Magnesium in PDB 4qg0: Crystal Structure of the Tetrameric Dgtp/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core

The structure of Crystal Structure of the Tetrameric Dgtp/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qg0 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)	42.91 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.856, 146.596, 98.686, 90.00, 114.62, 90.00
R / Rfree (%)	19.7 / 25

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Dgtp/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core (pdb code 4qg0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Tetrameric Dgtp/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qg0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:32.0 occ:0.80 O1G C:DGT702 2.0 42.5 0.9 O1B A:DUT703 2.0 34.2 0.9 O1A C:DGT702 2.0 34.7 0.9 O1B C:DGT702 2.1 33.7 0.9 O1G A:DUT703 2.1 33.9 0.9 O C:HOH805 2.2 30.1 0.9 PB C:DGT702 3.2 45.0 0.9 PG C:DGT702 3.2 36.4 0.9 PA C:DGT702 3.3 33.6 0.9 PB A:DUT703 3.3 32.5 0.9 PG A:DUT703 3.4 37.6 0.9 O3B C:DGT702 3.5 38.0 0.9 O3A C:DGT702 3.6 41.9 0.9 O3B A:DUT703 3.7 44.5 0.9 NZ B:LYS116 3.8 41.4 0.9 O3' C:DGT702 3.9 32.6 0.9 C5' C:DGT702 3.9 32.3 0.9 NZ A:LYS523 4.0 48.2 0.9 O2B A:DUT703 4.1 27.0 0.9 O2G C:DGT702 4.1 45.6 0.9 O5' C:DGT702 4.1 39.6 0.9 O3G C:DGT702 4.2 41.5 0.9 O3G A:DUT703 4.2 36.2 0.9 C3' C:DGT702 4.3 30.9 0.9 O3A A:DUT703 4.3 39.5 0.9 O2A C:DGT702 4.4 37.6 0.9 O2B C:DGT702 4.4 40.2 0.9 O2G A:DUT703 4.5 43.6 0.9 C4' C:DGT702 4.6 33.8 0.9 O C:HOH829 4.7 31.8 0.8 NZ C:LYS377 4.8 54.9 0.8 CE B:LYS116 4.9 37.3 0.9 CE A:LYS523 5.0 46.8 0.9

Magnesium binding site 2 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:26.2 occ:0.90 O2G B:DUT703 2.0 25.9 0.9 O1G D:DGT702 2.0 26.0 0.9 O1B D:DGT702 2.0 22.9 0.9 O1B B:DUT703 2.1 25.6 0.9 O1A D:DGT702 2.2 20.9 0.9 PB D:DGT702 3.2 31.6 0.9 PG D:DGT702 3.3 31.9 0.9 PG B:DUT703 3.3 27.8 0.9 PB B:DUT703 3.3 22.4 0.9 PA D:DGT702 3.5 29.6 0.9 O3B B:DUT703 3.6 30.5 0.9 O3B D:DGT702 3.6 35.1 0.9 O3A D:DGT702 3.8 30.8 0.9 NZ A:LYS116 3.9 30.0 0.9 O1G B:DUT703 4.0 28.8 0.9 O3' D:DGT702 4.0 27.0 0.9 O2B B:DUT703 4.1 31.3 0.9 O3G D:DGT702 4.1 30.2 0.9 C5' D:DGT702 4.2 25.1 0.9 O2G D:DGT702 4.3 34.9 0.9 NZ B:LYS523 4.3 38.9 0.8 O3A B:DUT703 4.3 32.2 0.9 O5' D:DGT702 4.4 29.4 0.9 O3G B:DUT703 4.4 34.2 0.9 O2B D:DGT702 4.5 29.9 0.9 O2A D:DGT702 4.6 26.0 0.9 C3' D:DGT702 4.6 28.3 0.9 O A:HOH801 4.8 24.7 1.0 O B:HOH840 4.9 35.1 0.9 C4' D:DGT702 4.9 27.7 0.9

Magnesium binding site 3 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:62.1 occ:0.97 O1B A:DUT702 2.0 40.9 0.7 O3G A:DUT702 2.1 59.6 0.7 O3B A:DUT702 2.9 53.6 0.7 PB A:DUT702 2.9 53.1 0.7 PG A:DUT702 3.0 46.9 0.7 O3A A:DUT702 3.8 49.0 0.7 O1G A:DUT702 3.8 44.6 0.7 NZ A:LYS312 3.8 35.7 0.9 NH2 A:ARG206 3.9 43.7 0.9 O2B A:DUT702 4.1 48.5 0.7 NH1 A:ARG206 4.2 35.1 0.9 O2G A:DUT702 4.3 55.4 0.7 OD2 A:ASP309 4.3 42.8 0.8 OD1 A:ASP309 4.5 39.2 0.8 OD2 A:ASP311 4.5 40.9 0.8 CZ A:ARG206 4.5 40.3 0.9 CG A:LYS312 4.8 36.3 0.9 CG A:ASP309 4.9 38.5 0.8

