Magnesium in PDB 7a5y: Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg, PDB code: 7a5y was solved by E.R.Morris, S.Kunzelmann, S.J.Caswell, A.Purkiss, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	153.15 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.193, 181.263, 286.331, 90, 90, 90
R / Rfree (%)	21 / 24

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg (pdb code 7a5y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg, PDB code: 7a5y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:22.8 occ:1.00 O A:HOH930 1.8 22.1 1.0 OD1 A:ASP207 2.0 23.3 1.0 O A:HOH905 2.2 18.0 1.0 NE2 A:HIS233 2.2 27.4 1.0 O A:HOH901 2.4 17.8 1.0 O2A A:T8T704 2.6 26.2 1.0 CG A:ASP207 3.1 22.6 1.0 CD2 A:HIS233 3.1 28.8 1.0 CE1 A:HIS233 3.2 29.5 1.0 OD2 A:ASP207 3.4 21.5 1.0 PA A:T8T704 3.6 25.9 1.0 O3A A:T8T704 3.8 24.9 1.0 FE A:FE701 3.8 21.5 1.0 CD2 A:HIS206 3.9 25.4 1.0 NE2 A:HIS210 3.9 28.7 1.0 OE2 A:GLU234 4.1 37.5 1.0 O A:HIS206 4.2 22.5 1.0 NE2 A:HIS206 4.3 25.8 1.0 CG A:HIS233 4.3 30.1 1.0 ND1 A:HIS233 4.3 30.4 1.0 CB A:ASP207 4.4 22.6 1.0 S1A A:T8T704 4.4 25.8 1.0 OD2 A:ASP311 4.4 21.5 1.0 CD2 A:HIS210 4.5 27.4 1.0 CD A:GLU234 4.5 36.0 1.0 O2B A:T8T704 4.5 24.1 1.0 CG A:GLU234 4.6 36.1 1.0 CA A:ASP207 4.6 23.9 1.0 PB A:T8T704 4.7 24.4 1.0 C A:HIS206 4.8 23.5 1.0 CE1 A:HIS210 4.9 27.4 1.0 NH2 A:ARG164 4.9 29.2 1.0 O1B A:T8T704 4.9 23.5 1.0 O5' A:T8T704 4.9 23.8 1.0 CG A:HIS206 5.0 24.7 1.0

Magnesium binding site 2 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:30.9 occ:1.00 O2B A:T8T704 1.8 24.1 1.0 O A:HOH942 1.9 20.8 1.0 O A:HOH926 1.9 15.7 1.0 O2G A:T8T704 2.0 24.6 1.0 O A:HOH912 2.2 16.5 1.0 O A:HOH918 2.2 22.5 1.0 PB A:T8T704 3.1 24.4 1.0 PG A:T8T704 3.3 24.3 1.0 O3B A:T8T704 3.5 22.9 1.0 O1G A:T8T704 4.0 24.1 1.0 O3A A:T8T704 4.0 24.9 1.0 O1B A:T8T704 4.1 23.5 1.0 OD2 A:ASP311 4.2 21.5 1.0 NZ A:LYS312 4.3 22.3 1.0 O A:HOH930 4.3 22.1 1.0 OD2 A:ASP309 4.4 26.9 1.0 O3G A:T8T704 4.4 23.6 1.0 OD1 A:ASP309 4.8 24.5 1.0

Magnesium binding site 3 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:20.9 occ:1.00 O3G D:T8T701 2.1 27.8 1.0 O D:HOH824 2.1 11.8 1.0 O2A A:T8T706 2.2 24.6 1.0 O1B D:T8T701 2.3 25.7 1.0 O3G A:T8T706 2.3 29.7 1.0 O2B A:T8T706 2.3 25.2 1.0 PG D:T8T701 3.2 28.2 1.0 O3B A:T8T706 3.3 26.7 1.0 PB D:T8T701 3.3 25.5 1.0 PG A:T8T706 3.3 29.5 1.0 PB A:T8T706 3.4 24.9 1.0 PA A:T8T706 3.5 23.9 1.0 O2G D:T8T701 3.5 28.4 1.0 O3B D:T8T701 3.6 26.9 1.0 O3' A:T8T706 3.8 22.3 1.0 NZ B:LYS116 3.8 37.0 1.0 O3A A:T8T706 3.9 23.9 1.0 O2B D:T8T701 4.0 25.1 1.0 O B:HOH823 4.3 19.7 1.0 O1G A:T8T706 4.3 30.0 1.0 O A:HOH933 4.3 20.4 1.0 O2G A:T8T706 4.4 30.7 1.0 O5' A:T8T706 4.5 22.7 1.0 C3' A:T8T706 4.5 22.2 1.0 C5' A:T8T706 4.5 22.6 1.0 O1G D:T8T701 4.6 29.1 1.0 O3A D:T8T701 4.6 24.6 1.0 O1B A:T8T706 4.7 25.8 1.0 NZ D:LYS523 4.7 54.3 1.0 NZ A:LYS377 4.8 38.4 1.0 S1A A:T8T706 4.9 24.3 1.0

