Magnesium in PDB 4qfx: Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core

The structure of Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qfx was solved by L.M.I.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.34 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.561, 147.264, 98.795, 90.00, 114.63, 90.00
R / Rfree (%)	22.8 / 27

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core (pdb code 4qfx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qfx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:41.7 occ:0.94 O1G A:DTP703 1.9 39.5 1.0 O1B A:DTP703 2.0 33.4 0.6 O1G C:DGT702 2.0 38.4 0.8 O1B C:DGT702 2.1 34.9 0.8 O1A C:DGT702 2.2 28.3 0.8 PG A:DTP703 3.2 38.8 0.8 PB C:DGT702 3.2 38.8 0.8 PG C:DGT702 3.2 37.5 0.8 PB A:DTP703 3.3 34.4 0.9 PA C:DGT702 3.5 31.6 0.8 O3B C:DGT702 3.5 35.3 0.8 O3B A:DTP703 3.6 43.7 0.8 NZ B:LYS116 3.7 32.6 0.9 O3A C:DGT702 3.8 33.4 0.8 NZ A:LYS523 3.9 47.8 0.9 O3G A:DTP703 3.9 37.5 1.0 O3' C:DGT702 4.1 32.9 0.8 O C:HOH862 4.1 51.9 1.0 O3G C:DGT702 4.2 35.5 0.8 C5' C:DGT702 4.2 32.6 0.8 O2G C:DGT702 4.2 39.4 0.8 O2B A:DTP703 4.2 29.7 0.9 O3A A:DTP703 4.3 37.0 0.8 O5' C:DGT702 4.4 34.9 0.8 O C:HOH812 4.4 34.5 0.9 O2G A:DTP703 4.4 41.6 0.8 O2B C:DGT702 4.5 36.2 0.8 O2A C:DGT702 4.5 34.0 0.8 CE A:LYS523 4.6 44.5 0.9 C3' C:DGT702 4.6 34.9 0.8 CE B:LYS116 4.9 32.5 0.9 C4' C:DGT702 4.9 31.6 0.8

Magnesium binding site 2 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:34.7 occ:0.96 O3G A:DGT704 2.0 32.4 0.8 O1B B:DTP703 2.0 25.8 0.8 O2B A:DGT704 2.1 25.3 0.8 O3G B:DTP703 2.1 28.5 1.0 O2A A:DGT704 2.3 21.4 0.8 PB A:DGT704 3.2 29.4 0.8 PG A:DGT704 3.3 39.5 0.8 PG B:DTP703 3.3 29.2 0.8 PB B:DTP703 3.3 26.7 0.9 PA A:DGT704 3.5 29.6 0.8 O3B B:DTP703 3.6 31.0 0.6 O3B A:DGT704 3.6 35.9 0.8 NZ A:LYS116 3.6 29.1 0.9 O3A A:DGT704 3.8 31.2 0.8 O1G B:DTP703 3.9 30.7 1.0 NZ B:LYS523 3.9 43.6 0.9 O3' A:DGT704 4.1 29.4 0.8 O1G A:DGT704 4.2 31.3 0.8 C5' A:DGT704 4.2 24.3 0.8 O2B B:DTP703 4.2 24.9 0.7 O2G A:DGT704 4.2 30.0 0.8 O3A B:DTP703 4.3 29.8 0.7 O5' A:DGT704 4.3 33.9 0.8 O A:HOH862 4.4 31.1 0.8 O1B A:DGT704 4.5 30.4 0.8 O2G B:DTP703 4.5 29.9 0.9 C3' A:DGT704 4.5 27.7 0.8 O A:HOH865 4.6 42.7 1.0 O1A A:DGT704 4.6 28.7 0.8 CE A:LYS116 4.8 40.0 0.9 C4' A:DGT704 4.9 25.9 0.8 CE B:LYS523 4.9 41.6 0.9 CD A:LYS116 5.0 35.9 0.9 O B:HOH815 5.0 40.6 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg707 b:48.0 occ:1.00 O A:HOH873 2.2 39.3 1.0 O2B A:DGT702 2.3 31.1 0.8 O2G A:DGT702 2.6 40.4 0.8 O A:HOH869 2.7 43.3 1.0 PB A:DGT702 3.5 37.3 0.8 OD1 A:ASP309 3.5 34.3 0.9 OD2 A:ASP311 3.6 43.4 0.7 NH1 A:ARG206 3.6 35.5 0.8 OD2 A:ASP309 3.6 40.3 0.9 PG A:DGT702 3.6 37.0 0.8 O3B A:DGT702 3.7 39.4 0.8 NH2 A:ARG206 3.8 34.4 0.8 NZ A:LYS312 3.8 40.4 0.9 CG A:ASP309 4.0 41.0 0.9 CZ A:ARG206 4.1 37.4 0.8 O3A A:DGT702 4.2 43.6 0.8 CG A:ASP311 4.3 33.7 0.7 O3G A:DGT702 4.3 39.2 0.8 CG A:LYS312 4.3 32.7 0.9 CB A:ASP311 4.4 32.1 0.7 O A:HOH851 4.6 38.7 0.8 O1B A:DGT702 4.7 36.3 0.8 O1G A:DGT702 4.9 33.4 0.8 N A:LYS312 4.9 23.8 0.9 CE A:LYS312 4.9 40.2 0.9

