Magnesium in PDB 6tx0: Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg, PDB code: 6tx0 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)	72.31 / 2.01
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.924, 105.924, 198.073, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.8

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg (pdb code 6tx0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg, PDB code: 6tx0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, 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 D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:29.1 occ:1.00 O2A A:DZ4705 2.0 25.9 1.0 OD1 A:ASP207 2.0 29.2 1.0 O A:HOH836 2.1 33.0 1.0 NE2 A:HIS233 2.2 35.2 1.0 O A:HOH808 2.2 18.5 1.0 O A:HOH817 2.3 29.5 1.0 CE1 A:HIS233 3.1 36.4 1.0 CG A:ASP207 3.2 27.5 1.0 CD2 A:HIS233 3.2 33.8 1.0 PA A:DZ4705 3.2 26.4 1.0 OD2 A:ASP207 3.7 23.0 1.0 O1A A:DZ4705 3.8 24.8 1.0 NE2 A:HIS210 3.8 37.8 1.0 N3A A:DZ4705 3.9 25.1 1.0 FE A:FE701 3.9 22.4 1.0 CD2 A:HIS206 3.9 24.6 1.0 ND1 A:HIS233 4.3 35.2 1.0 CG A:HIS233 4.3 34.9 1.0 NE2 A:HIS206 4.3 24.3 1.0 O A:HIS206 4.4 29.2 1.0 O1B A:DZ4705 4.4 24.4 1.0 O A:HOH853 4.4 41.5 1.0 CD2 A:HIS210 4.4 35.2 1.0 PB A:DZ4705 4.4 27.1 1.0 OE2 A:GLU234 4.5 37.9 1.0 CB A:ASP207 4.5 26.7 1.0 O5' A:DZ4705 4.5 24.7 1.0 O2B A:DZ4705 4.6 26.3 1.0 CA A:ASP207 4.7 26.6 1.0 CD A:GLU234 4.8 39.3 1.0 CG A:GLU234 4.8 38.9 1.0 O A:HOH847 4.8 39.4 1.0 CE1 A:HIS210 4.8 35.8 1.0 OD2 A:ASP311 4.9 35.2 1.0 NH2 A:ARG164 4.9 24.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, 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 D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:32.2 occ:1.00 O A:HOH812 1.8 33.5 1.0 O A:HOH802 1.9 39.0 1.0 O1G A:DZ4705 2.0 26.7 1.0 O A:HOH827 2.1 35.4 1.0 O A:HOH811 2.2 30.5 1.0 O1B A:DZ4705 2.2 24.4 1.0 PG A:DZ4705 3.4 26.1 1.0 PB A:DZ4705 3.5 27.1 1.0 O3B A:DZ4705 3.7 23.6 1.0 OD2 A:ASP309 3.9 29.4 1.0 NZ A:LYS312 4.0 27.8 1.0 OD2 A:ASP311 4.1 35.2 1.0 O3G A:DZ4705 4.2 25.7 1.0 OD1 A:ASP309 4.4 23.9 1.0 O A:HOH847 4.4 39.4 1.0 O A:HOH836 4.5 33.0 1.0 O2G A:DZ4705 4.5 24.7 1.0 OG A:SER302 4.5 27.9 1.0 N3A A:DZ4705 4.6 25.1 1.0 CG A:ASP309 4.6 26.0 1.0 O2B A:DZ4705 4.6 26.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, 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 D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:32.5 occ:1.00 O B:HOH823 1.9 32.2 1.0 O1B B:DZ4701 2.0 30.5 1.0 O2G B:DZ4701 2.1 35.8 1.0 O9 A:CZF706 2.1 29.1 1.0 O12 A:CZF706 2.1 26.4 1.0 O14 A:CZF706 2.2 33.1 1.0 P2 A:CZF706 3.1 31.1 1.0 PB B:DZ4701 3.3 32.4 1.0 P1 A:CZF706 3.3 31.2 1.0 P3 A:CZF706 3.3 33.1 1.0 PG B:DZ4701 3.3 35.8 1.0 O10 A:CZF706 3.4 28.1 1.0 O7 A:CZF706 3.5 31.8 1.0 O3B B:DZ4701 3.5 35.4 1.0 O3 A:CZF706 3.9 29.0 1.0 O1G B:DZ4701 4.0 31.0 1.0 O15 A:CZF706 4.1 31.3 1.0 O2B B:DZ4701 4.2 26.1 1.0 O5 A:CZF706 4.2 32.2 1.0 C8 A:CZF706 4.3 30.7 1.0 O B:HOH804 4.4 41.5 1.0 O11 A:CZF706 4.4 29.1 1.0 N3A B:DZ4701 4.4 28.1 1.0 O A:HOH838 4.4 34.8 1.0 O3G B:DZ4701 4.4 34.0 1.0 O13 