Magnesium in PDB 4zwg: Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant

The structure of Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant, PDB code: 4zwg 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 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.720, 136.970, 95.843, 90.00, 113.96, 90.00
R / Rfree (%)	20.5 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant (pdb code 4zwg). 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 the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant, PDB code: 4zwg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E 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 Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:26.5 occ:1.00 O2B B:GTP702 1.9 23.7 1.0 O3G B:GTP702 1.9 23.9 1.0 O A:HOH813 2.0 18.6 1.0 O2A B:GTP702 2.0 23.5 1.0 O1B A:DTP703 2.0 23.9 1.0 O1G A:DTP703 2.0 22.4 1.0 PB B:GTP702 3.0 24.9 1.0 PG B:GTP702 3.1 25.9 1.0 PB A:DTP703 3.2 25.1 1.0 PA B:GTP702 3.2 24.7 1.0 PG A:DTP703 3.3 24.4 1.0 O3B B:GTP702 3.4 25.1 1.0 O3A B:GTP702 3.5 24.6 1.0 O3B A:DTP703 3.6 24.5 1.0 NZ B:LYS116 3.7 32.2 1.0 NZ A:LYS523 3.9 48.9 1.0 O3' B:GTP702 3.9 23.8 1.0 O2G B:GTP702 4.0 27.4 1.0 C5' B:GTP702 4.0 24.8 1.0 O2B A:DTP703 4.1 25.6 1.0 O5' B:GTP702 4.1 25.1 1.0 O1G B:GTP702 4.1 27.7 1.0 O2G A:DTP703 4.1 22.5 1.0 O3A A:DTP703 4.4 24.1 1.0 O1B B:GTP702 4.4 24.0 1.0 O B:HOH835 4.5 30.0 1.0 O3G A:DTP703 4.5 23.4 1.0 C3' B:GTP702 4.5 24.4 1.0 O1A B:GTP702 4.5 24.1 1.0 O A:HOH826 4.6 47.0 1.0 O A:HOH872 4.6 30.0 1.0 C4' B:GTP702 4.7 24.3 1.0 CE B:LYS116 4.8 31.2 1.0 O A:HOH850 5.0 50.2 1.0 CE A:LYS523 5.0 46.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E 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 Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:29.3 occ:1.00 O2G B:DTP703 1.8 27.2 1.0 O1G A:GTP706 1.9 33.2 1.0 O1B A:GTP706 1.9 27.9 1.0 O1A A:GTP706 2.0 28.0 1.0 O A:HOH844 2.2 31.9 1.0 O2B B:DTP703 2.3 30.8 1.0 PB A:GTP706 3.1 31.5 1.0 PG B:DTP703 3.1 29.4 1.0 PB B:DTP703 3.2 29.4 1.0 PG A:GTP706 3.2 33.1 1.0 PA A:GTP706 3.3 28.6 1.0 O3B B:DTP703 3.5 30.3 1.0 O3A A:GTP706 3.5 31.6 1.0 O3B A:GTP706 3.6 30.5 1.0 O1B B:DTP703 3.6 35.0 1.0 NZ A:LYS116 3.6 36.4 1.0 O3' A:GTP706 3.7 27.3 1.0 O1G B:DTP703 3.9 27.8 1.0 NZ B:LYS523 4.0 60.2 1.0 O2G A:GTP706 4.0 35.2 1.0 O B:HOH821 4.2 24.3 1.0 C5' A:GTP706 4.2 26.2 1.0 O5' A:GTP706 4.2 28.7 1.0 O3G B:DTP703 4.2 33.1 1.0 O3G A:GTP706 4.2 35.6 1.0 O2B A:GTP706 4.4 33.0 1.0 O2A A:GTP706 4.4 27.6 1.0 O B:HOH833 4.5 40.5 1.0 C3' A:GTP706 4.6 26.3 1.0 O3A B:DTP703 4.6 29.1 1.0 O A:HOH875 4.7 40.0 1.0 CE A:LYS116 4.7 35.0 1.0 C4' A:GTP706 4.9 26.0 1.0 CD A:LYS116 4.9 34.