Magnesium in PDB 4to0: Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dctp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dctp Complex, PDB code: 4to0 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 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.418, 141.329, 97.519, 90.00, 114.58, 90.00
R / Rfree (%)	19.1 / 22.2

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dctp Complex (pdb code 4to0). 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-Datp-Dctp Complex, PDB code: 4to0:
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-Datp-Dctp 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-Datp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:32.8 occ:1.00 O3G C:GTP704 1.9 33.0 1.0 O3G A:DTP703 1.9 33.1 1.0 O1B A:DTP703 2.0 27.9 1.0 O2B C:GTP704 2.1 36.4 1.0 O A:HOH808 2.1 36.8 1.0 O1A C:GTP704 2.2 31.5 1.0 PG C:GTP704 3.1 35.6 1.0 PB C:GTP704 3.1 37.5 1.0 PG A:DTP703 3.2 34.1 1.0 PB A:DTP703 3.3 30.6 1.0 O C:HOH819 3.4 91.7 1.0 O3B C:GTP704 3.4 33.2 1.0 PA C:GTP704 3.5 34.3 1.0 O3B A:DTP703 3.6 30.9 1.0 NZ B:LYS116 3.6 46.3 1.0 NZ A:LYS523 3.7 56.0 1.0 O3A C:GTP704 3.7 34.2 1.0 O3' C:GTP704 4.0 30.2 1.0 O2G C:GTP704 4.1 31.2 1.0 O2G A:DTP703 4.1 32.4 1.0 O1G C:GTP704 4.2 35.6 1.0 O2B A:DTP703 4.2 28.6 1.0 C5' C:GTP704 4.2 33.2 1.0 O1G A:DTP703 4.3 35.8 1.0 O5' C:GTP704 4.4 31.5 1.0 O C:HOH816 4.4 42.8 1.0 O3A A:DTP703 4.4 30.8 1.0 O A:HOH831 4.5 61.4 1.0 O1B C:GTP704 4.5 39.1 1.0 C3' C:GTP704 4.6 29.5 1.0 O2A C:GTP704 4.7 37.5 1.0 CE B:LYS116 4.8 46.2 1.0 CE A:LYS523 4.9 52.9 1.0 C4' C:GTP704 4.9 29.7 1.0

Magnesium binding site 2 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dctp 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-Datp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:44.0 occ:1.00 O2G D:DTP703 1.8 40.7 1.0 O1G D:GTP704 1.9 46.2 1.0 O D:HOH813 2.0 51.6 1.0 O1B D:DTP703 2.0 38.6 1.0 O2A D:GTP704 2.2 33.2 1.0 O1B D:GTP704 2.3 43.0 1.0 PG D:DTP703 3.1 43.6 1.0 PG D:GTP704 3.2 44.5 1.0 PB D:DTP703 3.3 37.0 1.0 PB D:GTP704 3.4 41.2 1.0 NZ A:LYS116 3.5 56.6 1.0 O3B D:DTP703 3.6 42.2 1.0 PA D:GTP704 3.6 37.3 1.0 O3B D:GTP704 3.6 41.5 1.0 NZ B:LYS523 3.8 63.5 1.0 O1G D:DTP703 3.8 42.1 1.0 O3A D:GTP704 3.9 40.5 1.0 O3' D:GTP704 3.9 37.8 1.0 O D:HOH816 4.1 84.1 1.0 O3G D:GTP704 4.1 49.7 1.0 O2G D:GTP704 4.2 40.3 1.0 O2B D:DTP703 4.2 36.6 1.0 O3G D:DTP703 4.3 39.0 1.0 C5' D:GTP704 4.3 39.6 1.0 O3A D:DTP703 4.3 37.5 1.0 O D:HOH822 4.3 42.0 1.0 O5' D:GTP704 4.4 41.2 1.0 C3' D:GTP704 4.6 39.5 1.0 CE A:LYS116 4.7 56.1 1.0 O2B D:GTP704 4.7 48.2 1.0 O1A D:GTP704 4.8 35.4 1.0 C4' D:GTP704 4.9 41.7 1.0 CE B:LYS523 4.9 60.9 1.0

