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

The structure of Crystal Structure of the Tetrameric Dgtp/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qfy 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)	38.67 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.966, 147.021, 98.873, 90.00, 114.31, 90.00
R / Rfree (%)	22.6 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Dgtp/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core (pdb code 4qfy). 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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qfy:
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/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:34.5 occ:1.00 O1G A:DCP702 2.0 29.1 0.9 O1B A:DCP702 2.0 26.0 0.9 O A:HOH804 2.3 27.1 1.0 PG A:DCP702 3.2 31.2 0.9 PB A:DCP702 3.3 31.0 0.9 O3B A:DCP702 3.6 31.8 0.9 NZ A:LYS312 3.8 24.7 1.0 O2G A:DCP702 4.0 29.9 0.9 OD2 A:ASP309 4.0 28.7 0.8 O A:HOH869 4.0 33.4 0.9 O2B A:DCP702 4.2 31.8 0.9 NH1 A:ARG206 4.2 27.4 0.9 NH2 A:ARG206 4.2 29.7 0.9 O3A A:DCP702 4.4 30.2 0.9 O A:HOH856 4.4 35.7 0.9 O3G A:DCP702 4.4 31.0 0.9 OD1 A:ASP309 4.5 26.2 0.8 CG A:ASP309 4.7 31.0 0.8 CZ A:ARG206 4.7 29.1 0.9 OD2 A:ASP311 4.8 28.0 0.8

Magnesium binding site 2 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:19.4 occ:1.00 O2B B:DGT702 2.0 17.0 0.9 O2B A:DGT704 2.1 16.7 0.9 O1G B:DGT702 2.1 16.6 0.9 O3G A:DGT704 2.1 20.3 0.9 O2A A:DGT704 2.3 16.0 0.9 PG B:DGT702 3.2 21.1 0.9 PB B:DGT702 3.2 18.2 0.9 PB A:DGT704 3.3 23.4 0.9 PG A:DGT704 3.3 23.0 0.9 O3B B:DGT702 3.5 19.8 0.9 PA A:DGT704 3.6 17.7 0.9 O3B A:DGT704 3.6 21.5 0.9 NZ B:LYS523 3.7 26.1 0.9 NZ A:LYS116 3.8 20.4 1.0 O3A A:DGT704 3.8 17.5 0.9 O3' A:DGT704 3.9 17.4 0.9 O3G B:DGT702 3.9 17.2 0.9 O A:HOH838 4.2 26.1 1.0 O1B B:DGT702 4.2 17.4 0.9 O3A B:DGT702 4.2 22.3 0.9 C5' A:DGT704 4.3 16.6 0.9 O2G A:DGT704 4.3 25.8 0.9 O1G A:DGT704 4.3 20.5 0.9 O2G B:DGT702 4.4 22.0 0.9 O5' A:DGT704 4.4 22.1 0.9 O1B A:DGT704 4.5 22.2 0.9 O A:HOH803 4.5 16.1 1.0 C3' A:DGT704 4.5 16.7 0.9 CE B:LYS523 4.6 25.6 0.9 O1A A:DGT704 4.6 20.1 0.9 CE A:LYS116 4.9 24.8 1.0 C4' A:DGT704 4.9 16.9 0.9 O B:HOH830 4.9 22.3 0.9

