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

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dttp Complex, PDB code: 4tnz 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)	88.29 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.126, 141.749, 98.474, 90.00, 116.29, 90.00
R / Rfree (%)	21.2 / 24.3

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Dttp Complex (pdb code 4tnz). 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-Datp-Dttp Complex, PDB code: 4tnz:
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-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:77.6 occ:1.00 O1B C:TTP701 2.3 0.8 1.0 O2G C:TTP701 2.8 75.5 1.0 O2B C:TTP701 3.0 92.4 1.0 PB C:TTP701 3.0 92.9 1.0 O3G C:TTP701 3.5 75.8 1.0 PG C:TTP701 3.5 70.3 1.0 O3B C:TTP701 3.8 89.2 1.0 NH2 C:ARG206 3.9 57.9 1.0 O3A C:TTP701 4.5 87.7 1.0 NZ C:LYS312 4.6 51.0 1.0 NH1 C:ARG206 4.6 61.1 1.0 CZ C:ARG206 4.7 59.5 1.0 O1A C:TTP701 4.9 97.2 1.0 OD2 C:ASP309 4.9 56.9 1.0 O1G C:TTP701 5.0 78.2 1.0

Magnesium binding site 2 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:77.2 occ:1.00 O D:HOH805 1.7 53.5 1.0 O3G D:DTP705 1.8 74.1 1.0 O1B B:GTP704 1.8 75.6 1.0 O2B D:DTP705 1.9 59.8 1.0 O1G B:GTP704 2.0 78.3 1.0 O1A B:GTP704 2.2 71.2 1.0 PB B:GTP704 3.1 80.2 1.0 PG D:DTP705 3.2 70.1 1.0 PG B:GTP704 3.2 81.0 1.0 PB D:DTP705 3.3 62.2 1.0 NZ C:LYS116 3.5 85.1 1.0 PA B:GTP704 3.6 69.9 1.0 O3B B:GTP704 3.6 77.8 1.0 O3B D:DTP705 3.7 65.6 1.0 O3A B:GTP704 3.8 74.8 1.0 O1G D:DTP705 3.9 68.0 1.0 O3' B:GTP704 4.1 64.6 1.0 O3G B:GTP704 4.1 80.3 1.0 O2G B:GTP704 4.2 83.9 1.0 C5' B:GTP704 4.3 69.2 1.0 O1B D:DTP705 4.3 61.5 1.0 O3A D:DTP705 4.3 60.9 1.0 O2G D:DTP705 4.3 69.5 1.0 O2B B:GTP704 4.3 80.4 1.0 NZ D:LYS523 4.3 87.8 1.0 O5' B:GTP704 4.4 68.5 1.0 O B:HOH804 4.4 42.0 1.0 C3' B:GTP704 4.7 60.3 1.0 CE C:LYS116 4.7 82.6 1.0 O2A B:GTP704 4.7 69.6 1.0 CD C:LYS116 5.0 79.1 1.0 C4' B:GTP704 5.0 63.5 1.0

Magnesium binding site 3 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:54.0 occ:1.00 O3G A:DTP701 1.6 44.5 1.0 O1B C:GTP703 1.6 39.3 1.0 O1G C:GTP703 1.9 42.4 1.0 O1B A:DTP701 2.0 37.9 1.0 O C:HOH823 2.0 35.3 1.0 O1A C:GTP703 2.3 37.9 1.0 PG A:DTP701 3.0 41.3 1.0 PB C:GTP703 3.0 41.8 1.0 PB A:DTP701 3.1 35.7 1.0 PG C:GTP703 3.2 42.8 1.0 O3B A:DTP701 3.5 36.0 1.0 O3B C:GTP703 3.5 39.2 1.0 PA C:GTP703 3.6 39.9 1.0 NZ A:LYS523 3.6 63.0 1.0 O C:HOH815 3.8 72.2 1.0 NZ B:LYS116 3.8 52.7 1.0 O1G A:DTP701 3.8 37.3 1.0 O3A C:GTP703 3.8 39.5 1.0 O A:HOH817 4.0 51.9 1.0 O2G C:GTP703 4.0 42.5 1.0 O2B A:DTP701 4.0 35.9 1.0 O2G A:DTP701 4.1 37.6 1.0 O2B C:GTP703 4.2 44.5 1.0 O3' C:GTP703 4.2 45.2 1.0 O3G C:GTP703 4.2 47.6 1.0 C5' C:GTP703 4.2 36.9 1.0 O3A A:DTP701 4.3 35.4 1.0 O5' C:GTP703 4.5 37.8 1.0 C3' C:GTP703 4.7 39.1 1.0 O2A C:GTP703 4.8 37.7 1.0 CE A:LYS523 5.0 63.1 1.0 C4' C:GTP703 5.0 36.2 1.0 CE B:LYS116 5.0 52.0 1.0

Magnesium binding site 4 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:85.4 occ:1.00 O2B A:TTP703 1.9 0.4 1.0 NH2 A:ARG206 2.7 63.7 1.0 O3G A:TTP703 2.8 80.5 1.0 PB A:TTP703 3.2 1.0 1.0 NH1 A:ARG206 3.4 68.3 1.0 CZ A:ARG206 3.5 65.2 1.0 O1B A:TTP703 3.9 95.6 1.0 PG A:TTP703 3.9 72.6 1.0 O3B A:TTP703 4.0 89.0 1.0 OD2 A:ASP311 4.1 70.8 1.0 O1G A:TTP703 4.2 79.7 1.0 O2A A:TTP703 4.3 94.1 1.0 O3A A:TTP703 4.4 0.9 1.0 OD2 A:ASP309 4.5 60.1 1.0 NZ A:LYS312 4.7 61.1 1.0 CG A:ASP311 4.7 66.8 1.0 OD1 A:ASP309 4.8 54.2 1.0 NE A:ARG206 4.8 62.1 1.0 OG A:SER302 4.8 70.5 1.0 CB A:ASP311 5.0 56.4 1.0