Magnesium binding site 4 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:61.3 occ:1.00 O3B B:DUT702 2.0 57.0 0.7 O1B B:DUT702 2.8 51.9 0.7 PB B:DUT702 2.9 47.6 0.7 PG B:DUT702 3.0 40.7 0.7 O3G B:DUT702 3.3 40.8 0.7 O1G B:DUT702 3.5 40.1 0.7 O3A B:DUT702 3.7 49.6 0.7 NH2 B:ARG206 3.8 36.6 0.9 NZ B:LYS312 4.1 31.8 0.9 O2B B:DUT702 4.1 53.2 0.7 NH1 B:ARG206 4.3 34.3 0.9 O2G B:DUT702 4.4 53.0 0.7 CZ B:ARG206 4.5 38.3 0.9 OD2 B:ASP311 4.7 38.8 0.8 OD2 B:ASP309 4.7 35.9 0.8 OD1 B:ASP309 5.0 34.6 0.8

Magnesium binding site 5 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:42.9 occ:1.00 O1G B:DGT701 1.9 40.1 0.9 O1G D:DUT701 2.0 32.1 0.9 O1B D:DUT701 2.1 32.2 0.9 O1B B:DGT701 2.3 35.2 0.9 O1A B:DGT701 2.4 30.3 0.9 PG D:DUT701 3.2 30.8 0.9 PG B:DGT701 3.3 39.3 0.9 PB D:DUT701 3.3 29.8 0.9 PB B:DGT701 3.5 35.2 0.9 O3B D:DUT701 3.6 41.0 0.9 NZ C:LYS116 3.7 34.2 0.9 O3B B:DGT701 3.8 39.5 0.9 PA B:DGT701 3.8 31.1 0.9 O2G D:DUT701 3.8 33.9 0.9 O3' B:DGT701 4.0 29.5 0.9 O3A B:DGT701 4.1 34.6 0.9 NZ D:LYS523 4.1 45.1 0.9 O2G B:DGT701 4.1 36.9 0.9 O2B D:DUT701 4.2 27.0 0.9 O3G B:DGT701 4.2 32.8 0.9 O3A D:DUT701 4.3 41.7 0.9 O3G D:DUT701 4.5 37.2 0.9 C5' B:DGT701 4.5 30.2 0.9 O C:HOH820 4.5 28.1 0.8 O5' B:DGT701 4.7 34.7 0.9 O2B B:DGT701 4.7 35.1 0.9 C3' B:DGT701 4.7 33.5 0.9 O2A B:DGT701 4.7 32.5 0.9 CE C:LYS116 4.9 35.6 0.9

Magnesium binding site 6 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:31.4 occ:0.93 O1B A:DGT701 1.9 30.5 0.9 O2G C:DUT701 2.0 32.5 0.9 O2B C:DUT701 2.0 28.9 0.9 O1G A:DGT701 2.1 31.1 0.9 O A:HOH809 2.1 29.7 0.9 O1A A:DGT701 2.1 26.2 0.9 PB A:DGT701 3.1 44.8 0.9 PG A:DGT701 3.3 33.9 0.9 PB C:DUT701 3.3 31.2 0.9 PG C:DUT701 3.4 39.8 0.9 PA A:DGT701 3.4 32.3 0.9 O3B A:DGT701 3.6 36.4 0.9 NZ D:LYS116 3.6 32.2 0.9 O3A A:DGT701 3.7 31.2 0.9 O3B C:DUT701 3.7 43.2 0.9 O3' A:DGT701 3.9 32.6 0.9 O1G C:DUT701 4.1 38.4 0.9 O3G A:DGT701 4.2 29.6 0.9 O3A C:DUT701 4.3 37.6 0.9 C5' A:DGT701 4.3 27.5 0.9 O1B C:DUT701 4.3 31.1 0.9 O2B A:DGT701 4.3 35.3 0.9 O2G A:DGT701 4.3 39.6 0.9 O5' A:DGT701 4.4 34.0 0.9 O2A A:DGT701 4.4 33.1 0.9 O A:HOH804 4.5 32.0 1.0 C3' A:DGT701 4.5 30.8 0.9 O3G C:DUT701 4.5 41.3 0.9 NZ C:LYS523 4.7 57.6 0.9 CE D:LYS116 4.8 31.2 0.9 C4' A:DGT701 4.9 32.4 0.9 CD D:LYS116 4.9 42.0 0.9

Magnesium binding site 7 out of 7 in the Crystal Structure of the Tetrameric Dgtp/Dutp-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/Dutp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg705 b:58.9 occ:1.00 O3B D:DUT703 2.3 55.3 0.8 O2B D:DUT703 2.4 54.4 0.8 PB D:DUT703 2.9 43.4 0.8 PG D:DUT703 3.3 41.2 0.8 O2G D:DUT703 3.6 42.3 0.8 NH2 D:ARG206 3.8 41.5 0.9 O1G D:DUT703 3.8 42.4 0.8 O3A D:DUT703 3.9 47.1 0.8 NH1 D:ARG206 3.9 31.6 0.9 O1B D:DUT703 4.0 46.9 0.8 NZ D:LYS312 4.1 29.5 0.9 CZ D:ARG206 4.4 35.1 0.9 OD2 D:ASP309 4.5 31.4 0.8 O3G D:DUT703 4.7 59.4 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