Magnesium binding site 3 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:26.9 occ:1.00 O2B A:DGT703 2.0 28.0 0.9 O2G C:DGT703 2.0 30.3 0.9 O1B C:DGT703 2.1 25.1 0.9 O1A C:DGT703 2.1 21.5 0.9 O3G A:DGT703 2.2 29.1 0.9 PB C:DGT703 3.2 27.3 0.9 PG C:DGT703 3.2 27.0 0.9 PB A:DGT703 3.3 24.1 0.9 PG A:DGT703 3.4 30.2 0.9 PA C:DGT703 3.4 22.7 0.9 O3B C:DGT703 3.6 27.2 0.9 O3B A:DGT703 3.7 31.1 0.9 NZ B:LYS116 3.7 22.5 1.0 O3A C:DGT703 3.7 25.6 0.9 O3' C:DGT703 3.9 22.0 0.9 C5' C:DGT703 4.1 21.9 0.9 O1G A:DGT703 4.1 25.2 0.9 O1G C:DGT703 4.2 27.9 0.9 O1B A:DGT703 4.2 22.1 0.9 NZ A:LYS523 4.2 31.9 1.0 O5' C:DGT703 4.2 25.5 0.9 O3G C:DGT703 4.3 26.1 0.9 O3A A:DGT703 4.3 28.9 0.9 C3' C:DGT703 4.4 22.4 0.9 O C:HOH820 4.5 24.6 0.9 O2A C:DGT703 4.5 24.5 0.9 O2B C:DGT703 4.5 27.7 0.9 O2G A:DGT703 4.5 32.9 0.9 C4' C:DGT703 4.8 23.0 0.9 CE B:LYS116 4.9 21.4 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:23.4 occ:0.87 O2B B:DCP701 2.0 20.7 0.9 O3G B:DCP701 2.1 17.1 0.9 O B:HOH825 2.2 16.9 0.9 O B:HOH805 2.2 18.2 0.9 O B:HOH802 2.2 16.4 1.0 PB B:DCP701 3.3 23.4 0.9 PG B:DCP701 3.3 23.7 0.9 O3B B:DCP701 3.6 23.4 0.9 NZ B:LYS312 3.9 17.0 1.0 O1G B:DCP701 3.9 18.7 0.9 O B:HOH875 4.0 23.3 0.8 O1B B:DCP701 4.0 20.3 0.9 NH2 B:ARG206 4.0 21.6 1.0 OD2 B:ASP309 4.1 16.6 0.9 O B:HOH860 4.2 22.4 0.8 NH1 B:ARG206 4.2 18.0 1.0 O3A B:DCP701 4.4 21.2 0.9 O2G B:DCP701 4.5 19.9 0.9 CZ B:ARG206 4.6 21.7 1.0 OD1 B:ASP309 4.7 19.4 0.9 OD2 B:ASP311 4.8 18.4 0.9 OG B:SER302 4.9 27.3 0.9 CG B:ASP309 4.9 17.2 0.9

