Magnesium in PDB 4zwe: Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant

The structure of Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant, PDB code: 4zwe was solved by C.Tang, X.Ji, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.083, 146.091, 98.463, 90.00, 115.03, 90.00
R / Rfree (%)	20.8 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant (pdb code 4zwe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant, PDB code: 4zwe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant


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 Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:46.6 occ:1.00 O1G B:DGT705 1.9 47.3 1.0 O2A D:DGT704 2.0 44.2 1.0 O3G D:DGT704 2.1 44.4 1.0 O2B B:DGT705 2.1 45.6 1.0 O2B D:DGT704 2.4 40.8 1.0 NZ A:LYS116 3.2 51.5 1.0 PG D:DGT704 3.3 47.3 1.0 PG B:DGT705 3.3 46.8 1.0 PB D:DGT704 3.3 48.9 1.0 O3B D:DGT704 3.4 49.2 1.0 PA D:DGT704 3.4 44.3 1.0 PB B:DGT705 3.4 44.0 1.0 O3B B:DGT705 3.8 44.7 1.0 O3A D:DGT704 3.8 44.2 1.0 O3' D:DGT704 3.8 45.3 1.0 O3G B:DGT705 3.9 44.8 1.0 O2G D:DGT704 4.0 45.2 1.0 NZ B:LYS523 4.0 54.6 1.0 O3A B:DGT705 4.3 44.0 1.0 O5' D:DGT704 4.4 47.6 1.0 C3' D:DGT704 4.4 45.1 1.0 O1B B:DGT705 4.4 43.7 1.0 C5' D:DGT704 4.4 46.7 1.0 O2G B:DGT705 4.4 47.9 1.0 CE A:LYS116 4.5 52.6 1.0 O1G D:DGT704 4.5 49.5 1.0 O1A D:DGT704 4.6 47.1 1.0 O1B D:DGT704 4.8 46.7 1.0 CD A:LYS116 4.9 53.9 1.0 C4' D:DGT704 5.0 45.9 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant


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 Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:0.1 occ:1.00 NZ B:LYS312 2.0 99.1 1.0 O3G B:DGT701 2.3 1.0 1.0 NH2 B:ARG206 2.7 0.3 1.0 O3A B:DGT701 3.4 0.2 1.0 CE B:LYS312 3.4 91.9 1.0 PG B:DGT701 3.6 0.9 1.0 CZ B:ARG206 3.8 0.3 1.0 O1B B:DGT701 3.9 0.3 1.0 CG B:LYS312 3.9 77.7 1.0 OD2 B:ASP309 4.1 64.9 1.0 OD1 B:ASP311 4.1 83.2 1.0 NH1 B:ARG206 4.1 0.9 1.0 PB B:DGT701 4.1 0.7 1.0 OD1 B:ASP309 4.2 66.3 1.0 O2G B:DGT701 4.2 0.7 1.0 CD B:LYS312 4.2 82.6 1.0 O3B B:DGT701 4.3 0.6 1.0 O1A B:DGT701 4.5 0.9 1.0 CG B:ASP309 4.6 63.7 1.0 PA B:DGT701 4.7 0.6 1.0 CG B:ASP311 4.7 83.7 1.0 CB B:ASP311 4.7 75.2 1.0 CE2 B:TYR315 4.8 64.4 1.0 O1G B:DGT701 4.8 0.2 1.0 N B:LYS312 4.9 67.0 1.0 CB B:LYS312 5.0 71.6 1.0 NE B:ARG206 5.0 90.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant


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 Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:48.3 occ:1.00 O2G B:DGT704 1.9 65.0 1.0 O2B A:DGT704 2.0 56.2 1.0 O1A B:DGT704 2.1 47.7 1.0 O1B B:DGT704 2.3 54.4 1.0 O3G A:DGT704 2.4 47.7 1.0 NZ B:LYS116 3.1 71.1 1.0 PG B:DGT704 3.2 60.1 1.0 PB B:DGT704 3.4 60.0 1.0 PB A:DGT704 3.4 50.2 1.0 PG A:DGT704 3.4 52.0 1.0 PA B:DGT704 3.5 49.8 1.0 O3B B:DGT704 3.6 61.8 1.0 O3' B:DGT704 3.8 46.6 1.0 O1G A:DGT704 3.8 49.5 1.0 O1G B:DGT704 3.8 62.0 1.0 O3B A:DGT704 3.9 51.5 1.0 O3A B:DGT704 3.9 52.7 1.0 NZ A:LYS523 4.2 66.1 1.0 C3' B:DGT704 4.3 48.1 1.0 O3A A:DGT704 4.3 51.0 1.0 O3G B:DGT704 4.3 56.8 1.0 C5' B:DGT704 4.3 49.2 1.0 CE B:LYS116 4.4 70.6 1.0 O5' B:DGT704 4.4 50.9 1.0 O1B A:DGT704 4.4 50.5 1.0 O2A B:DGT704 4.6 49.7 1.0 CD B:LYS116 4.7 69.2 1.0 O2G A:DGT704 4.8 51.4 1.0 O2B B:DGT704 4.8 59.2 1.0 C4' B:DGT704 4.8 50.8 1.0 CG B:LYS116 4.8 70.5 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant


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 Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:60.6 occ:1.00 O3G D:DGT702 1.9 58.2 1.0 O2B D:DGT702 2.0 56.0 1.0 O1G C:DGT702 2.1 51.7 1.0 O1A C:DGT702 2.2 53.5 1.0 O1B C:DGT702 2.3 53.1 1.0 NZ C:LYS116 3.1 80.3 1.0 PG D:DGT702 3.2 56.2 1.0 PB D:DGT702 3.3 57.0 1.0 PG C:DGT702 3.5 53.0 1.0 PB C:DGT702 3.5 56.7 1.0 O3' C:DGT702 3.5 60.9 1.0 PA C:DGT702 3.6 54.1 1.0 O3B D:DGT702 3.6 56.8 1.0 O3B C:DGT702 3.8 55.6 1.0 O3A C:DGT702 4.0 54.3 1.0 NZ D:LYS523 4.1 89.8 1.0 C3' C:DGT702 4.1 55.1 1.0 O1G D:DGT702 4.1 54.0 1.0 O2G D:DGT702 4.2 55.0 1.0 O3A D:DGT702 4.3 55.6 1.0 C5' C:DGT702 4.3 56.3 1.0 O1B D:DGT702 4.4 57.2 1.0 O2G C:DGT702 4.4 53.4 1.0 O5' C:DGT702 4.4 56.2 1.0 O3G C:DGT702 4.5 56.9 1.0 CE C:LYS116 4.5 80.2 1.0 C4' C:DGT702 4.7 56.5 1.0 O2A C:DGT702 4.7 57.2 1.0 O2B C:DGT702 4.9 55.8 1.0 CD C:LYS116 4.9 76.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant


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 Dgtp-Bound Catalytic Core of SAMHD1 T592V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:39.1 occ:1.00 O3G A:DGT703 2.0 51.5 1.0 O1B A:DGT702 2.0 40.0 1.0 O2G A:DGT702 2.1 42.1 1.0 O2A A:DGT703 2.2 45.6 1.0 O2B A:DGT703 2.5 41.0 1.0 NZ D:LYS116 3.2 54.2 1.0 PB A:DGT702 3.3 39.3 1.0 PG A:DGT702 3.4 44.0 1.0 PG A:DGT703 3.4 50.3 1.0 O3' A:DGT703 3.6 46.1 1.0 PB A:DGT703 3.6 48.1 1.0 PA A:DGT703 3.7 47.4 1.0 O3B A:DGT702 3.7 41.8 1.0 O3B A:DGT703 3.9 51.8 1.0 O3G A:DGT702 4.0 38.9 1.0 C3' A:DGT703 4.1 42.7 1.0 O3A A:DGT703 4.2 43.4 1.0 O1G A:DGT703 4.2 48.6 1.0 O3A A:DGT702 4.2 40.0 1.0 NZ C:LYS523 4.3 66.9 1.0 O2B A:DGT702 4.5 44.0 1.0 CE D:LYS116 4.5 53.6 1.0 C5' A:DGT703 4.5 44.3 1.0 O2G A:DGT703 4.5 51.6 1.0 O1G A:DGT702 4.5 42.7 1.0 O1A A:DGT703 4.6 47.7 1.0 O5' A:DGT703 4.7 45.7 1.0 CD D:LYS116 4.7 55.0 1.0 CG D:LYS116 4.7 58.0 1.0 C4' A:DGT703 4.8 43.6 1.0

C.Tang, X.Ji, L.Wu, Y.Xiong. Impaired Dntpase Activity of SAMHD1 By Phosphomimetic Mutation of Thr-592. J.Biol.Chem. V. 290 26352 2015.
ISSN: ESSN 1083-351X
PubMed: 26294762
DOI: 10.1074/JBC.M115.677435