 O1G D:DTP701 2.3 4.1 1.0 O3G A:GTP701 2.7 1.2 1.0 O5' A:GTP701 3.3 1.2 1.0 PB D:DTP701 3.3 4.1 1.0 PB A:GTP701 3.4 1.2 1.0 O2A A:GTP701 3.4 1.2 1.0 PG D:DTP701 3.4 4.1 1.0 O3B D:DTP701 3.5 4.1 1.0 O3' A:GTP701 3.7 1.2 1.0 PA A:GTP701 3.8 1.2 1.0 PG A:GTP701 3.8 1.2 1.0 NZ A:LYS116 3.9 3.4 1.0 O3B A:GTP701 4.0 1.2 1.0 O3A A:GTP701 4.0 1.2 1.0 O3G D:DTP701 4.1 4.1 1.0 O3A D:DTP701 4.2 4.1 1.0 C3' A:GTP701 4.3 1.2 1.0 O1G A:GTP701 4.4 1.2 1.0 O2B A:GTP701 4.4 1.2 1.0 O2B D:DTP701 4.5 4.1 1.0 C5' A:GTP701 4.5 1.2 1.0 O2G D:DTP701 4.7 4.1 1.0 C4' A:GTP701 4.9 1.2 1.0 CG A:LYS116 5.0 3.4 1.0

Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:4.3 occ:1.00 OD1 C:ASP207 2.5 0.9 1.0 NE2 C:HIS233 2.6 1.9 1.0 O1A C:DCP706 2.8 5.3 1.0 CE1 C:HIS233 3.4 1.9 1.0 CG C:ASP207 3.5 0.9 1.0 CD2 C:HIS233 3.6 1.9 1.0 OD2 C:ASP207 3.8 0.9 1.0 PA C:DCP706 3.8 5.3 1.0 O2A C:DCP706 3.8 5.3 1.0 O1B C:DCP706 3.9 5.3 1.0 OE2 C:GLU234 3.9 2.1 1.0 CD2 C:HIS206 4.1 0.8 1.0 O C:HIS206 4.3 0.8 1.0 O3A C:DCP706 4.3 5.3 1.0 FE C:FE702 4.4 2.3 1.0 CD C:GLU234 4.4 2.1 1.0 PB C:DCP706 4.5 5.3 1.0 NE2 C:HIS210 4.5 1.2 1.0 OD2 C:ASP311 4.5 1.3 1.0 O2B C:DCP706 4.5 5.3 1.0 ND1 C:HIS233 4.6 1.9 1.0 NE2 C:HIS206 4.6 0.8 1.0 CG C:GLU234 4.7 2.1 1.0 CG C:HIS233 4.7 1.9 1.0 CB C:ASP207 4.8 0.9 1.0

Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:9.1 occ:1.00 OG C:SER302 3.7 4.3 1.0 O1G C:DCP706 3.8 5.3 1.0 OD2 C:ASP309 3.9 2.4 1.0 O1B C:DCP706 4.0 5.3 1.0 CB C:SER302 4.4 4.3 1.0 O2B C:DCP706 4.5 5.3 1.0 CA C:SER302 4.6 4.3 1.0 OD2 C:ASP311 4.7 1.3 1.0 PB C:DCP706 4.8 5.3 1.0 CG C:ASP309 4.9 2.4 1.0 PG C:DCP706 5.0 5.3 1.0

Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:2.1 occ:1.00 O1B C:GTP701 2.0 1.9 1.0 O1B B:DTP701 2.1 4.1 1.0 O1G B:DTP701 2.3 4.1 1.0 O3G C:GTP701 2.7 1.9 1.0 PB B:DTP701 3.3 4.1 1.0 O5' C:GTP701 3.3 1.9 1.0 PG B:DTP701 3.4 4.1 1.0 PB C:GTP701 3.4 1.9 1.0 O2A C:GTP701 3.4 1.9 1.0 O3B B:DTP701 3.5 4.1 1.0 O3' C:GTP701 3.7 1.9 1.0 PA C:GTP701 3.8 1.9 1.0 PG C:GTP701 3.8 1.9 1.0 O3B C:GTP701 4.0 1.9 1.0 NZ C:LYS116 4.0 3.6 1.0 O3A C:GTP701 4.0 1.9 1.0 O3G B:DTP701 4.1 4.1 1.0 O3A B:DTP701 4.2 4.1 1.0 C3' C:GTP701 4.4 1.9 1.0 O1G C:GTP701 4.4 1.9 1.0 O2B C:GTP701 4.4 1.9 1.0 O2B B:DTP701 4.5 4.1 1.0 C5' C:GTP701 4.5 1.9 1.0 O2G B:DTP701 4.6 4.1 1.0 CG C:LYS116 4.9 3.6 1.0 C4' C:GTP701 4.9 1.9 1.0

Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:5.3 occ:1.00 NE2 B:HIS233 2.6 2.0 1.0 OD1 B:ASP207 2.6 0.9 1.0 O1A B:DCP707 2.9 4.7 1.0 CE1 B:HIS233 3.4 2.0 1.0 CG B:ASP207 3.6 0.9 1.0 CD2 B:HIS233 3.7 2.0 1.0 PA B:DCP707 3.8 4.7 1.0 O1B B:DCP707 3.8 4.7 1.0 O2A B:DCP707 3.9 4.7 1.0 OE2 B:GLU234 3.9 2.2 1.0 OD2 B:ASP207 3.9 0.9 1.0 CD2 B:HIS206 4.1 0.9 1.0 O B:HIS206 4.3 0.9 1.0 O3A B:DCP707 4.3 4.7 1.0 CD B:GLU234 4.4 2.2 1.0 FE B:FE703 4.4 2.5 1.0 PB B:DCP707 4.4 4.7 1.0 NE2 B:HIS210 4.5 1.2 1.0 OD2 B:ASP311 4.5 1.4 1.0 O2B B:DCP707 4.5 4.7 1.0 NE2 B:HIS206 4.6 0.9 1.0 ND1 B:HIS233 4.6 2.0 1.0 CG B:GLU234 4.7 2.2 1.0 CG B:HIS233 4.7 2.0 1.0 CB B:ASP207 4.9 0.9 1.0

Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


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 I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:8.1 occ:1.00 OG B:SER302 3.7 4.4 1.0 O1G B:DCP707 3.8 4.7 1.0 OD2 B:ASP309 3.9 2.5 1.0 O1B B:DCP707 3.9 4.7 1.0 CB B:SER302 4.4 4.4 1.0 O2B B:DCP707 4.5 4.7 1.0 CA B:SER302 4.6 4.4 1.0 OD2 B:ASP311 4.7 1.4 1.0 PB B:DCP707 4.8 4.7 1.0 PG B:DCP707 4.9 4.7 1.0 O3G B:DCP707 4.9 4.7 1.0 CG B:ASP309 5.0 2.5 1.0

Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg706 b:3.2 occ:1.00 O1B B:GTP702 2.0 4.1 1.0 O1B C:DTP707 2.1 4.1 1.0 O1G C:DTP707 2.3 4.1 1.0 O3G B:GTP702 2.7 4.1 1.0 PB C:DTP707 3.3 4.1 1.0 O5' B:GTP702 3.3 4.1 1.0 O2A B:GTP702 3.4 4.1 1.0 PG C:DTP707 3.4 4.1 1.0 PB B:GTP702 3.4 4.1 1.0 O3B C:DTP707 3.5 4.1 1.0 O3' B:GTP702 3.7 4.1 1.0 PA B:GTP702 3.8 4.1 1.0 PG B:GTP702 3.8 4.1 1.0 O3B B:GTP702 4.0 4.1 1.0 O3A B:GTP702 4.0 4.1 1.0 NZ B:LYS116 4.1 3.9 1.0 O3G C:DTP707 4.1 4.1 1.0 O3A C:DTP707 4.2 4.1 1.0 C3' B:GTP702 4.4 4.1 1.0 O1G B:GTP702 4.4 4.1 1.0 O2B B:GTP702 4.4 4.1 1.0 O2B C:DTP707 4.5 4.1 1.0 C5' B:GTP702 4.5 4.1 1.0 O2G C:DTP707 4.6 4.1 1.0 CG B:LYS116 4.9 3.9 1.0 C4' B:GTP702 4.9 4.1 1.0

Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Tetrameric Human SAMHD1 State I - Tense within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:4.8 occ:1.00 OD1 D:ASP207 2.5 0.9 1.0 NE2 D:HIS233 2.6 1.9 1.0 O2A D:DCP707 3.2 4.7 1.0 CE1 D:HIS233 3.4 1.9 1.0 CG D:ASP207 3.5 0.9 1.0 O1A D:DCP707 3.6 4.7 1.0 CD2 D:HIS233 3.6 1.9 1.0 O2B D:DCP707 3.8 4.7 1.0 PA D:DCP707 3.9 4.7 1.0 OD2 D:ASP207 3.9 0.9 1.0 OE2 D:GLU234 3.9 2.1 1.0 CD2 D:HIS206 4.1 0.8 1.0 O3A D:DCP707 4.3 4.7 1.0 O D:HIS206 4.3 0.8 1.0 CE1 D:HIS210 4.3 1.4 1.0 FE D:FE703 4.4 3.4 1.0 CD D:GLU234 4.4 2.1 1.0 PB D:DCP707 4.4 4.7 1.0 OD2 D:ASP311 4.5 1.4 1.0 O1B D:DCP707 4.6 4.7 1.0 ND1 D:HIS233 4.6 1.9 1.0 CG D:GLU234 4.7 2.1 1.0 NE2 D:HIS210 4.7 1.4 1.0 NE2 D:HIS206 4.7 0.8 1.0 CG D:HIS233 4.7 1.9 1.0 CB D:ASP207 4.8 0.9 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.