Magnesium binding site 4 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:41.1 occ:0.99 O1B B:DGT702 2.0 35.7 0.7 O2G B:DGT702 2.2 28.3 0.7 O B:HOH878 2.2 36.6 1.0 O B:HOH905 2.2 39.1 1.0 PB B:DGT702 3.3 32.1 0.7 PG B:DGT702 3.3 32.4 0.7 O3B B:DGT702 3.7 36.6 0.7 O3G B:DGT702 3.9 28.8 0.7 NZ B:LYS312 4.0 29.4 0.9 O2B B:DGT702 4.1 34.1 0.7 NH2 B:ARG206 4.1 34.3 0.9 O B:HOH829 4.1 36.8 0.9 O B:HOH845 4.1 43.4 0.9 OD2 B:ASP309 4.2 29.5 0.8 NH1 B:ARG206 4.2 28.0 0.9 O B:HOH893 4.4 41.1 1.0 O3A B:DGT702 4.4 29.8 0.7 O1G B:DGT702 4.5 37.4 0.7 CZ B:ARG206 4.7 33.0 0.9 OD1 B:ASP309 4.8 29.5 0.8 OG B:SER302 4.8 40.2 0.8 O B:HOH890 4.9 43.1 1.0 CG B:ASP309 4.9 27.9 0.8 OD2 B:ASP311 5.0 26.9 0.7

Magnesium binding site 5 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:33.7 occ:0.99 O3G A:DGT701 2.0 34.5 0.8 O2B C:DTP701 2.0 30.3 1.0 O3G C:DTP701 2.1 31.5 1.0 O2B A:DGT701 2.2 28.8 0.8 O2A A:DGT701 2.2 30.2 0.8 PG A:DGT701 3.3 36.8 0.8 PB A:DGT701 3.3 34.4 0.8 PG C:DTP701 3.3 29.8 0.8 PB C:DTP701 3.4 32.7 0.9 PA A:DGT701 3.5 31.7 0.8 NZ D:LYS116 3.6 32.8 0.9 O3B A:DGT701 3.6 30.6 0.8 NZ C:LYS523 3.7 47.2 0.9 O3B C:DTP701 3.7 33.1 0.5 O3A A:DGT701 3.9 36.0 0.8 O3' A:DGT701 3.9 31.1 0.8 O1G C:DTP701 3.9 36.2 0.8 O2G A:DGT701 4.2 39.8 0.8 C5' A:DGT701 4.2 26.7 0.8 O1G A:DGT701 4.3 32.5 0.8 O3A C:DTP701 4.3 36.4 0.6 O1B C:DTP701 4.4 30.8 0.8 O5' A:DGT701 4.4 30.4 0.8 O D:HOH855 4.5 29.3 0.8 CE C:LYS523 4.5 46.9 0.9 O2G C:DTP701 4.5 38.5 0.9 O1B A:DGT701 4.6 32.3 0.8 C3' A:DGT701 4.6 35.0 0.8 O1A A:DGT701 4.6 24.0 0.8 O D:HOH889 4.6 44.5 1.0 O C:HOH803 4.8 41.1 1.0 CE D:LYS116 4.9 31.5 0.9 C4' A:DGT701 4.9 31.4 0.8

