Magnesium in PDB 4to5: Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dctp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dctp Complex, PDB code: 4to5 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 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.459, 145.121, 98.233, 90.00, 114.13, 90.00
R / Rfree (%)	27.1 / 28.5

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dctp Complex (pdb code 4to5). 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-Dttp-Dctp Complex, PDB code: 4to5:
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-Dttp-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-Dttp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:0.5 occ:1.00 O3G B:GTP701 1.9 97.2 1.0 O2B A:TTP703 1.9 82.3 1.0 O2G A:TTP703 1.9 94.0 1.0 O A:HOH801 2.0 88.9 1.0 O1B B:GTP701 2.0 99.2 1.0 O2A B:GTP701 2.1 91.8 1.0 PB B:GTP701 3.2 98.3 1.0 PG B:GTP701 3.2 0.7 1.0 PG A:TTP703 3.3 98.9 1.0 PB A:TTP703 3.3 89.0 1.0 NZ A:LYS523 3.3 0.1 1.0 PA B:GTP701 3.5 89.2 1.0 NZ B:LYS116 3.5 99.0 1.0 O3B B:GTP701 3.7 93.2 1.0 O3B A:TTP703 3.7 81.4 1.0 O3A B:GTP701 3.8 96.5 1.0 CE B:LYS116 3.9 98.8 1.0 O1G A:TTP703 3.9 0.6 1.0 O2G B:GTP701 4.0 0.0 1.0 O3' B:GTP701 4.0 89.2 1.0 C5' B:GTP701 4.1 78.8 1.0 O1B A:TTP703 4.2 81.9 1.0 O3A A:TTP703 4.3 83.6 1.0 O5' B:GTP701 4.3 73.7 1.0 O1G B:GTP701 4.4 0.1 1.0 O3G A:TTP703 4.4 0.7 1.0 O2B B:GTP701 4.5 0.8 1.0 C3' B:GTP701 4.5 80.8 1.0 O1A B:GTP701 4.6 88.4 1.0 CE A:LYS523 4.7 0.2 1.0 C4' B:GTP701 4.8 80.1 1.0

Magnesium binding site 2 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-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-Dttp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:93.4 occ:1.00 O3G D:GTP703 1.8 98.1 1.0 O2A D:GTP703 2.0 78.9 1.0 O1B B:TTP702 2.0 69.3 1.0 O2G B:TTP702 2.0 56.2 1.0 O1B D:GTP703 2.4 83.3 1.0 O B:HOH801 2.4 68.4 1.0 NZ A:LYS116 3.2 99.2 1.0 PG D:GTP703 3.2 86.5 1.0 PA D:GTP703 3.4 91.3 1.0 PB D:GTP703 3.4 90.2 1.0 PB B:TTP702 3.4 80.8 1.0 PG B:TTP702 3.4 82.3 1.0 NZ B:LYS523 3.5 0.9 1.0 O3B D:GTP703 3.6 78.3 1.0 O3A D:GTP703 3.8 96.0 1.0 O3B B:TTP702 3.9 69.1 1.0 O3' D:GTP703 3.9 73.8 1.0 C5' D:GTP703 4.0 85.5 1.0 O2G D:GTP703 4.1 0.5 1.0 O1G D:GTP703 4.2 85.5 1.0 O5' D:GTP703 4.2 81.9 1.0 O3G B:TTP702 4.3 95.1 1.0 O2B B:TTP702 4.3 65.3 1.0 CE B:LYS523 4.3 0.7 1.0 O3A B:TTP702 4.4 86.4 1.0 C3' D:GTP703 4.4 78.4 1.0 O1G B:TTP702 4.4 69.6 1.0 O1A D:GTP703 4.5 78.8 1.0 CE A:LYS116 4.6 0.6 1.0 C4' D:GTP703 4.7 84.0 1.0 O2B D:GTP703 4.7 0.9 1.0

Magnesium binding site 3 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-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-Dttp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:0.6 occ:1.00 O3G B:GTP704 1.8 96.3 1.0 O2A B:GTP704 2.0 0.4 1.0 O D:HOH801 2.0 72.8 1.0 O2B D:TTP704 2.0 85.2 1.0 O3G D:TTP704 2.1 92.8 1.0 O1B B:GTP704 2.2 0.9 1.0 PG B:GTP704 3.2 0.9 1.0 NZ C:LYS116 3.3 99.2 1.0 PB B:GTP704 3.3 0.5 1.0 PA B:GTP704 3.4 0.4 1.0 PG D:TTP704 3.4 85.2 1.0 PB D:TTP704 3.4 88.5 1.0 O3B B:GTP704 3.6 0.8 1.0 O3' B:GTP704 3.8 82.6 1.0 O3B D:TTP704 3.9 81.5 1.0 O3A B:GTP704 3.9 0.8 1.0 NZ D:LYS523 3.9 0.4 1.0 O1G D:TTP704 3.9 83.5 1.0 O1G B:GTP704 4.1 0.3 1.0 C5' B:GTP704 4.1 88.2 1.0 O1B D:TTP704 4.2 84.2 1.0 O2G B:GTP704 4.2 0.3 1.0 O5' B:GTP704 4.3 88.4 1.0 C3' B:GTP704 4.4 80.8 1.0 O1A B:GTP704 4.4 0.5 1.0 O2G D:TTP704 4.5 89.5 1.0 O3A D:TTP704 4.5 79.1 1.0 O2B B:GTP704 4.6 0.6 1.0 CE C:LYS116 4.7 97.3 1.0 C4' B:GTP704 4.8 83.0 1.0

Magnesium binding site 4 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-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-Dttp-Dctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:85.4 occ:1.00 O1B A:GTP702 1.7 80.0 1.0 O1B C:TTP701 1.8 66.4 1.0 O3G C:TTP701 1.9 90.6 1.0 O3G A:GTP702 2.2 73.6 1.0 O2A A:GTP702 2.2 82.5 1.0 O C:HOH801 2.2 67.3 1.0 PB A:GTP702 3.0 83.6 1.0 PB C:TTP701 3.1 79.0 1.0 PG C:TTP701 3.3 79.2 1.0 PA A:GTP702 3.4 80.0 1.0 PG A:GTP702 3.4 92.1 1.0 O3B C:TTP701 3.6 81.1 1.0 O3A A:GTP702 3.6 81.3 1.0 O3B A:GTP702 3.7 83.0 1.0 NZ C:LYS523 3.7 0.9 1.0 O3' A:GTP702 3.8 84.6 1.0 O2B C:TTP701 3.9 69.5 1.0 C5' A:GTP702 4.0 70.7 1.0 NZ D:LYS116 4.1 0.2 1.0 O1G C:TTP701 4.1 73.2 1.0 O2G C:TTP701 4.1 74.9 1.0 O5' A:GTP702 4.2 70.9 1.0 O3A C:TTP701 4.3 68.2 1.0 O2B A:GTP702 4.3 78.7 1.0 CE D:LYS116 4.3 0.4 1.0 O1G A:GTP702 4.4 0.5 1.0 C3' A:GTP702 4.4 75.8 1.0 O2G A:GTP702 4.4 97.6 1.0 C4' A:GTP702 4.6 73.2 1.0 O1A A:GTP702 4.7 88.9 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