Magnesium in PDB 4to4: Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex, PDB code: 4to4 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 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.712, 145.843, 98.654, 90.00, 114.75, 90.00
R / Rfree (%)	19.7 / 22.5

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex (pdb code 4to4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex, PDB code: 4to4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-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-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:73.7 occ:1.00 O A:HOH889 2.1 48.7 1.0 O A:HOH890 2.2 48.5 1.0 O2G A:DCP701 2.2 48.1 1.0 O A:HOH892 2.2 50.0 1.0 O2B A:DCP701 2.5 56.9 1.0 PG A:DCP701 3.4 56.8 1.0 PB A:DCP701 3.5 68.7 1.0 O3B A:DCP701 3.8 58.6 1.0 NH2 A:ARG206 3.9 36.5 1.0 NZ A:LYS312 3.9 40.9 1.0 NH1 A:ARG206 3.9 36.7 1.0 O3G A:DCP701 4.0 47.4 1.0 OD2 A:ASP309 4.1 42.3 1.0 O A:HOH891 4.1 44.6 1.0 O1B A:DCP701 4.2 72.4 1.0 CZ A:ARG206 4.4 36.7 1.0 OD1 A:ASP309 4.6 39.6 1.0 O A:HOH834 4.7 45.7 1.0 O1G A:DCP701 4.7 48.1 1.0 OD2 A:ASP311 4.7 51.4 1.0 CG A:ASP309 4.8 40.9 1.0 O2A A:DCP701 4.8 78.5 1.0 O3A A:DCP701 4.9 72.5 1.0 OG A:SER302 4.9 50.9 1.0

Magnesium binding site 2 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-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-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:41.7 occ:1.00 O1G D:GTP705 1.7 40.6 1.0 O1B B:DGT706 1.8 36.0 1.0 O2G B:DGT706 1.9 34.3 1.0 O B:HOH844 2.0 35.7 1.0 O1B D:GTP705 2.0 37.3 1.0 O2A D:GTP705 2.1 38.4 1.0 PG B:DGT706 3.1 36.3 1.0 PB B:DGT706 3.2 35.7 1.0 PG D:GTP705 3.2 41.3 1.0 PB D:GTP705 3.2 41.0 1.0 PA D:GTP705 3.5 36.1 1.0 O3B B:DGT706 3.5 36.6 1.0 O3B D:GTP705 3.5 41.5 1.0 O3A D:GTP705 3.7 41.1 1.0 O1G B:DGT706 3.8 35.4 1.0 O3' D:GTP705 3.9 33.3 1.0 NZ A:LYS116 3.9 51.5 1.0 NZ B:LYS523 4.0 58.9 1.0 O3G D:GTP705 4.1 47.0 1.0 O2B B:DGT706 4.1 34.9 1.0 O2G D:GTP705 4.2 43.5 1.0 O D:HOH870 4.2 60.2 1.0 O D:HOH825 4.3 34.3 1.0 O D:HOH871 4.3 49.7 1.0 O3A B:DGT706 4.3 34.3 1.0 O B:HOH885 4.3 50.4 1.0 C5' D:GTP705 4.3 38.4 1.0 O3G B:DGT706 4.4 42.6 1.0 O5' D:GTP705 4.4 38.8 1.0 C3' D:GTP705 4.5 36.1 1.0 O1A D:GTP705 4.5 39.0 1.0 O2B D:GTP705 4.6 43.5 1.0 C4' D:GTP705 4.8 36.4 1.0

Magnesium binding site 3 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-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-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:0.8 occ:1.00 O B:HOH862 1.5 50.7 1.0 O1G B:DCP701 1.9 59.4 1.0 O1B B:DCP701 2.0 66.9 1.0 O B:HOH861 2.0 53.2 1.0 PB B:DCP701 3.2 71.2 1.0 PG B:DCP701 3.2 71.3 1.0 O3B B:DCP701 3.5 63.5 1.0 NH2 B:ARG206 3.6 44.2 1.0 NH1 B:ARG206 3.8 45.2 1.0 O3A B:DCP701 3.9 73.2 1.0 NZ B:LYS312 4.0 42.2 1.0 O2G B:DCP701 4.1 57.6 1.0 OD2 B:ASP309 4.1 42.3 1.0 OD2 B:ASP311 4.1 63.1 1.0 CZ B:ARG206 4.2 45.5 1.0 O3G B:DCP701 4.3 62.8 1.0 OD1 B:ASP309 4.4 41.4 1.0 O2B B:DCP701 4.5 66.0 1.0 CG B:ASP309 4.7 43.4 1.0 O B:HOH879 4.8 52.8 1.0 CG B:ASP311 4.9 52.6 1.0 CB B:ASP311 5.0 45.9 1.0 CG B:LYS312 5.0 36.9 1.0

