Magnesium in PDB 4to3: Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex

The structure of Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex, PDB code: 4to3 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)	40.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.411, 146.032, 98.106, 90.00, 114.52, 90.00
R / Rfree (%)	16.8 / 20.4

The binding sites of Magnesium atom in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex (pdb code 4to3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex, PDB code: 4to3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:0.3 occ:1.00 O1G A:DCP701 1.8 63.8 1.0 O2B A:DCP701 1.9 78.8 1.0 O A:HOH891 2.0 56.3 1.0 O A:HOH890 2.3 49.2 1.0 O A:HOH892 2.3 63.6 1.0 PG A:DCP701 3.1 74.1 1.0 PB A:DCP701 3.2 80.5 1.0 O3B A:DCP701 3.6 72.4 1.0 NZ A:LYS312 3.7 52.3 1.0 O2G A:DCP701 3.9 72.3 1.0 O3A A:DCP701 4.0 89.2 1.0 O A:HOH863 4.1 62.1 1.0 NH2 A:ARG206 4.2 53.8 1.0 O3G A:DCP701 4.2 58.8 1.0 O1B A:DCP701 4.3 74.3 1.0 NH1 A:ARG206 4.3 56.1 1.0 OD2 A:ASP309 4.4 56.5 1.0 OD2 A:ASP311 4.7 64.2 1.0 CZ A:ARG206 4.7 53.3 1.0 OD1 A:ASP309 4.7 58.0 1.0 O A:HOH866 4.8 55.3 1.0 CE A:LYS312 5.0 48.0 1.0

Magnesium binding site 2 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:43.9 occ:1.00 O2B B:DGT704 1.8 41.0 1.0 O2G A:DGT704 1.8 45.0 1.0 O1G B:DGT704 1.8 47.1 1.0 O B:HOH911 2.0 33.4 1.0 O1B A:DGT704 2.1 38.1 1.0 O2A B:DGT704 2.2 39.9 1.0 PB B:DGT704 3.0 42.3 1.0 PG B:DGT704 3.1 45.9 1.0 PG A:DGT704 3.1 43.2 1.0 PB A:DGT704 3.2 38.8 1.0 O3B B:DGT704 3.4 41.5 1.0 PA B:DGT704 3.5 39.7 1.0 O3B A:DGT704 3.6 41.2 1.0 O3A B:DGT704 3.7 42.8 1.0 NZ A:LYS523 3.8 67.2 1.0 O3G A:DGT704 3.9 39.1 1.0 NZ B:LYS116 3.9 52.9 1.0 O3G B:DGT704 3.9 49.8 1.0 O3' B:DGT704 4.1 37.9 1.0 O2B A:DGT704 4.2 33.5 1.0 O2G B:DGT704 4.2 45.7 1.0 O1G A:DGT704 4.3 46.0 1.0 O1B B:DGT704 4.3 40.3 1.0 C5' B:DGT704 4.3 40.3 1.0 O5' B:DGT704 4.4 42.6 1.0 O3A A:DGT704 4.4 40.7 1.0 O A:HOH885 4.4 49.5 1.0 O1A B:DGT704 4.7 45.0 1.0 C3' B:DGT704 4.7 38.7 1.0 C4' B:DGT704 5.0 41.2 1.0

Magnesium binding site 3 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:33.9 occ:1.00 O1G D:DGT705 1.9 37.8 1.0 O2B D:DGT705 2.0 35.2 1.0 O1B B:DGT705 2.1 34.7 1.0 O D:HOH852 2.1 36.8 1.0 O2A D:DGT705 2.1 33.8 1.0 O2G B:DGT705 2.2 34.9 1.0 PB D:DGT705 3.1 37.1 1.0 PG D:DGT705 3.2 41.6 1.0 PB B:DGT705 3.3 35.9 1.0 PA D:DGT705 3.4 35.4 1.0 PG B:DGT705 3.4 37.4 1.0 O3B D:DGT705 3.4 36.8 1.0 O3A D:DGT705 3.6 34.5 1.0 NZ A:LYS116 3.7 53.6 1.0 O3B B:DGT705 3.7 34.0 1.0 O3' D:DGT705 3.9 32.8 1.0 NZ B:LYS523 3.9 58.6 1.0 O3G D:DGT705 4.1 43.8 1.0 O2G D:DGT705 4.1 37.7 1.0 O3G B:DGT705 4.1 37.9 1.0 O2B B:DGT705 4.2 36.8 1.0 C5' D:DGT705 4.2 33.0 1.0 O5' D:DGT705 4.2 33.9 1.0 O D:HOH920 4.3 64.4 1.0 O3A B:DGT705 4.4 35.4 1.0 O1B D:DGT705 4.5 39.2 1.0 O D:HOH861 4.5 31.6 1.0 O1A D:DGT705 4.5 37.0 1.0 C3' D:DGT705 4.6 33.9 1.0 O1G B:DGT705 4.6 40.6 1.0 CE A:LYS116 4.8 52.1 1.0 C4' D:DGT705 4.9 33.9 1.0 O B:HOH842 5.0 39.1 1.0

