Magnesium in PDB 6xu1: Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg, PDB code: 6xu1 was solved by E.R.Morris, S.Kunzelmann, S.J.Caswell, L.H.Arnold, A.G.Purkiss, G.Kelly, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.30 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	137.369, 171.860, 179.572, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.2

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 - 25;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg (pdb code 6xu1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 25 binding sites of Magnesium where determined in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg, PDB code: 6xu1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:8.2 occ:1.00 O A:HOH866 2.0 15.7 1.0 O A:HOH865 2.0 11.1 1.0 OD1 A:ASP207 2.1 13.5 1.0 O A:HOH845 2.1 11.1 1.0 O2A A:DZ4705 2.1 15.1 1.0 NE2 A:HIS233 2.2 19.1 1.0 CE1 A:HIS233 3.1 19.6 1.0 CG A:ASP207 3.2 13.2 1.0 PA A:DZ4705 3.2 14.4 1.0 CD2 A:HIS233 3.2 19.6 1.0 OD2 A:ASP207 3.6 12.3 1.0 FE A:FE701 3.7 15.0 1.0 N3A A:DZ4705 3.7 14.0 1.0 O1A A:DZ4705 3.8 13.6 1.0 NE2 A:HIS210 3.8 16.1 1.0 CD2 A:HIS206 3.9 13.4 1.0 ND1 A:HIS233 4.3 19.7 1.0 NE2 A:HIS206 4.3 13.5 1.0 CG A:HIS233 4.3 19.3 1.0 PB A:DZ4705 4.3 14.2 1.0 OE2 A:GLU234 4.4 25.2 1.0 O A:HIS206 4.4 15.2 1.0 O1B A:DZ4705 4.4 13.0 1.0 O2B A:DZ4705 4.5 13.2 1.0 CD2 A:HIS210 4.5 16.4 1.0 CB A:ASP207 4.5 13.3 1.0 O5' A:DZ4705 4.5 14.3 1.0 O A:HOH889 4.6 17.8 1.0 CD A:GLU234 4.7 24.3 1.0 O A:HOH884 4.7 18.1 1.0 CG A:GLU234 4.8 21.9 1.0 CE1 A:HIS210 4.8 17.2 1.0 CA A:ASP207 4.8 13.8 1.0 OD2 A:ASP311 4.9 14.1 1.0 NH2 A:ARG164 4.9 14.6 1.0 OD1 A:ASP311 5.0 13.7 1.0

Magnesium binding site 2 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:14.7 occ:1.00 O1G A:DZ4705 2.0 15.6 1.0 O1B A:DZ4705 2.0 13.0 1.0 O A:HOH824 2.0 15.6 1.0 O A:HOH864 2.0 10.7 1.0 O A:HOH858 2.1 15.8 1.0 O A:HOH805 2.1 12.9 1.0 PG A:DZ4705 3.3 15.7 1.0 PB A:DZ4705 3.4 14.2 1.0 O3B A:DZ4705 3.6 14.4 1.0 NZ A:LYS312 3.9 16.0 1.0 OD2 A:ASP309 4.0 15.2 1.0 O A:HOH812 4.1 32.1 1.0 OD2 A:ASP311 4.1 14.1 1.0 O A:HOH884 4.2 18.1 1.0 O3G A:DZ4705 4.3 16.8 1.0 N3A A:DZ4705 4.3 14.0 1.0 O2G A:DZ4705 4.3 16.7 1.0 O A:HOH865 4.4 11.1 1.0 OD1 A:ASP309 4.4 16.1 1.0 O2B A:DZ4705 4.5 13.2 1.0 CG A:ASP309 4.6 15.5 1.0 OG A:SER302 4.7 19.9 1.0 O A:HOH835 5.0 21.8 1.0