Magnesium binding site 4 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-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-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:30.2 occ:1.00 O3G B:GTP705 1.8 33.1 1.0 O2B B:GTP705 2.0 30.1 1.0 O A:HOH822 2.0 27.6 1.0 O1A B:GTP705 2.0 32.0 1.0 O1B A:DGT704 2.0 29.2 1.0 O1G A:DGT704 2.1 29.4 1.0 PG B:GTP705 3.1 36.0 1.0 PB B:GTP705 3.1 34.4 1.0 PA B:GTP705 3.3 31.8 1.0 PB A:DGT704 3.4 31.8 1.0 PG A:DGT704 3.4 33.2 1.0 O3B B:GTP705 3.4 34.5 1.0 O3A B:GTP705 3.7 32.9 1.0 NZ B:LYS116 3.7 44.2 1.0 O3B A:DGT704 3.8 30.7 1.0 O2G B:GTP705 3.9 37.9 1.0 O3' B:GTP705 4.0 27.6 1.0 NZ A:LYS523 4.0 49.4 1.0 O3G A:DGT704 4.1 31.8 1.0 O1G B:GTP705 4.2 36.9 1.0 C5' B:GTP705 4.2 31.6 1.0 O5' B:GTP705 4.3 35.0 1.0 O2B A:DGT704 4.3 32.3 1.0 O B:HOH814 4.4 26.2 1.0 O3A A:DGT704 4.4 31.0 1.0 O1B B:GTP705 4.4 29.5 1.0 O B:HOH884 4.5 54.2 1.0 O2A B:GTP705 4.5 31.1 1.0 C3' B:GTP705 4.6 31.8 1.0 O2G A:DGT704 4.7 37.8 1.0 CE B:LYS116 4.9 45.6 1.0 C4' B:GTP705 4.9 30.7 1.0 O A:HOH873 5.0 33.6 1.0 CD B:LYS116 5.0 45.4 1.0

Magnesium binding site 5 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:37.3 occ:1.00 O1G B:GTP703 1.8 40.5 1.0 O1B D:DGT702 1.9 36.3 1.0 O B:HOH828 2.0 33.6 1.0 O3G D:DGT702 2.0 35.8 1.0 O1A B:GTP703 2.1 30.9 1.0 O1B B:GTP703 2.1 31.5 1.0 PG B:GTP703 3.2 39.5 1.0 PB B:GTP703 3.2 36.6 1.0 PB D:DGT702 3.3 38.5 1.0 PG D:DGT702 3.4 38.7 1.0 PA B:GTP703 3.4 34.6 1.0 O3B B:GTP703 3.5 36.4 1.0 NZ C:LYS116 3.7 45.8 1.0 O3B D:DGT702 3.8 39.0 1.0 O3A B:GTP703 3.8 35.5 1.0 O3' B:GTP703 4.0 30.3 1.0 NZ D:LYS523 4.0 56.7 1.0 O2G B:GTP703 4.2 34.8 1.0 O3G B:GTP703 4.2 45.3 1.0 O1G D:DGT702 4.2 35.5 1.0 O2B D:DGT702 4.2 33.1 1.0 C5' B:GTP703 4.3 34.9 1.0 O5' B:GTP703 4.4 34.7 1.0 O3A D:DGT702 4.4 34.5 1.0 C3' B:GTP703 4.5 34.1 1.0 O2A B:GTP703 4.5 37.8 1.0 O C:HOH848 4.5 35.0 1.0 O2G D:DGT702 4.6 42.4 1.0 O2B B:GTP703 4.6 39.1 1.0 CE C:LYS116 4.8 45.2 1.0 C4' B:GTP703 4.9 34.0 1.0 CD C:LYS116 4.9 45.6 1.0

