Magnesium in PDB 6yom: Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg, PDB code: 6yom 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)	92.72 / 3.25
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.298, 105.298, 195.629, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.6

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

Manganese	(Mn)	2 atoms
Iron	(Fe)	2 atoms

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

Magnesium binding site 1 out of 4 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn 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, Datp, Dcmpnpp, Mn and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:45.6 occ:1.00 O3G A:0KX705 2.2 60.1 1.0 O1B A:0KX705 2.5 66.4 1.0 PB A:0KX705 3.5 62.9 1.0 O3B A:0KX705 3.5 58.7 1.0 PG A:0KX705 3.5 59.5 1.0 OD2 A:ASP311 3.6 71.9 1.0 OD2 A:ASP309 3.7 71.6 1.0 OD1 A:ASP309 3.7 68.7 1.0 OG A:SER302 3.8 72.0 1.0 CG A:ASP309 4.1 67.6 1.0 NZ A:LYS312 4.1 67.2 1.0 N3A A:0KX705 4.3 62.5 1.0 O2G A:0KX705 4.4 62.6 1.0 O1G A:0KX705 4.6 53.1 1.0 CG A:ASP311 4.7 65.9 1.0 O2B A:0KX705 4.7 64.2 1.0 CB A:ASP311 4.9 64.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn 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, Datp, Dcmpnpp, Mn and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:45.4 occ:1.00 O14 A:CZF706 2.2 69.5 1.0 O9 A:CZF706 2.2 66.3 1.0 O2B B:DTP701 2.3 71.8 1.0 O12 A:CZF706 2.4 61.5 1.0 O1G B:DTP701 2.5 66.8 1.0 O3 A:CZF706 3.5 60.2 1.0 P3 A:CZF706 3.5 68.3 1.0 PG B:DTP701 3.5 71.7 1.0 P2 A:CZF706 3.6 67.5 1.0 PB B:DTP701 3.6 66.9 1.0 P1 A:CZF706 3.6 66.1 1.0 O3G B:DTP701 3.7 65.7 1.0 O3B B:DTP701 3.8 70.1 1.0 O13 A:CZF706 3.9 69.9 1.0 O10 A:CZF706 3.9 66.8 1.0 O7 A:CZF706 4.1 65.2 1.0 C4 A:CZF706 4.2 61.1 1.0 CE A:LYS116 4.2 67.2 1.0 C8 A:CZF706 4.3 62.7 1.0 O5 A:CZF706 4.5 64.9 1.0 O3A B:DTP701 4.6 58.4 1.0 O1B B:DTP701 4.7 64.5 1.0 C6 A:CZF706 4.7 60.8 1.0 O15 A:CZF706 4.7 67.2 1.0 O8 A:CZF706 4.8 65.2 1.0 O2G B:DTP701 4.9 68.1 1.0 O11 A:CZF706 4.9 72.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn 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, Datp, Dcmpnpp, Mn and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:50.2 occ:1.00 O3G B:0KX706 2.1 68.8 1.0 O1B B:0KX706 2.5 71.7 1.0 OD2 B:ASP309 3.2 71.2 1.0 OD1 B:ASP309 3.3 68.1 1.0 PG B:0KX706 3.4 66.9 1.0 O3B B:0KX706 3.6 65.8 1.0 PB B:0KX706 3.6 70.3 1.0 NZ B:LYS312 3.6 69.2 1.0 CG B:ASP309 3.7 70.5 1.0 OD2 B:ASP311 3.9 77.8 1.0 OG B:SER302 4.0 77.9 1.0 O1G B:0KX706 4.0 60.8 1.0 N3A B:0KX706 4.6 69.4 1.0 O2G B:0KX706 4.6 69.3 1.0 O2B B:0KX706 4.8 69.4 1.0 CG B:ASP311 4.9 68.1 1.0 CB B:ASP311 4.9 65.0 1.0 CE B:LYS312 5.0 67.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn 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, Datp, Dcmpnpp, Mn and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:58.5 occ:1.00 O1B A:DTP707 2.0 73.7 1.0 O9 B:CZF707 2.2 73.3 1.0 O12 B:CZF707 2.3 68.4 1.0 O14 B:CZF707 2.4 74.9 1.0 O3G A:DTP707 2.4 69.6 1.0 P2 B:CZF707 3.3 74.5 1.0 PB A:DTP707 3.4 70.3 1.0 P1 B:CZF707 3.5 74.2 1.0 P3 B:CZF707 3.5 72.3 1.0 O10 B:CZF707 3.6 73.5 1.0 O3 B:CZF707 3.6 60.6 1.0 PG A:DTP707 3.7 66.9 1.0 O7 B:CZF707 3.7 71.9 1.0 O3B A:DTP707 3.9 68.9 1.0 CE B:LYS116 4.0 76.5 1.0 O13 B:CZF707 4.0 71.0 1.0 C8 B:CZF707 4.2 65.6 1.0 C4 B:CZF707 4.3 59.9 1.0 O5 B:CZF707 4.3 72.3 1.0 O2B A:DTP707 4.3 66.3 1.0 O3A A:DTP707 4.4 65.6 1.0 O2G A:DTP707 4.5 63.1 1.0 O8 B:CZF707 4.6 77.5 1.0 NZ B:LYS116 4.7 76.2 1.0 O11 B:CZF707 4.7 74.5 1.0 O1G A:DTP707 4.7 69.1 1.0 O15 B:CZF707 4.8 74.4 1.0 C6 B:CZF707 4.8 61.2 1.0 CG B:LYS116 5.0 74.1 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