Magnesium binding site 6 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:37.8 occ:0.83 O B:HOH842 2.7 32.7 0.9 O1G B:DGT701 2.9 38.4 0.9 O2B D:DTP701 2.9 35.7 1.0 O1A B:DGT701 2.9 30.8 0.9 O1G D:DTP701 3.2 36.5 1.0 NZ C:LYS116 3.3 23.5 0.8 O3' B:DGT701 3.3 30.6 0.9 CG C:LYS116 3.8 30.2 0.8 O D:HOH843 3.9 37.8 0.9 O3G D:DTP701 3.9 33.1 1.0 CD C:LYS116 3.9 34.9 0.8 PG D:DTP701 4.1 31.8 0.8 CE C:LYS116 4.2 28.0 0.8 PB D:DTP701 4.2 32.9 0.9 C3' B:DGT701 4.2 30.4 0.9 O1B B:DGT701 4.2 31.8 0.9 CB C:LYS116 4.4 32.1 0.8 PG B:DGT701 4.4 32.6 0.9 PA B:DGT701 4.4 32.1 0.9 O3A D:DTP701 4.5 33.5 0.6 CA C:LYS116 4.6 33.5 0.8 O3B D:DTP701 4.7 32.0 0.6 NZ D:LYS523 4.7 47.0 0.9 O C:MET115 4.8 37.5 0.8 O3G B:DGT701 4.8 29.7 0.9 C5' B:DGT701 5.0 36.2 0.9

Magnesium binding site 7 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg706 b:42.0 occ:0.94 O2G C:DGT703 2.0 34.9 0.8 O1B C:DGT703 2.0 41.3 0.8 O C:HOH860 2.2 49.8 1.0 O C:HOH857 2.3 49.4 1.0 PG C:DGT703 3.2 36.1 0.8 NZ C:LYS312 3.2 30.4 0.9 PB C:DGT703 3.2 41.6 0.8 O3B C:DGT703 3.5 38.1 0.8 OD2 C:ASP309 3.8 36.8 0.8 NH2 C:ARG206 3.9 41.9 0.9 O3G C:DGT703 4.0 42.0 0.8 NH1 C:ARG206 4.0 38.1 0.9 OD1 C:ASP309 4.1 33.4 0.8 O3A C:DGT703 4.2 49.1 0.8 O2B C:DGT703 4.3 45.0 0.8 O1G C:DGT703 4.3 38.8 0.8 O C:HOH845 4.3 41.7 1.0 CG C:ASP309 4.4 39.1 0.8 CE C:LYS312 4.4 34.3 0.9 CZ C:ARG206 4.4 44.0 0.9 OD2 C:ASP311 4.6 42.0 0.8 CG C:LYS312 4.6 34.3 0.9 OG C:SER302 5.0 56.0 0.9

Magnesium binding site 8 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


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 the Tetrameric Dgtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:40.0 occ:1.00 O2B D:DGT702 2.1 29.0 0.8 O2G D:DGT702 2.1 26.7 0.8 O D:HOH890 2.3 38.9 1.0 PG D:DGT702 3.3 31.3 0.8 PB D:DGT702 3.3 34.2 0.8 NZ D:LYS312 3.6 27.8 0.9 O3B D:DGT702 3.7 33.2 0.8 O1G D:DGT702 3.9 27.8 0.8 OD2 D:ASP309 3.9 31.2 0.9 O D:HOH884 3.9 43.2 1.0 NH1 D:ARG206 4.1 31.3 0.9 O1B D:DGT702 4.1 30.9 0.8 NH2 D:ARG206 4.2 35.3 0.9 O D:HOH883 4.3 37.5 1.0 OD1 D:ASP309 4.4 38.5 0.9 O3A D:DGT702 4.5 41.5 0.8 O3G D:DGT702 4.5 28.1 0.8 CG D:ASP309 4.6 30.8 0.9 O D:HOH825 4.6 37.9 0.9 CZ D:ARG206 4.7 31.1 0.9 CE D:LYS312 4.8 28.6 0.9 OD2 D:ASP311 4.8 28.6 0.8

L.M.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn. Structural Basis of Allosteric Activation of Sterile Alpha Motif and Histidine-Aspartate Domain Containing Protein 1 (SAMHD1) By Nucleoside Triphosphates. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25288794
DOI: 10.1074/JBC.M114.591958