Magnesium binding site 5 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:76.7 occ:1.00 O1G B:DTP701 1.6 58.3 1.0 O2B D:GTP704 1.7 59.1 1.0 O A:HOH808 2.0 58.7 1.0 O2G D:GTP704 2.0 64.3 1.0 O1B B:DTP701 2.1 61.3 1.0 O2A D:GTP704 2.3 57.2 1.0 PG B:DTP701 3.0 60.6 1.0 PB D:GTP704 3.1 65.7 1.0 PG D:GTP704 3.2 68.8 1.0 PB B:DTP701 3.3 55.1 1.0 NZ A:LYS116 3.5 86.6 1.0 O3B B:DTP701 3.5 60.0 1.0 O3B D:GTP704 3.6 64.0 1.0 NZ B:LYS523 3.6 86.1 1.0 PA D:GTP704 3.6 59.3 1.0 O2G B:DTP701 3.7 60.5 1.0 O D:HOH813 3.8 75.3 1.0 O3A D:GTP704 3.8 58.9 1.0 O3' D:GTP704 4.0 54.0 1.0 O3G D:GTP704 4.2 68.9 1.0 O1G D:GTP704 4.2 71.4 1.0 O3G B:DTP701 4.2 60.3 1.0 O1B D:GTP704 4.2 60.0 1.0 O2B B:DTP701 4.3 60.0 1.0 O3A B:DTP701 4.4 54.0 1.0 O D:HOH806 4.4 50.2 1.0 C5' D:GTP704 4.4 57.3 1.0 O5' D:GTP704 4.6 57.4 1.0 CE A:LYS116 4.7 85.2 1.0 C3' D:GTP704 4.7 54.0 1.0 O1A D:GTP704 4.8 56.8 1.0 CE B:LYS523 4.9 88.4 1.0

Magnesium binding site 6 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:52.2 occ:1.00 O2B A:GTP705 1.8 53.7 1.0 O2G A:GTP705 1.8 50.6 1.0 O1G C:DTP704 1.9 51.0 1.0 O C:HOH803 2.0 48.5 1.0 O2B C:DTP704 2.1 45.3 1.0 O2A A:GTP705 2.2 45.3 1.0 PG A:GTP705 3.0 53.8 1.0 PB A:GTP705 3.1 51.4 1.0 PG C:DTP704 3.2 48.6 1.0 O3B A:GTP705 3.4 50.7 1.0 PB C:DTP704 3.4 44.0 1.0 NZ D:LYS116 3.5 61.3 1.0 PA A:GTP705 3.5 46.2 1.0 NZ C:LYS523 3.5 68.8 1.0 O3B C:DTP704 3.7 46.7 1.0 O3A A:GTP705 3.8 49.7 1.0 O3G A:GTP705 4.0 54.3 1.0 O1G A:GTP705 4.0 53.3 1.0 O2G C:DTP704 4.0 52.9 1.0 O3' A:GTP705 4.1 41.4 1.0 O A:HOH829 4.2 63.5 1.0 O1B C:DTP704 4.3 40.8 1.0 C5' A:GTP705 4.4 46.0 1.0 O1B A:GTP705 4.4 51.6 1.0 O3G C:DTP704 4.4 52.4 1.0 O5' A:GTP705 4.4 48.5 1.0 O3A C:DTP704 4.5 43.3 1.0 O A:HOH810 4.5 44.7 1.0 CE D:LYS116 4.6 58.4 1.0 O1A A:GTP705 4.7 45.4 1.0 C3' A:GTP705 4.7 41.6 1.0 CE C:LYS523 4.9 68.7 1.0 CD D:LYS116 4.9 54.6 1.0

Magnesium binding site 7 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:85.1 occ:1.00 O2B D:TTP702 2.7 91.7 1.0 O2G D:TTP702 2.8 88.2 1.0 O1G D:TTP702 3.8 88.4 1.0 PG D:TTP702 3.9 81.2 1.0 NZ D:LYS312 4.1 72.7 1.0 PB D:TTP702 4.2 0.5 1.0 OD2 D:ASP309 4.3 59.2 1.0 NH2 D:ARG206 4.5 72.3 1.0 O3B D:TTP702 4.6 93.8 1.0 NH1 D:ARG206 4.8 69.8 1.0 OG D:SER302 4.9 59.0 1.0

Magnesium binding site 8 out of 8 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-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-Gtp-Datp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:92.0 occ:1.00 O3G B:TTP702 2.6 98.0 1.0 O3B B:TTP702 3.0 98.7 1.0 PG B:TTP702 3.3 0.1 1.0 O1B B:TTP702 3.3 0.1 1.0 NZ B:LYS312 3.5 0.3 1.0 PB B:TTP702 3.5 0.0 1.0 O1G B:TTP702 3.7 0.9 1.0 OD2 B:ASP309 3.8 88.5 1.0 O2B B:TTP702 3.8 0.9 1.0 NH2 B:ARG206 4.5 92.2 1.0 OD1 B:ASP309 4.6 74.9 1.0 NH1 B:ARG206 4.6 87.9 1.0 CG B:ASP309 4.7 83.8 1.0 O2G B:TTP702 4.7 90.4 1.0 CE B:LYS312 4.9 95.0 1.0 O B:GLY307 5.0 83.6 1.0 CA B:GLY307 5.0 81.1 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