Magnesium binding site 6 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:61.0 occ:1.00 O2G C:DCP703 1.9 54.7 1.0 O C:HOH913 2.1 50.2 1.0 O2B C:DCP703 2.1 55.1 1.0 O C:HOH815 2.1 39.6 1.0 O C:HOH891 2.2 51.7 1.0 O C:HOH892 2.2 46.1 1.0 PG C:DCP703 3.3 47.5 1.0 PB C:DCP703 3.5 57.5 1.0 NZ C:LYS312 3.7 34.3 1.0 O3B C:DCP703 3.8 59.2 1.0 OD2 C:ASP309 3.8 35.8 1.0 O C:HOH914 4.0 57.4 1.0 O3G C:DCP703 4.0 56.9 1.0 NH1 C:ARG206 4.1 35.8 1.0 NH2 C:ARG206 4.2 36.8 1.0 O1B C:DCP703 4.4 51.0 1.0 O1G C:DCP703 4.4 54.6 1.0 OD1 C:ASP309 4.5 35.7 1.0 O3A C:DCP703 4.5 53.7 1.0 CG C:ASP309 4.6 34.4 1.0 CZ C:ARG206 4.6 35.9 1.0 O C:HOH915 4.7 42.3 1.0 OD2 C:ASP311 4.9 46.1 1.0 OG C:SER302 4.9 50.8 1.0 CE C:LYS312 5.0 33.5 1.0

Magnesium binding site 7 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:37.8 occ:1.00 O3G A:GTP703 1.9 38.2 1.0 O A:HOH814 1.9 26.0 1.0 O1B C:DGT701 2.0 30.4 1.0 O2B A:GTP703 2.0 36.7 1.0 O1A A:GTP703 2.0 34.0 1.0 O3G C:DGT701 2.1 32.0 1.0 PB A:GTP703 3.1 38.0 1.0 PG A:GTP703 3.2 38.5 1.0 PB C:DGT701 3.3 30.9 1.0 PG C:DGT701 3.3 35.7 1.0 PA A:GTP703 3.3 33.8 1.0 O3B A:GTP703 3.5 36.4 1.0 O A:HOH893 3.5 79.2 1.0 O3A A:GTP703 3.6 38.8 1.0 NZ D:LYS116 3.7 43.0 1.0 O3B C:DGT701 3.8 32.2 1.0 O3' A:GTP703 3.8 31.2 1.0 NZ C:LYS523 4.0 45.5 1.0 O C:HOH911 4.1 49.7 1.0 O2G C:DGT701 4.1 30.1 1.0 O1G A:GTP703 4.1 40.8 1.0 O2G A:GTP703 4.2 45.2 1.0 O2B C:DGT701 4.2 29.8 1.0 O5' A:GTP703 4.3 35.3 1.0 C5' A:GTP703 4.3 33.6 1.0 O2A A:GTP703 4.4 35.5 1.0 C3' A:GTP703 4.4 33.5 1.0 O3A C:DGT701 4.4 32.1 1.0 O1B A:GTP703 4.5 39.9 1.0 O D:HOH853 4.5 40.0 1.0 O1G C:DGT701 4.5 35.6 1.0 CE D:LYS116 4.8 43.0 1.0 C4' A:GTP703 4.8 32.9 1.0 CD D:LYS116 4.9 41.8 1.0 O C:HOH890 5.0 41.0 1.0

Magnesium binding site 8 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:0.5 occ:1.00 O1B D:DCP703 1.6 71.9 1.0 O2G D:DCP703 1.7 63.4 1.0 O D:HOH855 2.1 53.7 1.0 O D:HOH833 2.2 45.7 1.0 PB D:DCP703 2.9 70.1 1.0 PG D:DCP703 3.0 67.0 1.0 O3B D:DCP703 3.3 69.8 1.0 O3A D:DCP703 3.7 80.3 1.0 NH2 D:ARG206 3.8 43.7 1.0 O1G D:DCP703 3.9 70.7 1.0 NZ D:LYS312 3.9 46.9 1.0 O2B D:DCP703 4.0 69.3 1.0 O3G D:DCP703 4.0 68.5 1.0 NH1 D:ARG206 4.1 48.0 1.0 OD2 D:ASP311 4.4 55.1 1.0 OD2 D:ASP309 4.4 44.0 1.0 CZ D:ARG206 4.4 45.3 1.0 OD1 D:ASP309 4.7 43.5 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