Magnesium binding site 3 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:14.8 occ:1.00 O3G A:GTP706 2.0 17.0 1.0 O1B A:GTP706 2.0 16.4 1.0 O A:HOH823 2.0 8.7 1.0 O2A A:GTP706 2.0 14.1 1.0 O1B C:DZ4701 2.1 16.2 1.0 O2G C:DZ4701 2.1 15.4 1.0 PB A:GTP706 3.1 16.8 1.0 PG A:GTP706 3.2 18.1 1.0 PG C:DZ4701 3.2 16.6 1.0 PB C:DZ4701 3.3 17.9 1.0 PA A:GTP706 3.4 14.6 1.0 O3B A:GTP706 3.5 16.8 1.0 O3B C:DZ4701 3.5 16.4 1.0 O3A A:GTP706 3.7 15.4 1.0 NZ A:LYS116 3.7 22.3 1.0 O1G C:DZ4701 4.0 16.6 1.0 O3' A:GTP706 4.1 13.2 1.0 NZ C:LYS523 4.1 37.0 1.0 O2B C:DZ4701 4.2 15.6 1.0 O1G A:GTP706 4.2 18.3 1.0 C5' A:GTP706 4.2 13.5 1.0 O2G A:GTP706 4.3 19.9 1.0 O A:HOH867 4.3 26.1 1.0 O5' A:GTP706 4.3 14.0 1.0 O3G C:DZ4701 4.4 18.9 1.0 N3A C:DZ4701 4.4 15.9 1.0 O2B A:GTP706 4.4 16.1 1.0 O1A A:GTP706 4.7 14.2 1.0 CE A:LYS116 4.7 22.3 1.0 C3' A:GTP706 4.8 13.1 1.0 C4' A:GTP706 5.0 13.2 1.0

Magnesium binding site 4 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:9.6 occ:1.00 O B:HOH849 2.1 9.8 1.0 OD1 B:ASP207 2.1 14.2 1.0 O B:HOH822 2.2 11.7 1.0 O B:HOH850 2.2 11.9 1.0 O2A B:DZ4705 2.2 16.8 1.0 NE2 B:HIS233 2.2 15.3 1.0 CE1 B:HIS233 3.2 15.2 1.0 PA B:DZ4705 3.2 14.8 1.0 CD2 B:HIS233 3.2 15.2 1.0 CG B:ASP207 3.2 14.2 1.0 OD2 B:ASP207 3.7 13.2 1.0 FE B:FE701 3.7 13.9 1.0 O1A B:DZ4705 3.7 14.6 1.0 N3A B:DZ4705 3.7 14.8 1.0 CD2 B:HIS206 3.9 14.7 1.0 NE2 B:HIS210 3.9 15.3 1.0 O B:HOH895 4.2 13.6 1.0 NE2 B:HIS206 4.3 14.3 1.0 OE2 B:GLU234 4.3 24.4 1.0 ND1 B:HIS233 4.3 14.5 1.0 O1B B:DZ4705 4.3 14.7 1.0 CG B:HIS233 4.3 14.9 1.0 PB B:DZ4705 4.4 15.0 1.0 O B:HIS206 4.4 14.2 1.0 O B:HOH901 4.4 22.2 1.0 O2B B:DZ4705 4.5 13.5 1.0 O5' B:DZ4705 4.5 13.7 1.0 CD2 B:HIS210 4.6 15.6 1.0 CB B:ASP207 4.6 14.1 1.0 CD B:GLU234 4.6 23.8 1.0 CG B:GLU234 4.7 22.5 1.0 OD2 B:ASP311 4.8 15.4 1.0 CA B:ASP207 4.8 14.3 1.0 CE1 B:HIS210 4.8 15.8 1.0 OD1 B:ASP311 5.0 13.3 1.0 NH1 B:ARG164 5.0 13.5 1.0

Magnesium binding site 5 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:16.9 occ:1.00 O1G B:DZ4705 1.9 13.5 1.0 O B:HOH877 2.0 14.8 1.0 O B:HOH829 2.0 14.6 1.0 O B:HOH848 2.0 16.4 1.0 O1B B:DZ4705 2.1 14.7 1.0 O B:HOH842 2.1 14.6 1.0 PG B:DZ4705 3.3 13.6 1.0 PB B:DZ4705 3.4 15.0 1.0 O3B B:DZ4705 3.6 13.9 1.0 NZ B:LYS312 3.9 18.3 1.0 OD2 B:ASP309 4.0 20.1 1.0 O3G B:DZ4705 4.1 14.1 1.0 OD2 B:ASP311 4.2 15.4 1.0 O B:HOH901 4.3 22.2 1.0 O B:HOH849 4.3 9.8 1.0 O2G B:DZ4705 4.3 14.4 1.0 N3A B:DZ4705 4.4 14.8 1.0 OD1 B:ASP309 4.5 16.5 1.0 OG B:SER302 4.5 20.3 1.0 O2B B:DZ4705 4.5 13.5 1.0 CG B:ASP309 4.7 17.7 1.0 O B:HOH831 4.8 18.9 1.0