Magnesium binding site 4 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg707 b:20.6 occ:1.00 O2B D:T8T702 1.9 25.4 1.0 O3G A:T8T708 2.1 26.4 1.0 O3G D:T8T702 2.1 28.1 1.0 O2A D:T8T702 2.2 23.5 1.0 O A:HOH924 2.2 25.3 1.0 O1B A:T8T708 2.2 25.4 1.0 PB D:T8T702 3.1 25.8 1.0 PG D:T8T702 3.2 28.6 1.0 PA D:T8T702 3.2 23.8 1.0 PB A:T8T708 3.3 24.7 1.0 O3B D:T8T702 3.3 26.9 1.0 PG A:T8T708 3.4 26.7 1.0 O3A D:T8T702 3.5 24.7 1.0 O3B A:T8T708 3.7 25.2 1.0 NZ C:LYS116 3.9 29.0 1.0 O3' D:T8T702 3.9 25.5 1.0 O2B A:T8T708 4.0 26.2 1.0 O1G D:T8T702 4.1 29.0 1.0 O1G A:T8T708 4.1 25.4 1.0 NZ D:LYS377 4.2 38.4 1.0 O5' D:T8T702 4.3 24.3 1.0 NZ A:LYS523 4.3 51.9 1.0 C5' D:T8T702 4.3 24.8 1.0 O2G D:T8T702 4.4 30.2 1.0 O1B D:T8T702 4.4 26.2 1.0 C3' D:T8T702 4.5 25.1 1.0 O D:HOH807 4.5 18.5 1.0 O3A A:T8T708 4.5 23.2 1.0 O2G A:T8T708 4.6 27.0 1.0 O A:HOH908 4.8 19.4 1.0 C4' D:T8T702 4.9 24.3 1.0 S1A D:T8T702 4.9 24.3 1.0

Magnesium binding site 5 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:32.1 occ:1.00 O B:HOH809 2.0 8.4 1.0 O B:HOH815 2.0 13.4 1.0 OD1 B:ASP207 2.1 19.2 1.0 NE2 B:HIS233 2.2 29.1 1.0 O B:HOH825 2.3 16.3 1.0 O2A B:T8T706 2.4 23.1 1.0 CG B:ASP207 3.2 18.2 1.0 CE1 B:HIS233 3.2 28.9 1.0 CD2 B:HIS233 3.2 28.8 1.0 PA B:T8T706 3.4 22.5 1.0 OD2 B:ASP207 3.4 17.4 1.0 O3A B:T8T706 3.6 22.5 1.0 FE B:FE703 3.7 18.9 1.0 NE2 B:HIS210 3.9 24.2 1.0 CD2 B:HIS206 3.9 15.7 1.0 OE2 B:GLU234 4.1 32.8 1.0 O B:HOH845 4.1 19.7 1.0 S1A B:T8T706 4.2 20.1 1.0 ND1 B:HIS233 4.3 29.1 1.0 PB B:T8T706 4.3 24.3 1.0 O2B B:T8T706 4.3 23.6 1.0 OD2 B:ASP311 4.3 21.4 1.0 NE2 B:HIS206 4.4 14.6 1.0 CG B:HIS233 4.4 29.0 1.0 O B:HIS206 4.4 18.9 1.0 O1B B:T8T706 4.4 21.9 1.0 CB B:ASP207 4.5 18.2 1.0 CD2 B:HIS210 4.5 23.4 1.0 CD B:GLU234 4.5 32.0 1.0 CG B:GLU234 4.7 31.9 1.0 O5' B:T8T706 4.7 22.1 1.0 CA B:ASP207 4.8 18.8 1.0 NH1 B:ARG164 4.8 23.9 1.0 CE1 B:HIS210 4.9 25.2 1.0