Magnesium binding site 3 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dctp 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-Datp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:36.0 occ:1.00 O1G B:GTP703 1.7 38.4 1.0 O1B B:GTP703 1.9 34.5 1.0 O3G B:DTP702 1.9 37.1 1.0 O B:HOH811 1.9 38.9 1.0 O1B B:DTP702 2.0 31.8 1.0 O1A B:GTP703 2.0 33.5 1.0 PB B:GTP703 3.0 37.2 1.0 PG B:GTP703 3.0 38.9 1.0 PG B:DTP702 3.3 36.5 1.0 PA B:GTP703 3.3 35.7 1.0 PB B:DTP702 3.4 32.1 1.0 O3B B:GTP703 3.4 33.0 1.0 O3A B:GTP703 3.5 36.4 1.0 NZ C:LYS116 3.6 53.0 1.0 O3B B:DTP702 3.8 32.9 1.0 NZ D:LYS523 3.9 60.0 1.0 O3G B:GTP703 4.0 41.5 1.0 O2G B:DTP702 4.0 34.4 1.0 O3' B:GTP703 4.0 36.3 1.0 O2G B:GTP703 4.1 38.1 1.0 C5' B:GTP703 4.2 32.6 1.0 O2B B:DTP702 4.3 29.7 1.0 O B:HOH806 4.3 57.3 1.0 O5' B:GTP703 4.3 33.2 1.0 O2B B:GTP703 4.4 30.9 1.0 O3A B:DTP702 4.4 32.1 1.0 O1G B:DTP702 4.4 39.2 1.0 O2A B:GTP703 4.4 35.2 1.0 C3' B:GTP703 4.5 35.5 1.0 CE C:LYS116 4.8 47.3 1.0 C4' B:GTP703 4.8 34.5 1.0

Magnesium binding site 4 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dctp 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-Datp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:38.5 occ:1.00 O3G A:GTP702 1.8 36.5 1.0 O2B C:DTP701 1.9 34.5 1.0 O2B A:GTP702 1.9 37.7 1.0 O A:HOH805 1.9 34.8 1.0 O1A A:GTP702 1.9 38.2 1.0 O2G C:DTP701 2.0 40.3 1.0 PB A:GTP702 3.0 38.9 1.0 PG A:GTP702 3.2 36.5 1.0 PB C:DTP701 3.2 36.2 1.0 PA A:GTP702 3.2 39.4 1.0 PG C:DTP701 3.3 41.5 1.0 O3B A:GTP702 3.4 35.2 1.0 NZ D:LYS116 3.5 48.3 1.0 O3A A:GTP702 3.5 40.0 1.0 O3B C:DTP701 3.6 40.7 1.0 O3' A:GTP702 3.9 36.0 1.0 NZ C:LYS523 3.9 53.1 1.0 O A:HOH816 4.0 61.8 1.0 C5' A:GTP702 4.1 36.9 1.0 O1G A:GTP702 4.1 39.6 1.0 O A:HOH832 4.1 49.5 1.0 O3G C:DTP701 4.1 38.1 1.0 O5' A:GTP702 4.1 40.1 1.0 O1B C:DTP701 4.2 32.7 1.0 O2G A:GTP702 4.2 37.0 1.0 O3A C:DTP701 4.3 36.9 1.0 O2A A:GTP702 4.3 41.6 1.0 O1B A:GTP702 4.4 34.4 1.0 C3' A:GTP702 4.4 34.9 1.0 O1G C:DTP701 4.4 38.1 1.0 CE D:LYS116 4.6 43.8 1.0 C4' A:GTP702 4.7 36.4 1.0 CD D:LYS116 4.9 44.0 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