Magnesium binding site 6 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:18.0 occ:1.00 O2G D:DZ4701 1.9 18.0 1.0 O1B D:DZ4701 2.0 18.3 1.0 O3G B:GTP706 2.0 25.8 1.0 O1B B:GTP706 2.0 19.6 1.0 O B:HOH818 2.1 10.7 1.0 O2A B:GTP706 2.2 17.0 1.0 PB B:GTP706 3.1 22.5 1.0 PB D:DZ4701 3.1 19.3 1.0 PG D:DZ4701 3.1 18.4 1.0 PG B:GTP706 3.3 25.2 1.0 O3B D:DZ4701 3.3 18.2 1.0 O3B B:GTP706 3.4 23.2 1.0 PA B:GTP706 3.5 17.3 1.0 O3A B:GTP706 3.6 19.3 1.0 O2B D:DZ4701 3.9 17.4 1.0 NZ B:LYS116 3.9 25.0 1.0 O3' B:GTP706 4.0 13.9 1.0 NZ D:LYS523 4.0 41.3 1.0 O1G D:DZ4701 4.1 19.1 1.0 O2G B:GTP706 4.2 25.1 1.0 C5' B:GTP706 4.2 15.9 1.0 O3G D:DZ4701 4.2 19.8 1.0 N3A D:DZ4701 4.3 17.6 1.0 O1G B:GTP706 4.3 24.1 1.0 O5' B:GTP706 4.4 17.0 1.0 C3' B:GTP706 4.6 14.8 1.0 O2B B:GTP706 4.6 22.2 1.0 O1A B:GTP706 4.7 18.1 1.0 C4' B:GTP706 4.8 15.3 1.0

Magnesium binding site 7 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:9.2 occ:1.00 O C:HOH825 2.0 18.6 1.0 OD1 C:ASP207 2.0 13.1 1.0 O C:HOH832 2.1 13.7 1.0 O C:HOH841 2.1 13.1 1.0 O2A C:DZ4706 2.1 14.0 1.0 NE2 C:HIS233 2.2 15.5 1.0 CG C:ASP207 3.1 13.4 1.0 CD2 C:HIS233 3.2 15.9 1.0 PA C:DZ4706 3.2 14.2 1.0 CE1 C:HIS233 3.2 15.5 1.0 OD2 C:ASP207 3.6 12.5 1.0 FE C:FE702 3.7 13.4 1.0 N3A C:DZ4706 3.7 13.8 1.0 O1A C:DZ4706 3.8 13.6 1.0 NE2 C:HIS210 3.8 14.0 1.0 CD2 C:HIS206 3.9 11.8 1.0 O C:HOH909 4.2 28.5 1.0 NE2 C:HIS206 4.2 11.5 1.0 ND1 C:HIS233 4.3 15.2 1.0 O1B C:DZ4706 4.3 13.6 1.0 CG C:HIS233 4.3 16.1 1.0 O C:HIS206 4.4 14.8 1.0 OE2 C:GLU234 4.4 22.9 1.0 PB C:DZ4706 4.4 14.8 1.0 CD2 C:HIS210 4.5 14.5 1.0 CB C:ASP207 4.5 13.5 1.0 O5' C:DZ4706 4.5 14.1 1.0 O2B C:DZ4706 4.5 13.6 1.0 O C:HOH895 4.6 16.0 1.0 CD C:GLU234 4.7 21.7 1.0 CA C:ASP207 4.7 13.8 1.0 CE1 C:HIS210 4.8 14.9 1.0 CG C:GLU234 4.8 20.2 1.0 OD2 C:ASP311 4.8 15.4 1.0 NH2 C:ARG164 4.9 15.0 1.0 OD1 C:ASP311 4.9 13.5 1.0

Magnesium binding site 8 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:13.8 occ:1.00 O1G C:DZ4706 2.0 14.9 1.0 O1B C:DZ4706 2.0 13.6 1.0 O C:HOH878 2.0 13.4 1.0 O C:HOH860 2.1 17.2 1.0 O C:HOH826 2.1 13.5 1.0 O C:HOH808 2.1 11.5 1.0 PB C:DZ4706 3.3 14.8 1.0 PG C:DZ4706 3.3 14.7 1.0 O3B C:DZ4706 3.5 14.4 1.0 NZ C:LYS312 4.0 15.3 1.0 O C:HOH833 4.0 28.4 1.0 OD2 C:ASP309 4.1 16.7 1.0 O C:HOH870 4.1 24.9 1.0 O3G C:DZ4706 4.1 14.4 1.0 OD2 C:ASP311 4.1 15.4 1.0 O C:HOH832 4.2 13.7 1.0 N3A C:DZ4706 4.2 13.8 1.0 O2G C:DZ4706 4.3 14.2 1.0 O C:HOH895 4.3 16.0 1.0 O2B C:DZ4706 4.4 13.6 1.0 OD1 C:ASP309 4.5 15.4 1.0 OG C:SER302 4.6 21.9 1.0 CG C:ASP309 4.7 16.8 1.0