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E 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 Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:31.1 occ:1.00 O2B D:DTP702 1.9 27.2 1.0 O2B C:GTP703 1.9 26.2 1.0 O D:HOH820 2.0 26.6 1.0 O1G D:DTP702 2.0 24.4 1.0 O2A C:GTP703 2.2 25.1 1.0 O3G C:GTP703 2.2 27.0 1.0 PB D:DTP702 3.1 29.4 1.0 PB C:GTP703 3.1 27.1 1.0 PG D:DTP702 3.2 28.3 1.0 PA C:GTP703 3.3 24.1 1.0 PG C:GTP703 3.3 28.8 1.0 O5' C:GTP703 3.4 28.7 1.0 O3B D:DTP702 3.4 28.1 1.0 O3B C:GTP703 3.5 28.2 1.0 O3A C:GTP703 3.6 26.5 1.0 NZ C:LYS116 3.7 34.6 1.0 O3' C:GTP703 3.9 23.5 1.0 NZ D:LYS523 3.9 48.6 1.0 O1B D:DTP702 4.0 29.0 1.0 O3G D:DTP702 4.0 27.5 1.0 O C:HOH812 4.1 24.6 1.0 O3A D:DTP702 4.2 29.8 1.0 O1G C:GTP703 4.2 30.5 1.0 O2G C:GTP703 4.3 28.6 1.0 O2G D:DTP702 4.4 31.8 1.0 O1B C:GTP703 4.5 27.7 1.0 C3' C:GTP703 4.6 23.8 1.0 C5' C:GTP703 4.7 26.3 1.0 O1A C:GTP703 4.7 25.8 1.0 CE C:LYS116 4.8 32.8 1.0 C4' C:GTP703 5.0 24.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E 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 Gtp-Datp-Bound Catalytic Core of SAMHD1 Phosphomimetic T592E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:27.6 occ:1.00 O2B C:DTP701 1.9 21.8 1.0 O1G A:GTP702 1.9 28.4 1.0 O1B A:GTP702 2.0 28.8 1.0 O1A A:GTP702 2.1 25.5 1.0 O A:HOH829 2.1 12.4 1.0 O2G C:DTP701 2.1 29.3 1.0 PB A:GTP702 3.1 29.4 1.0 PB C:DTP701 3.1 23.5 1.0 PG A:GTP702 3.2 30.4 1.0 PA A:GTP702 3.2 27.1 1.0 PG C:DTP701 3.4 26.5 1.0 O5' A:GTP702 3.5 26.4 1.0 O3B A:GTP702 3.5 28.4 1.0 O3A A:GTP702 3.6 29.1 1.0 O3B C:DTP701 3.7 26.4 1.0 NZ D:LYS116 3.7 33.1 1.0 O3' A:GTP702 3.7 23.7 1.0 O A:HOH811 3.9 26.1 1.0 NZ C:LYS523 4.0 50.1 1.0 O1B C:DTP701 4.1 26.9 1.0 O1G C:DTP701 4.1 27.1 1.0 O2G A:GTP702 4.2 30.1 1.0 O3G A:GTP702 4.2 28.6 1.0 O3A C:DTP701 4.3 24.1 1.0 O3G C:DTP701 4.4 29.7 1.0 C3' A:GTP702 4.5 23.7 1.0 O2B A:GTP702 4.5 29.4 1.0 O2A A:GTP702 4.6 26.6 1.0 C5' A:GTP702 4.6 26.8 1.0 CE D:LYS116 4.7 34.3 1.0 C4' A:GTP702 4.8 24.6 1.0 O D:HOH827 4.9 36.4 1.0 CD D:LYS116 4.9 32.8 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