Magnesium in PDB 4to2: Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp Complex, PDB code: 4to2 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 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.313, 145.798, 98.257, 90.00, 114.22, 90.00
R / Rfree (%)	20.6 / 23.4

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp Complex (pdb code 4to2). 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-Dgtp-Dgtp- Dgtp/Dttp Complex, PDB code: 4to2:
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-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:81.5 occ:1.00 O2B A:DGT701 2.0 92.9 1.0 O1G A:DGT701 2.7 76.8 1.0 PB A:DGT701 3.5 92.5 1.0 O3G A:DGT701 3.7 82.7 1.0 PG A:DGT701 3.7 78.8 1.0 NH2 A:ARG206 3.7 64.8 1.0 O3B A:DGT701 4.2 84.7 1.0 NZ A:LYS312 4.2 59.2 1.0 NH1 A:ARG206 4.3 68.7 1.0 OD2 A:ASP309 4.4 63.2 1.0 O3A A:DGT701 4.4 93.2 1.0 CZ A:ARG206 4.5 65.5 1.0 O1B A:DGT701 4.5 87.5 1.0 OG A:SER302 4.8 71.1 1.0 O A:HOH824 4.9 72.6 1.0

Magnesium binding site 2 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:58.1 occ:1.00 O1G A:DGT704 1.4 54.6 1.0 O1G C:DGT706 1.8 58.0 1.0 O A:HOH805 2.0 47.4 1.0 O2B A:DGT704 2.0 52.1 1.0 O1B C:DGT706 2.1 55.5 1.0 O1A C:DGT706 2.1 53.4 1.0 PG A:DGT704 2.8 54.6 1.0 PB A:DGT704 3.1 52.0 1.0 PG C:DGT706 3.2 58.9 1.0 PB C:DGT706 3.2 55.5 1.0 O3B A:DGT704 3.3 53.4 1.0 PA C:DGT706 3.5 53.1 1.0 O2G A:DGT704 3.5 54.7 1.0 O3B C:DGT706 3.7 57.0 1.0 NZ A:LYS523 3.8 63.4 1.0 O3A C:DGT706 3.9 54.0 1.0 O3G A:DGT704 3.9 55.3 1.0 NZ B:LYS116 3.9 62.2 1.0 O2G C:DGT706 3.9 60.3 1.0 O1B A:DGT704 3.9 51.7 1.0 O3' C:DGT706 4.1 51.1 1.0 O3G C:DGT706 4.2 58.6 1.0 O3A A:DGT704 4.3 51.1 1.0 C5' C:DGT706 4.3 51.6 1.0 O5' C:DGT706 4.4 52.2 1.0 O2B C:DGT706 4.6 55.6 1.0 O2A C:DGT706 4.7 52.8 1.0 C3' C:DGT706 4.7 50.9 1.0 O A:HOH806 4.7 55.7 1.0 O C:HOH808 4.7 46.6 1.0 CE A:LYS523 4.8 64.1 1.0 O A:HOH823 4.8 56.2 1.0 C4' C:DGT706 4.9 50.9 1.0

Magnesium binding site 3 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:45.4 occ:1.00 O2B B:DGT704 1.9 44.9 1.0 O1B D:DGT704 1.9 46.1 1.0 O1A D:DGT704 2.0 45.5 1.0 O2G B:DGT704 2.0 45.6 1.0 O3G D:DGT704 2.1 46.9 1.0 O D:HOH810 2.2 39.6 1.0 PB D:DGT704 3.1 46.2 1.0 PB B:DGT704 3.1 44.7 1.0 PA D:DGT704 3.3 45.4 1.0 PG B:DGT704 3.3 45.3 1.0 PG D:DGT704 3.4 47.2 1.0 O3B D:DGT704 3.6 46.7 1.0 O3B B:DGT704 3.6 44.9 1.0 O3A D:DGT704 3.6 45.7 1.0 NZ A:LYS116 3.7 53.6 1.0 O3' D:DGT704 3.8 44.5 1.0 O D:HOH849 3.8 54.5 1.0 O1B B:DGT704 4.0 44.5 1.0 C5' D:DGT704 4.0 44.6 1.0 O3G B:DGT704 4.1 45.3 1.0 NZ B:LYS523 4.1 55.9 1.0 O5' D:DGT704 4.1 44.9 1.0 O3A B:DGT704 4.2 44.3 1.0 O2G D:DGT704 4.3 47.5 1.0 O2B D:DGT704 4.3 46.3 1.0 O1G D:DGT704 4.3 47.5 1.0 O1G B:DGT704 4.4 45.5 1.0 C3' D:DGT704 4.4 44.6 1.0 O2A D:DGT704 4.5 45.6 1.0 O D:HOH828 4.5 40.2 1.0 C4' D:DGT704 4.7 44.4 1.0 CE A:LYS116 4.9 54.4 1.0

Magnesium binding site 4 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:75.0 occ:1.00 O1B B:DGT701 1.8 75.9 1.0 O B:HOH828 2.3 56.7 1.0 O3G B:DGT701 2.5 64.9 1.0 O B:HOH827 3.2 57.6 1.0 PB B:DGT701 3.3 77.6 1.0 PG B:DGT701 3.6 65.5 1.0 O2G B:DGT701 3.7 67.6 1.0 NH2 B:ARG206 3.9 54.8 1.0 O3B B:DGT701 4.0 70.5 1.0 O2B B:DGT701 4.2 77.0 1.0 O3A B:DGT701 4.3 79.3 1.0 NZ B:LYS312 4.5 45.1 1.0 O B:HOH846 4.6 57.4 1.0 NH1 B:ARG206 4.7 54.6 1.0 CZ B:ARG206 4.8 54.3 1.0 OD2 B:ASP309 4.9 49.2 1.0 O1G B:DGT701 5.0 68.0 1.0 OE2 B:GLU234 5.0 75.8 1.0