A:CZF706 4.5 34.8 1.0 CE A:LYS116 4.5 34.1 1.0 O8 A:CZF706 4.5 29.8 1.0 C4 A:CZF706 4.6 28.1 1.0 C6 A:CZF706 4.9 29.7 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, 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 D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:36.0 occ:1.00 O B:HOH822 2.2 37.2 1.0 O2A B:DZ4706 2.2 28.7 1.0 O B:HOH818 2.3 39.3 1.0 NE2 B:HIS233 2.3 41.6 1.0 OD1 B:ASP207 2.3 33.5 1.0 O B:HOH812 2.4 32.5 1.0 CE1 B:HIS233 3.1 40.6 1.0 PA B:DZ4706 3.3 28.5 1.0 CD2 B:HIS233 3.3 37.9 1.0 CG B:ASP207 3.4 30.2 1.0 N3A B:DZ4706 3.8 27.5 1.0 OD2 B:ASP207 3.8 27.8 1.0 FE B:FE702 3.9 28.7 1.0 O1A B:DZ4706 4.0 26.7 1.0 CD2 B:HIS206 4.0 34.9 1.0 NE2 B:HIS210 4.0 30.3 1.0 OE2 B:GLU234 4.2 43.1 1.0 O2B B:DZ4706 4.3 27.3 1.0 ND1 B:HIS233 4.3 40.7 1.0 PB B:DZ4706 4.3 30.7 1.0 O B:HOH860 4.4 40.4 1.0 O B:HIS206 4.4 30.3 1.0 NE2 B:HIS206 4.4 35.8 1.0 CG B:HIS233 4.4 37.5 1.0 O1B B:DZ4706 4.5 29.5 1.0 CD B:GLU234 4.6 42.7 1.0 O5' B:DZ4706 4.6 25.8 1.0 CG B:GLU234 4.6 40.0 1.0 CD2 B:HIS210 4.7 29.7 1.0 CB B:ASP207 4.7 29.8 1.0 OD2 B:ASP311 4.7 27.1 1.0 O B:HOH851 4.8 30.4 1.0 CA B:ASP207 4.9 30.8 1.0 O B:HOH844 4.9 43.2 1.0 OD1 B:ASP311 5.0 30.1 1.0 CE1 B:HIS210 5.0 30.9 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, 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 D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:37.9 occ:1.00 O B:HOH820 1.7 38.3 1.0 O1B B:DZ4706 1.9 29.5 1.0 O B:HOH829 2.1 35.2 1.0 O1G B:DZ4706 2.1 30.4 1.0 O B:HOH844 2.1 43.2 1.0 O B:HOH847 2.2 46.8 1.0 PB B:DZ4706 3.2 30.7 1.0 PG B:DZ4706 3.3 31.8 1.0 O3B B:DZ4706 3.6 30.4 1.0 O B:HOH822 3.8 37.2 1.0 OD2 B:ASP311 4.0 27.1 1.0 NZ B:LYS312 4.0 29.9 1.0 OD2 B:ASP309 4.1 37.8 1.0 O B:HOH851 4.2 30.4 1.0 N3A B:DZ4706 4.2 27.5 1.0 O3G B:DZ4706 4.3 31.4 1.0 O2G B:DZ4706 4.4 30.7 1.0 O2B B:DZ4706 4.4 27.3 1.0 OD1 B:ASP309 4.4 33.8 1.0 O B:HOH807 4.5 36.9 1.0 CG B:ASP309 4.7 36.0 1.0 O B:HOH805 4.8 36.6 1.0 OG B:SER302 4.8 34.5 1.0 O B:HOH828 4.9 37.2 1.0 O B:HOH812 4.9 32.5 1.0 CG B:ASP311 5.0 29.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, 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 D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:35.4 occ:1.00 O14 B:CZF707 1.9 36.8 1.0 O2G A:DZ4707 2.1 32.2 1.0 O1B A:DZ4707 2.1 30.9 1.0 O12 B:CZF707 2.2 33.7 1.0 O9 B:CZF707 2.2 33.0 1.0 O A:HOH845 2.2 27.9 1.0 P3 B:CZF707 3.1 38.4 1.0 P2 B:CZF707 3.2 34.6 1.0 PG A:DZ4707 3.3 35.4 1.0 O10 B:CZF707 3.4 36.6 1.0 PB A:DZ4707 3.4 32.0 1.0 P1 B:CZF707 3.4 39.6 1.0 O3B A:DZ4707 3.5 33.2 1.0 O7 B:CZF707 3.6 37.3 1.0 O3 B:CZF707 3.9 28.0 1.0 O15 B:CZF707 4.1 38.8 1.0 O1G A:DZ4707 4.1 33.0 1.0 O13 B:CZF707 4.1 42.9 1.0 O2B A:DZ4707 4.2 29.8 1.0 C8 B:CZF707 4.3 33.7 1.0 O5 B:CZF707 4.4 36.9 1.0 O3G A:DZ4707 4.5 34.3 1.0 O8 B:CZF707 4.5 38.5 1.0 O11 B:CZF707 4.6 35.6 1.0 C4 B:CZF707 4.6 29.7 1.0 N3A A:DZ4707 4.6 29.1 1.0 NZ B:LYS116 4.8 32.2 1.0 O B:HOH866 4.8 42.0 1.0 CE B:LYS116 4.9 33.4 1.0 C6 B:CZF707 4.9 31.0 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