Magnesium in PDB 4tnx: Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex, PDB code: 4tnx was solved by X.Ji, C.Tang, Q.Zhao, W.Wang, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.886, 140.734, 97.603, 90.00, 114.71, 90.00
R / Rfree (%)	18.8 / 22.6

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex (pdb code 4tnx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex, PDB code: 4tnx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:34.9 occ:1.00 O1G B:DGT703 1.7 36.1 1.0 O3G A:GTP704 1.9 32.1 1.0 O2B B:DGT703 1.9 31.6 1.0 O A:HOH813 2.0 24.6 1.0 O2B A:GTP704 2.1 31.2 1.0 O1A A:GTP704 2.3 31.9 1.0 PG B:DGT703 3.0 34.9 1.0 PB B:DGT703 3.2 31.8 1.0 PB A:GTP704 3.3 31.5 1.0 PG A:GTP704 3.3 32.4 1.0 O3B B:DGT703 3.4 33.4 1.0 O3B A:GTP704 3.6 31.5 1.0 PA A:GTP704 3.6 31.2 1.0 NZ A:LYS116 3.8 39.6 1.0 NZ B:LYS523 3.8 51.9 1.0 O3A A:GTP704 3.9 31.4 1.0 O3' A:GTP704 3.9 29.8 1.0 O3G B:DGT703 4.0 34.6 1.0 O2G B:DGT703 4.1 36.4 1.0 O1G A:GTP704 4.2 32.8 1.0 O1B B:DGT703 4.2 31.0 1.0 O A:HOH814 4.2 32.7 1.0 O3A B:DGT703 4.3 31.4 1.0 C5' A:GTP704 4.3 30.4 1.0 O2G A:GTP704 4.3 32.1 1.0 O5' A:GTP704 4.5 30.9 1.0 O1B A:GTP704 4.6 31.6 1.0 C3' A:GTP704 4.6 29.9 1.0 CE B:LYS523 4.6 51.5 1.0 O2A A:GTP704 4.8 32.3 1.0 O A:HOH864 4.9 48.0 1.0 C4' A:GTP704 4.9 29.9 1.0 CE A:LYS116 4.9 39.4 1.0

Magnesium binding site 2 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:49.8 occ:1.00 O3G C:GTP704 1.7 45.5 1.0 O1G C:DGT703 1.8 49.5 1.0 O2B C:DGT703 2.0 45.6 1.0 O C:HOH824 2.0 44.6 1.0 O1A C:GTP704 2.0 43.3 1.0 O2B C:GTP704 2.2 43.5 1.0 PG C:GTP704 3.1 49.6 1.0 PG C:DGT703 3.2 47.4 1.0 PB C:DGT703 3.3 45.0 1.0 PB C:GTP704 3.3 47.0 1.0 PA C:GTP704 3.4 42.5 1.0 NZ B:LYS116 3.5 51.8 1.0 O3B C:GTP704 3.6 45.5 1.0 O3B C:DGT703 3.6 47.0 1.0 O3A C:GTP704 3.8 45.1 1.0 O3' C:GTP704 3.8 38.4 1.0 NZ A:LYS523 4.0 50.5 1.0 O3G C:DGT703 4.0 48.5 1.0 O2G C:GTP704 4.0 46.7 1.0 O1G C:GTP704 4.1 48.0 1.0 O1B C:DGT703 4.2 44.6 1.0 O2G C:DGT703 4.2 49.1 1.0 C5' C:GTP704 4.3 41.1 1.0 O3A C:DGT703 4.4 42.7 1.0 O5' C:GTP704 4.4 43.1 1.0 O C:HOH817 4.4 32.5 1.0 C3' C:GTP704 4.5 39.2 1.0 O2A C:GTP704 4.6 42.9 1.0 O1B C:GTP704 4.7 48.9 1.0 C4' C:GTP704 4.8 40.2 1.0 O C:HOH841 4.9 51.2 1.0 CE B:LYS116 4.9 50.9 1.0