Magnesium binding site 5 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:22.6 occ:0.89 O3G A:DGT701 1.9 25.6 1.0 O2G C:DGT701 2.0 20.1 1.0 O2B A:DGT701 2.0 26.1 1.0 O1B C:DGT701 2.0 20.8 1.0 O C:HOH801 2.2 17.2 1.0 O2A A:DGT701 2.3 23.4 1.0 PB A:DGT701 3.1 30.7 1.0 PG A:DGT701 3.2 28.2 1.0 PG C:DGT701 3.2 28.1 1.0 PB C:DGT701 3.3 22.8 1.0 O3B A:DGT701 3.4 25.8 1.0 PA A:DGT701 3.5 24.0 1.0 O3B C:DGT701 3.5 29.0 1.0 O3A A:DGT701 3.7 23.5 1.0 NZ D:LYS116 3.8 22.1 1.0 NZ C:LYS523 3.8 30.5 0.9 O2G A:DGT701 4.0 30.7 1.0 O3G C:DGT701 4.0 27.0 1.0 O3' A:DGT701 4.1 21.1 1.0 O2B C:DGT701 4.2 21.6 1.0 C5' A:DGT701 4.2 20.3 1.0 O1G A:DGT701 4.3 19.8 1.0 O3A C:DGT701 4.3 26.6 1.0 O1B A:DGT701 4.4 25.6 1.0 O5' A:DGT701 4.4 19.2 1.0 O1G C:DGT701 4.4 25.8 1.0 O A:HOH834 4.6 21.3 0.9 O1A A:DGT701 4.6 17.4 1.0 C3' A:DGT701 4.7 22.1 1.0 CE C:LYS523 4.8 33.8 0.9 C4' A:DGT701 5.0 20.4 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg706 b:35.9 occ:1.00 O3G C:DCP704 2.0 26.1 0.9 O2B C:DCP704 2.0 27.0 0.9 O C:HOH809 2.2 26.5 1.0 PG C:DCP704 3.3 30.0 0.9 PB C:DCP704 3.3 30.9 0.9 O3B C:DCP704 3.6 30.4 0.9 NZ C:LYS312 3.7 23.6 1.0 O1G C:DCP704 3.9 29.6 0.9 O C:HOH854 3.9 35.7 0.9 NH2 C:ARG206 4.1 26.2 1.0 O1B C:DCP704 4.1 32.2 0.9 OD2 C:ASP309 4.1 26.7 1.0 O C:HOH861 4.3 32.3 0.9 NH1 C:ARG206 4.4 22.9 1.0 O3A C:DCP704 4.4 34.2 0.9 O C:HOH871 4.4 34.2 1.0 O2G C:DCP704 4.5 28.4 0.9 CZ C:ARG206 4.7 25.9 1.0 CE C:LYS312 4.7 25.7 1.0 OD1 C:ASP309 4.8 26.1 1.0 CG C:ASP309 4.9 27.1 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg707 b:22.9 occ:0.95 O3G D:DGT701 2.0 22.0 1.0 O1G C:DGT702 2.0 24.1 1.0 O1B D:DGT701 2.0 21.4 1.0 O1B C:DGT702 2.0 22.8 1.0 O C:HOH873 2.2 20.6 1.0 O1A C:DGT702 2.2 21.6 1.0 PB C:DGT702 3.1 24.5 1.0 PG D:DGT701 3.2 25.2 1.0 PG C:DGT702 3.2 26.0 1.0 PB D:DGT701 3.3 22.3 1.0 PA C:DGT702 3.5 21.8 1.0 O3B D:DGT701 3.5 26.4 1.0 O3B C:DGT702 3.5 28.3 1.0 O3A C:DGT702 3.7 23.4 1.0 NZ C:LYS116 3.9 21.6 1.0 O2G D:DGT701 3.9 22.3 1.0 NZ D:LYS523 4.0 26.8 0.9 O3' C:DGT702 4.1 21.4 1.0 O2B D:DGT701 4.1 19.9 1.0 O2G C:DGT702 4.1 27.6 1.0 C5' C:DGT702 4.2 19.3 1.0 O3G C:DGT702 4.3 23.1 1.0 O3A D:DGT701 4.3 27.3 1.0 O D:HOH916 4.3 30.2 0.7 O5' C:DGT702 4.3 20.4 1.0 O1G D:DGT701 4.4 26.5 1.0 O2B C:DGT702 4.4 23.0 1.0 O2A C:DGT702 4.6 21.9 1.0 O C:HOH805 4.6 21.2 1.0 C3' C:DGT702 4.6 18.6 1.0 C4' C:DGT702 4.9 19.2 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of the Tetrameric Dgtp/Dctp-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/Dctp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:17.4 occ:0.84 O1B D:DCP702 1.9 21.2 0.9 O D:HOH851 2.1 20.0 0.9 O D:HOH811 2.1 18.8 1.0 O3G D:DCP702 2.1 18.0 0.9 O D:HOH803 2.1 18.0 0.9 O D:HOH823 2.1 18.4 0.9 PB D:DCP702 3.2 19.1 0.9 PG D:DCP702 3.3 21.1 0.9 O3B D:DCP702 3.6 21.1 0.9 O2G D:DCP702 3.9 21.3 0.9 NZ D:LYS312 4.0 18.3 1.0 O2B D:DCP702 4.0 20.2 0.9 NH1 D:ARG206 4.0 17.2 1.0 NH2 D:ARG206 4.0 20.9 1.0 OD2 D:ASP309 4.1 18.8 1.0 O D:HOH863 4.1 23.5 0.8 O D:HOH861 4.2 22.3 0.9 O D:HOH883 4.2 25.3 0.8 O3A D:DCP702 4.3 22.2 0.9 O1G D:DCP702 4.5 22.3 0.9 CZ D:ARG206 4.5 18.9 1.0 OD2 D:ASP311 4.6 18.4 0.9 OD1 D:ASP309 4.7 21.6 1.0 CG D:ASP309 4.8 22.4 1.0 O D:HOH850 4.9 22.4 0.9

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