Magnesium binding site 9 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:17.9 occ:1.00 O1B A:DZ4707 1.9 16.5 1.0 O2G A:DZ4707 1.9 17.6 1.0 O1B C:GTP707 2.0 17.6 1.0 O A:HOH811 2.0 14.4 1.0 O3G C:GTP707 2.0 22.0 1.0 O2A C:GTP707 2.3 15.3 1.0 PB C:GTP707 3.1 21.5 1.0 PB A:DZ4707 3.2 18.2 1.0 PG A:DZ4707 3.2 18.5 1.0 PG C:GTP707 3.3 22.5 1.0 O3B A:DZ4707 3.4 18.7 1.0 O3B C:GTP707 3.4 19.8 1.0 PA C:GTP707 3.5 15.9 1.0 O3A C:GTP707 3.8 18.2 1.0 O3' C:GTP707 3.9 15.1 1.0 O1G A:DZ4707 3.9 19.3 1.0 NZ C:LYS116 4.0 28.4 1.0 O2B A:DZ4707 4.0 16.5 1.0 NZ A:LYS523 4.0 36.6 1.0 O1G C:GTP707 4.3 22.9 1.0 O2G C:GTP707 4.3 23.4 1.0 C5' C:GTP707 4.3 16.0 1.0 O3G A:DZ4707 4.4 21.0 1.0 O5' C:GTP707 4.4 15.6 1.0 N3A A:DZ4707 4.4 16.5 1.0 O2B C:GTP707 4.5 20.2 1.0 CE C:LYS116 4.6 28.5 1.0 C3' C:GTP707 4.7 15.3 1.0 O1A C:GTP707 4.8 16.8 1.0 C4' C:GTP707 5.0 15.5 1.0

Magnesium binding site 10 out of 25 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:8.9 occ:1.00 O D:HOH822 2.1 13.1 1.0 NE2 D:HIS233 2.1 17.7 1.0 OD1 D:ASP207 2.1 15.3 1.0 O2A D:DZ4706 2.1 14.1 1.0 O D:HOH847 2.2 13.6 1.0 O D:HOH840 2.2 14.1 1.0 CE1 D:HIS233 3.1 18.5 1.0 CD2 D:HIS233 3.1 18.0 1.0 PA D:DZ4706 3.1 15.0 1.0 CG D:ASP207 3.2 15.3 1.0 N3A D:DZ4706 3.6 15.5 1.0 OD2 D:ASP207 3.7 13.8 1.0 FE D:FE702 3.7 15.5 1.0 O1A D:DZ4706 3.8 13.7 1.0 NE2 D:HIS210 3.8 14.7 1.0 CD2 D:HIS206 4.0 16.3 1.0 ND1 D:HIS233 4.2 18.3 1.0 CG D:HIS233 4.2 18.6 1.0 OE2 D:GLU234 4.2 28.9 1.0 O1B D:DZ4706 4.3 17.2 1.0 PB D:DZ4706 4.3 16.7 1.0 NE2 D:HIS206 4.4 16.3 1.0 O D:HIS206 4.4 16.7 1.0 O2B D:DZ4706 4.4 16.4 1.0 CD2 D:HIS210 4.4 14.4 1.0 O D:HOH876 4.5 21.9 1.0 O5' D:DZ4706 4.5 14.4 1.0 CB D:ASP207 4.6 15.4 1.0 CD D:GLU234 4.6 27.6 1.0 CE1 D:HIS210 4.7 14.9 1.0 CG D:GLU234 4.7 24.8 1.0 CA D:ASP207 4.8 15.7 1.0 O D:HOH863 4.8 20.7 1.0 OD2 D:ASP311 4.8 17.5 1.0 NH1 D:ARG164 4.9 15.5 1.0 OD1 D:ASP311 5.0 16.3 1.0

E.R.Morris, S.Kunzelmann, S.J.Caswell, L.H.Arnold, A.G.Purkiss, G.Kelly, I.A.Taylor. Crystal Structures of SAMHD1 Inhibitor Complexes Reveal the Mechanism of Water-Mediated Dntp Hydrolysis Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-16983-2