Magnesium binding site 5 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:50.5 occ:1.00 O1B A:DGT703 1.6 55.1 1.0 O1G C:DGT701 2.0 53.0 1.0 O1A A:DGT703 2.0 51.3 1.0 O2G A:DGT703 2.0 56.7 1.0 O2B C:DGT701 2.1 50.1 1.0 O A:HOH804 2.3 50.3 1.0 PB A:DGT703 2.8 55.3 1.0 PG A:DGT703 3.2 57.2 1.0 PB C:DGT701 3.2 50.3 1.0 PA A:DGT703 3.2 51.1 1.0 PG C:DGT701 3.3 53.6 1.0 O3A A:DGT703 3.4 52.7 1.0 O3B A:DGT703 3.4 56.2 1.0 O3B C:DGT701 3.6 51.5 1.0 NZ D:LYS116 3.8 60.3 1.0 O3' A:DGT703 3.9 48.1 1.0 NZ C:LYS523 3.9 80.7 1.0 O1B C:DGT701 4.0 49.8 1.0 O2B A:DGT703 4.1 55.3 1.0 O3G A:DGT703 4.1 56.5 1.0 C5' A:DGT703 4.1 48.7 1.0 O5' A:DGT703 4.2 49.5 1.0 O2G C:DGT701 4.2 53.1 1.0 O1G A:DGT703 4.3 59.7 1.0 O3G C:DGT701 4.4 53.7 1.0 O3A C:DGT701 4.5 49.1 1.0 O2A A:DGT703 4.5 51.0 1.0 C3' A:DGT703 4.5 47.6 1.0 O A:HOH836 4.7 42.2 1.0 C4' A:DGT703 4.8 47.7 1.0 CE C:LYS523 5.0 79.7 1.0

Magnesium binding site 6 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:48.1 occ:1.00 O1B B:DGT703 1.5 53.3 1.0 O3G B:DGT703 1.9 53.7 1.0 O2A B:DGT703 1.9 49.8 1.0 O1G D:DGT701 2.0 46.4 1.0 O2B D:DGT701 2.1 45.3 1.0 O D:HOH807 2.2 41.8 1.0 PB B:DGT703 2.7 52.8 1.0 PG B:DGT703 3.1 55.9 1.0 PA B:DGT703 3.1 50.1 1.0 O3B B:DGT703 3.2 53.9 1.0 PB D:DGT701 3.3 44.7 1.0 O3A B:DGT703 3.3 51.1 1.0 PG D:DGT701 3.3 45.9 1.0 O3B D:DGT701 3.6 45.2 1.0 NZ C:LYS116 3.6 64.1 1.0 O2B B:DGT703 3.9 54.2 1.0 NZ D:LYS523 4.0 61.0 1.0 O3' B:DGT703 4.0 46.3 1.0 C5' B:DGT703 4.0 47.9 1.0 O5' B:DGT703 4.0 49.0 1.0 O1G B:DGT703 4.0 55.9 1.0 O1B D:DGT701 4.1 44.7 1.0 O2G B:DGT703 4.1 55.2 1.0 O2G D:DGT701 4.2 45.7 1.0 O1A B:DGT703 4.4 50.2 1.0 O3G D:DGT701 4.4 46.0 1.0 O3A D:DGT701 4.5 43.7 1.0 C3' B:DGT703 4.6 46.7 1.0 O D:HOH808 4.6 55.5 1.0 C4' B:DGT703 4.8 47.0 1.0 CE C:LYS116 4.8 64.3 1.0

Magnesium binding site 7 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:92.0 occ:1.00 O2B C:TTP704 2.9 97.5 1.0 O1G C:TTP704 2.9 84.2 1.0 OD2 C:ASP309 3.2 79.2 1.0 NZ C:LYS312 3.7 68.9 1.0 NH1 C:ARG206 3.9 70.0 1.0 NH2 C:ARG206 4.0 68.4 1.0 CG C:ASP309 4.1 75.5 1.0 PG C:TTP704 4.1 81.1 1.0 OD1 C:ASP309 4.2 80.2 1.0 O3G C:TTP704 4.2 84.8 1.0 PB C:TTP704 4.4 0.5 1.0 OG C:SER302 4.4 69.1 1.0 CZ C:ARG206 4.4 69.1 1.0 O3B C:TTP704 4.8 92.6 1.0 O C:GLY307 4.9 70.4 1.0 CA C:GLY307 4.9 75.2 1.0

Magnesium binding site 8 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Dgtp- Dgtp/Dttp 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-Dgtp-Dgtp- Dgtp/Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:66.0 occ:1.00 O1B D:DGT702 1.9 82.5 1.0 O D:HOH875 2.2 62.4 1.0 O3G D:DGT702 2.4 65.3 1.0 O D:HOH865 2.7 62.9 1.0 PB D:DGT702 3.3 86.1 1.0 PG D:DGT702 3.4 65.1 1.0 O1G D:DGT702 3.6 65.8 1.0 O D:HOH830 3.6 60.1 1.0 O3B D:DGT702 3.9 74.5 1.0 NZ D:LYS312 4.0 44.3 1.0 O2B D:DGT702 4.1 81.7 1.0 O3A D:DGT702 4.4 84.9 1.0 NH2 D:ARG206 4.5 45.5 1.0 O2G D:DGT702 4.7 64.7 1.0 OD2 D:ASP309 4.9 47.9 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