Magnesium in PDB 4to1: Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex, PDB code: 4to1 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 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.204, 141.586, 98.187, 90.00, 115.79, 90.00
R / Rfree (%)	22.1 / 23.5

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-Dctp Complex (pdb code 4to1). 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-Dctp Complex, PDB code: 4to1:
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-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-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:28.6 occ:1.00 O3G C:GTP706 1.9 24.7 1.0 O3G A:DTP702 1.9 20.4 1.0 O1B A:DTP702 2.0 19.1 1.0 O C:HOH808 2.0 32.8 1.0 O2B C:GTP706 2.0 21.4 1.0 O1A C:GTP706 2.2 16.9 1.0 PG C:GTP706 3.2 24.6 1.0 PB C:GTP706 3.2 20.4 1.0 PB A:DTP702 3.3 19.6 1.0 PG A:DTP702 3.3 23.1 1.0 O3B C:GTP706 3.5 21.9 1.0 PA C:GTP706 3.5 18.7 1.0 NZ B:LYS116 3.6 62.2 1.0 O3B A:DTP702 3.6 21.1 1.0 O3A C:GTP706 3.8 20.5 1.0 O3' C:GTP706 3.8 19.4 1.0 NZ A:LYS523 3.9 51.4 1.0 O2G C:GTP706 4.0 25.9 1.0 O2G A:DTP702 4.1 21.1 1.0 O1G C:GTP706 4.2 24.6 1.0 C5' C:GTP706 4.2 20.0 1.0 O2B A:DTP702 4.2 20.7 1.0 O3A A:DTP702 4.3 18.7 1.0 O5' C:GTP706 4.4 19.5 1.0 O1G A:DTP702 4.4 21.1 1.0 O1B C:GTP706 4.5 23.4 1.0 C3' C:GTP706 4.5 20.2 1.0 O2A C:GTP706 4.7 17.3 1.0 CE B:LYS116 4.9 60.7 1.0 C4' C:GTP706 4.9 20.1 1.0 CE A:LYS523 5.0 50.6 1.0

Magnesium binding site 2 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-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-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:48.7 occ:1.00 O2G B:DTP702 1.7 23.0 1.0 O1G D:GTP704 1.8 26.8 1.0 O1B B:DTP702 2.0 17.9 1.0 O A:HOH805 2.2 48.0 1.0 O1B D:GTP704 2.2 20.3 1.0 O2A D:GTP704 2.3 18.8 1.0 PG B:DTP702 3.1 22.5 1.0 PG D:GTP704 3.2 25.7 1.0 PB B:DTP702 3.2 17.9 1.0 PB D:GTP704 3.4 20.1 1.0 O3B B:DTP702 3.5 20.8 1.0 NZ B:LYS523 3.6 82.3 1.0 O3B D:GTP704 3.6 21.6 1.0 O1G B:DTP702 3.7 19.4 1.0 NZ A:LYS116 3.7 80.7 1.0 PA D:GTP704 3.7 20.4 1.0 O3A D:GTP704 4.0 22.1 1.0 O3' D:GTP704 4.0 21.9 1.0 O2G D:GTP704 4.1 26.5 1.0 O3G D:GTP704 4.1 26.3 1.0 O B:HOH804 4.1 61.5 1.0 O3G B:DTP702 4.2 23.2 1.0 O2B B:DTP702 4.2 19.3 1.0 O3A B:DTP702 4.3 18.4 1.0 C5' D:GTP704 4.4 22.1 1.0 O5' D:GTP704 4.6 21.4 1.0 C3' D:GTP704 4.6 21.5 1.0 O2B D:GTP704 4.7 23.4 1.0 CE B:LYS523 4.7 84.2 1.0 O1A D:GTP704 4.9 19.9 1.0 CE A:LYS116 5.0 79.1 1.0 C4' D:GTP704 5.0 21.8 1.0

Magnesium binding site 3 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-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-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:32.2 occ:1.00 O1B C:DCP701 1.8 23.5 1.0 O2B D:GTP701 1.9 23.8 1.0 O3G D:GTP701 1.9 22.9 1.0 O2G C:DCP701 2.0 23.8 1.0 O1A D:GTP701 2.1 23.7 1.0 O D:HOH802 2.2 50.6 1.0 PB D:GTP701 3.1 22.6 1.0 PG D:GTP701 3.2 24.1 1.0 PB C:DCP701 3.3 21.8 1.0 PG C:DCP701 3.3 24.1 1.0 PA D:GTP701 3.4 23.9 1.0 O3B D:GTP701 3.5 22.1 1.0 NZ D:LYS116 3.5 64.0 1.0 O3A D:GTP701 3.6 23.2 1.0 O3B C:DCP701 3.7 24.2 1.0 NZ C:LYS523 3.8 69.9 1.0 O3' D:GTP701 3.9 28.1 1.0 O1G C:DCP701 4.0 25.5 1.0 C5' D:GTP701 4.0 27.6 1.0 O1G D:GTP701 4.1 23.4 1.0 O5' D:GTP701 4.2 25.4 1.0 O2G D:GTP701 4.2 23.9 1.0 O2B C:DCP701 4.2 21.3 1.0 O3A C:DCP701 4.3 21.8 1.0 O D:HOH803 4.4 35.4 1.0 C3' D:GTP701 4.4 29.0 1.0 O3G C:DCP701 4.5 29.0 1.0 O1B D:GTP701 4.5 22.0 1.0 O2A D:GTP701 4.6 22.8 1.0 C4' D:GTP701 4.7 29.5 1.0 O D:HOH801 4.8 53.8 1.0 CE D:LYS116 4.8 62.4 1.0 CE C:LYS523 5.0 70.4 1.0

Magnesium binding site 4 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp/Dctp-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-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:15.9 occ:1.00 O1G C:GTP704 1.8 28.3 1.0 O1B D:DCP702 1.9 18.1 1.0 O2G D:DCP702 1.9 17.9 1.0 O1B C:GTP704 2.0 25.8 1.0 O1A C:GTP704 2.2 26.9 1.0 O C:HOH821 2.2 74.7 1.0 PG C:GTP704 3.1 30.2 1.0 PB C:GTP704 3.1 26.4 1.0 PB D:DCP702 3.3 18.1 1.0 PG D:DCP702 3.3 18.0 1.0 O3B C:GTP704 3.3 28.0 1.0 PA C:GTP704 3.4 25.4 1.0 NZ C:LYS116 3.5 92.6 1.0 O3A C:GTP704 3.6 25.4 1.0 O3B D:DCP702 3.7 18.3 1.0 NZ D:LYS523 3.8 96.6 1.0 O3G C:GTP704 4.0 31.2 1.0 O1G D:DCP702 4.1 16.4 1.0 O3' C:GTP704 4.1 23.5 1.0 O2G C:GTP704 4.1 28.5 1.0 C5' C:GTP704 4.2 24.7 1.0 O2B D:DCP702 4.3 17.4 1.0 O3A D:DCP702 4.3 17.9 1.0 O5' C:GTP704 4.3 25.1 1.0 O3G D:DCP702 4.4 19.5 1.0 O2B C:GTP704 4.5 26.3 1.0 O C:HOH822 4.5 53.4 1.0 O2A C:GTP704 4.5 25.5 1.0 C3' C:GTP704 4.7 23.7 1.0 CE C:LYS116 4.8 88.7 1.0 CE D:LYS523 4.9 0.3 1.0 C4' C:GTP704 5.0 24.1 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