Magnesium binding site 6 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:23.6 occ:1.00 O B:HOH833 1.7 18.0 1.0 O B:HOH830 2.0 29.2 1.0 O2G B:T8T706 2.0 27.0 1.0 O2B B:T8T706 2.1 23.6 1.0 O B:HOH803 2.3 14.1 1.0 O B:HOH835 2.3 15.8 1.0 PG B:T8T706 3.3 26.0 1.0 PB B:T8T706 3.4 24.3 1.0 O3B B:T8T706 3.6 25.0 1.0 NZ B:LYS312 3.8 22.6 1.0 O1G B:T8T706 4.0 26.8 1.0 OD2 B:ASP309 4.0 25.3 1.0 O B:HOH801 4.0 32.2 1.0 O B:HOH819 4.2 16.8 1.0 OD2 B:ASP311 4.2 21.4 1.0 O3A B:T8T706 4.3 22.5 1.0 O B:HOH815 4.4 13.4 1.0 O3G B:T8T706 4.5 25.4 1.0 OD1 B:ASP309 4.5 25.6 1.0 O1B B:T8T706 4.6 21.9 1.0 CG B:ASP309 4.7 25.4 1.0 OG B:SER302 5.0 25.1 1.0

Magnesium binding site 7 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg707 b:24.0 occ:1.00 O3G C:T8T706 2.0 27.9 1.0 O3G B:T8T708 2.1 29.6 1.0 O B:HOH834 2.1 18.1 1.0 O2B C:T8T706 2.1 26.8 1.0 O1B B:T8T708 2.2 25.4 1.0 O2A C:T8T706 2.5 25.4 1.0 PG C:T8T706 3.2 28.0 1.0 PG B:T8T708 3.2 29.3 1.0 PB B:T8T708 3.2 25.1 1.0 PB C:T8T706 3.2 26.6 1.0 O3B C:T8T706 3.4 27.5 1.0 O3B B:T8T708 3.4 27.6 1.0 PA C:T8T706 3.6 25.3 1.0 O2G B:T8T708 3.7 29.2 1.0 O3A C:T8T706 3.8 25.9 1.0 O3' C:T8T706 3.8 23.6 1.0 NZ D:LYS116 3.9 37.3 1.0 O2B B:T8T708 4.1 26.1 1.0 O1G C:T8T706 4.1 27.8 1.0 O2G C:T8T706 4.2 29.8 1.0 NZ B:LYS523 4.2 54.3 1.0 O C:HOH922 4.3 24.1 1.0 O B:HOH829 4.5 16.1 1.0 O3A B:T8T708 4.5 25.3 1.0 C5' C:T8T706 4.5 24.5 1.0 O1G B:T8T708 4.5 30.3 1.0 O1B C:T8T706 4.5 27.1 1.0 C3' C:T8T706 4.6 23.5 1.0 O5' C:T8T706 4.6 24.1 1.0 NZ C:LYS377 4.8 48.5 1.0 O B:HOH814 4.9 27.5 1.0 CD B:LYS523 5.0 51.5 1.0 C4' C:T8T706 5.0 23.4 1.0