Magnesium binding site 4 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:80.4 occ:1.00 O B:HOH910 1.8 76.0 1.0 O B:HOH909 1.9 64.2 1.0 O1B B:DCP701 1.9 68.0 1.0 O1G B:DCP701 2.2 55.8 1.0 O B:HOH908 2.3 55.2 1.0 O B:HOH907 2.5 59.0 1.0 PB B:DCP701 3.3 71.4 1.0 PG B:DCP701 3.5 56.7 1.0 O3B B:DCP701 3.9 60.6 1.0 NH1 B:ARG206 3.9 45.3 1.0 NH2 B:ARG206 3.9 49.1 1.0 NZ B:LYS312 4.0 48.1 1.0 OD2 B:ASP309 4.1 50.7 1.0 O3A B:DCP701 4.1 76.9 1.0 O B:HOH854 4.2 66.6 1.0 O2G B:DCP701 4.2 54.0 1.0 O B:HOH876 4.3 75.8 1.0 O B:HOH887 4.3 62.7 1.0 O2B B:DCP701 4.3 72.6 1.0 CZ B:ARG206 4.4 47.9 1.0 OD1 B:ASP309 4.5 46.5 1.0 O3G B:DCP701 4.6 60.3 1.0 OD2 B:ASP311 4.6 58.2 1.0 CG B:ASP309 4.8 51.3 1.0

Magnesium binding site 5 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:44.5 occ:1.00 O B:HOH833 1.8 33.6 1.0 O1G B:DGT703 1.9 46.3 1.0 O1B D:DGT702 2.0 38.8 1.0 O2A B:DGT703 2.0 35.4 1.0 O2B B:DGT703 2.1 40.0 1.0 O2G D:DGT702 2.2 33.8 1.0 PB B:DGT703 3.2 44.5 1.0 PG B:DGT703 3.2 44.2 1.0 PB D:DGT702 3.3 38.1 1.0 PA B:DGT703 3.3 38.0 1.0 PG D:DGT702 3.4 40.3 1.0 O3B B:DGT703 3.5 40.8 1.0 NZ C:LYS116 3.6 51.8 1.0 O3A B:DGT703 3.7 40.1 1.0 O3B D:DGT702 3.7 37.4 1.0 O3' B:DGT703 3.8 36.6 1.0 O3G D:DGT702 4.1 39.3 1.0 O3G B:DGT703 4.1 50.5 1.0 NZ D:LYS523 4.1 64.5 1.0 O2B D:DGT702 4.1 39.6 1.0 C5' B:DGT703 4.2 39.7 1.0 O2G B:DGT703 4.2 41.3 1.0 O5' B:DGT703 4.2 36.2 1.0 O B:HOH827 4.3 38.7 1.0 O D:HOH931 4.3 52.7 1.0 O3A D:DGT702 4.4 38.3 1.0 O B:HOH920 4.4 63.9 1.0 C3' B:DGT703 4.4 36.9 1.0 O1A B:DGT703 4.4 39.1 1.0 O1B B:DGT703 4.6 43.0 1.0 O1G D:DGT702 4.6 37.8 1.0 CE C:LYS116 4.7 51.6 1.0 C4' B:DGT703 4.8 39.2 1.0 CD C:LYS116 4.9 49.2 1.0