Magnesium binding site 3 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:43.7 occ:1.00 O1G A:DGT701 1.8 38.7 1.0 O2B A:GTP702 1.9 34.6 1.0 O2B A:DGT701 2.0 35.1 1.0 O3G A:GTP702 2.0 35.5 1.0 O A:HOH810 2.1 34.2 1.0 O1A A:GTP702 2.2 31.6 1.0 PB A:GTP702 3.1 34.0 1.0 PG A:DGT701 3.1 39.4 1.0 PB A:DGT701 3.2 36.3 1.0 PG A:GTP702 3.3 34.8 1.0 PA A:GTP702 3.5 31.4 1.0 O3B A:DGT701 3.5 37.8 1.0 O3B A:GTP702 3.6 33.8 1.0 O3A A:GTP702 3.6 32.7 1.0 NZ C:LYS523 3.8 48.3 1.0 NZ D:LYS116 3.9 42.9 1.0 O A:HOH862 4.0 54.5 1.0 O3' A:GTP702 4.0 31.0 1.0 O A:HOH857 4.0 42.9 1.0 O3G A:DGT701 4.0 38.4 1.0 O1B A:DGT701 4.1 35.8 1.0 O1G A:GTP702 4.1 35.3 1.0 O2G A:DGT701 4.2 39.7 1.0 O2G A:GTP702 4.3 34.3 1.0 C5' A:GTP702 4.3 31.5 1.0 O A:HOH855 4.3 49.1 1.0 O3A A:DGT701 4.3 35.0 1.0 O1B A:GTP702 4.4 33.7 1.0 O A:HOH811 4.4 31.4 1.0 O5' A:GTP702 4.4 31.5 1.0 O2A A:GTP702 4.6 31.2 1.0 C3' A:GTP702 4.6 31.2 1.0 CE C:LYS523 4.9 49.1 1.0 C4' A:GTP702 4.9 31.3 1.0 O A:HOH812 4.9 34.3 1.0

Magnesium binding site 4 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:49.3 occ:1.00 O1G D:DGT800 1.8 38.8 1.0 O2B B:GTP701 1.9 38.8 1.0 O2B D:DGT800 1.9 37.9 1.0 O D:HOH908 1.9 33.8 1.0 O3G B:GTP701 2.0 39.3 1.0 O1A B:GTP701 2.2 37.6 1.0 PB B:GTP701 3.0 39.0 1.0 PB D:DGT800 3.2 36.6 1.0 PG D:DGT800 3.2 38.2 1.0 PG B:GTP701 3.2 41.3 1.0 PA B:GTP701 3.4 39.6 1.0 O3B B:GTP701 3.4 38.5 1.0 O3B D:DGT800 3.5 38.8 1.0 NZ C:LYS116 3.6 47.9 1.0 O3A B:GTP701 3.7 39.2 1.0 O B:HOH834 4.0 52.7 1.0 O3' B:GTP701 4.0 39.8 1.0 NZ D:LYS523 4.1 47.4 1.0 O2G B:GTP701 4.1 40.5 1.0 O1B D:DGT800 4.1 35.8 1.0 O3G D:DGT800 4.1 38.3 1.0 C5' B:GTP701 4.2 40.4 1.0 O1G B:GTP701 4.3 41.3 1.0 O2G D:DGT800 4.3 38.4 1.0 O5' B:GTP701 4.3 40.8 1.0 O3A D:DGT800 4.3 36.4 1.0 O1B B:GTP701 4.4 40.1 1.0 O B:HOH803 4.4 31.4 1.0 C3' B:GTP701 4.6 38.9 1.0 O2A B:GTP701 4.6 41.0 1.0 C4' B:GTP701 4.9 39.4 1.0 CE C:LYS116 4.9 48.3 1.0

X.Ji, C.Tang, Q.Zhao, W.Wang, Y.Xiong. Structural Basis of Cellular Dntp Regulation By SAMHD1. Proc.Natl.Acad.Sci.Usa V. 111 E4305 2014.
ISSN: ESSN 1091-6490
PubMed: 25267621
DOI: 10.1073/PNAS.1412289111