Magnesium binding site 8 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:23.9 occ:1.00 O3G B:T8T702 1.9 27.4 1.0 O3G B:T8T701 1.9 26.1 1.0 O2B B:T8T701 2.0 24.4 1.0 O B:HOH827 2.1 20.6 1.0 O2A B:T8T701 2.3 23.9 1.0 O1B B:T8T702 2.3 24.2 1.0 PG B:T8T701 3.1 26.4 1.0 PB B:T8T701 3.2 24.9 1.0 PG B:T8T702 3.2 27.2 1.0 O3B B:T8T701 3.3 25.4 1.0 PB B:T8T702 3.3 24.4 1.0 O3B B:T8T702 3.4 26.0 1.0 PA B:T8T701 3.5 24.4 1.0 O3A B:T8T701 3.7 24.3 1.0 NZ A:LYS116 4.0 29.8 1.0 O2G B:T8T702 4.1 26.6 1.0 O1G B:T8T701 4.1 26.9 1.0 O2G B:T8T701 4.1 26.9 1.0 O3' B:T8T701 4.1 24.4 1.0 O2B B:T8T702 4.2 25.7 1.0 O1G B:T8T702 4.3 27.3 1.0 NZ B:LYS377 4.4 46.3 1.0 NZ C:LYS523 4.4 55.2 1.0 CE C:LYS523 4.5 54.8 1.0 O5' B:T8T701 4.5 22.9 1.0 O1B B:T8T701 4.5 25.7 1.0 O3A B:T8T702 4.5 23.3 1.0 C5' B:T8T701 4.5 23.1 1.0 C3' B:T8T701 4.6 23.6 1.0

Magnesium binding site 9 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:23.1 occ:1.00 O C:HOH917 2.0 17.1 1.0 OD1 C:ASP207 2.1 22.3 1.0 O C:HOH907 2.2 29.5 1.0 NE2 C:HIS233 2.3 26.4 1.0 O C:HOH901 2.3 17.4 1.0 O2A C:T8T705 2.7 27.8 1.0 CG C:ASP207 3.1 21.0 1.0 CD2 C:HIS233 3.2 27.6 1.0 CE1 C:HIS233 3.3 26.9 1.0 OD2 C:ASP207 3.4 21.0 1.0 PA C:T8T705 3.6 28.6 1.0 FE C:FE702 3.8 23.6 1.0 CD2 C:HIS206 3.8 21.9 1.0 O3A C:T8T705 3.9 25.5 1.0 NE2 C:HIS210 4.0 23.8 1.0 O C:HIS206 4.1 24.2 1.0 OE2 C:GLU234 4.1 37.7 1.0 NE2 C:HIS206 4.3 21.6 1.0 CG C:HIS233 4.4 29.0 1.0 ND1 C:HIS233 4.4 27.9 1.0 OD2 C:ASP311 4.4 21.1 1.0 CB C:ASP207 4.4 21.4 1.0 S1A C:T8T705 4.4 26.6 1.0 CD C:GLU234 4.5 36.2 1.0 CG C:GLU234 4.5 35.5 1.0 O2B C:T8T705 4.6 25.6 1.0 CD2 C:HIS210 4.6 23.1 1.0 CA C:ASP207 4.6 22.3 1.0 PB C:T8T705 4.6 25.5 1.0 C C:HIS206 4.7 23.4 1.0 CG C:HIS206 4.9 22.2 1.0 O1B C:T8T705 4.9 24.0 1.0 N C:ASP207 5.0 22.5 1.0

Magnesium binding site 10 out of 24 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Rp-Dgtp-Alphas (T8T) and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:23.9 occ:1.00 O2B C:T8T705 1.8 25.6 1.0 O C:HOH906 1.9 16.6 1.0 O C:HOH914 2.0 27.1 1.0 O C:HOH905 2.1 14.9 1.0 O2G C:T8T705 2.1 26.8 1.0 O C:HOH934 2.2 11.2 1.0 PB C:T8T705 3.1 25.5 1.0 PG C:T8T705 3.3 25.4 1.0 O3B C:T8T705 3.4 25.8 1.0 O3A C:T8T705 4.0 25.5 1.0 O1G C:T8T705 4.1 26.8 1.0 NZ C:LYS312 4.1 24.5 1.0 OD2 C:ASP311 4.1 21.1 1.0 O1B C:T8T705 4.1 24.0 1.0 O C:HOH936 4.2 22.1 1.0 O C:HOH920 4.2 18.6 1.0 OD2 C:ASP309 4.2 23.2 1.0 O C:HOH917 4.3 17.1 1.0 O3G C:T8T705 4.5 24.7 1.0 OD1 C:ASP309 4.6 23.0 1.0 CG C:ASP309 4.9 23.0 1.0

E.R.Morris, S.Kunzelmann, S.J.Caswell, A.G.Purkiss, G.Kelly, I.A.Taylor. Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R P - and S P -Dntp Alpha S Diastereomers. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33988981
DOI: 10.1021/ACS.BIOCHEM.0C00944