Magnesium binding site 6 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:85.2 occ:1.00 O2B C:DCP703 1.9 77.3 1.0 O C:HOH870 2.1 66.1 1.0 O1G C:DCP703 2.2 58.9 1.0 O C:HOH871 2.9 53.2 1.0 PB C:DCP703 3.3 72.5 1.0 PG C:DCP703 3.5 64.7 1.0 O C:HOH881 3.6 57.0 1.0 O3B C:DCP703 3.9 67.4 1.0 O2G C:DCP703 4.0 75.5 1.0 NZ C:LYS312 4.1 47.6 1.0 NH2 C:ARG206 4.2 60.5 1.0 O3A C:DCP703 4.3 85.2 1.0 O1B C:DCP703 4.3 72.0 1.0 NH1 C:ARG206 4.4 56.4 1.0 OD2 C:ASP309 4.4 53.8 1.0 O C:HOH879 4.5 62.4 1.0 O C:HOH853 4.5 56.9 1.0 O3G C:DCP703 4.7 64.7 1.0 CZ C:ARG206 4.8 56.8 1.0

Magnesium binding site 7 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:38.9 occ:1.00 O1G A:DGT703 1.9 41.3 1.0 O2G C:DGT701 2.0 40.2 1.0 O1B C:DGT701 2.0 37.8 1.0 O2B A:DGT703 2.0 40.3 1.0 O2A A:DGT703 2.1 34.1 1.0 O C:HOH826 2.2 35.5 1.0 PB A:DGT703 3.1 42.7 1.0 PG A:DGT703 3.2 42.0 1.0 PG C:DGT701 3.2 42.7 1.0 PB C:DGT701 3.3 39.2 1.0 O3B A:DGT703 3.4 39.6 1.0 PA A:DGT703 3.4 35.2 1.0 O3B C:DGT701 3.6 39.7 1.0 O3A A:DGT703 3.7 38.2 1.0 NZ D:LYS116 3.8 51.1 1.0 NZ C:LYS523 3.9 59.5 1.0 O3' A:DGT703 3.9 35.3 1.0 O3G A:DGT703 4.1 46.6 1.0 O3G C:DGT701 4.1 40.9 1.0 O2B C:DGT701 4.2 36.0 1.0 O2G A:DGT703 4.2 36.0 1.0 C5' A:DGT703 4.2 38.9 1.0 O5' A:DGT703 4.3 36.5 1.0 O1G C:DGT701 4.4 43.8 1.0 O3A C:DGT701 4.4 37.5 1.0 O1B A:DGT703 4.5 43.1 1.0 C3' A:DGT703 4.5 35.8 1.0 O A:HOH852 4.6 40.0 1.0 O1A A:DGT703 4.6 40.1 1.0 O D:HOH908 4.8 63.3 1.0 C4' A:DGT703 4.9 34.8 1.0 CE D:LYS116 4.9 45.9 1.0

Magnesium binding site 8 out of 8 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-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 Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:81.9 occ:1.00 O1G D:DCP703 1.9 62.8 1.0 O D:HOH938 2.0 64.7 1.0 O2B D:DCP703 2.0 58.1 1.0 O D:HOH937 2.1 54.4 1.0 O D:HOH939 2.2 59.2 1.0 O D:HOH940 2.4 56.6 1.0 PB D:DCP703 3.2 62.0 1.0 PG D:DCP703 3.2 52.4 1.0 O3B D:DCP703 3.7 58.7 1.0 NZ D:LYS312 3.7 42.2 1.0 OD2 D:ASP309 4.0 43.8 1.0 NH1 D:ARG206 4.1 41.4 1.0 NH2 D:ARG206 4.1 43.0 1.0 O2G D:DCP703 4.1 56.3 1.0 O3A D:DCP703 4.2 64.0 1.0 O3G D:DCP703 4.2 54.1 1.0 O1B D:DCP703 4.2 56.3 1.0 O D:HOH874 4.3 64.0 1.0 OD1 D:ASP309 4.5 44.6 1.0 CZ D:ARG206 4.6 41.8 1.0 CG D:ASP309 4.7 42.8 1.0 OD2 D:ASP311 4.7 56.5 1.0 O D:HOH866 4.7 53.2 1.0 CE D:LYS312 5.0 39.2 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