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

The structure of Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp-Dgtp Complex, PDB code: 4tny 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 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.253, 141.874, 98.333, 90.00, 116.38, 90.00
R / Rfree (%)	21.4 / 24.4

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

Magnesium binding site 1 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp-Dgtp 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-Datp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:28.7 occ:1.00 O3G B:DTP704 1.6 25.0 1.0 O1B D:DGT705 1.8 28.9 1.0 O1B B:DTP704 1.8 21.2 1.0 O2A D:DGT705 1.9 30.5 1.0 O2G D:DGT705 2.1 30.4 1.0 O D:HOH802 2.2 40.4 1.0 PG B:DTP704 2.9 24.6 1.0 PB B:DTP704 2.9 22.6 1.0 PB D:DGT705 3.1 29.8 1.0 PA D:DGT705 3.3 29.3 1.0 O3B B:DTP704 3.3 23.4 1.0 PG D:DGT705 3.4 31.0 1.0 O2G B:DTP704 3.6 22.7 1.0 O3A D:DGT705 3.6 27.7 1.0 O3B D:DGT705 3.7 30.9 1.0 O2B B:DTP704 3.8 23.3 1.0 O3' D:DGT705 3.8 28.1 1.0 NZ A:LYS116 3.9 0.4 1.0 NZ B:LYS523 3.9 81.0 1.0 O3G D:DGT705 4.0 35.5 1.0 O1G B:DTP704 4.0 23.8 1.0 O3A B:DTP704 4.2 22.6 1.0 C5' D:DGT705 4.3 28.6 1.0 O1A D:DGT705 4.3 28.5 1.0 O5' D:DGT705 4.3 28.2 1.0 C3' D:DGT705 4.4 28.5 1.0 O2B D:DGT705 4.4 30.6 1.0 O1G D:DGT705 4.6 29.2 1.0 O D:HOH803 4.6 38.0 1.0 C4' D:DGT705 4.6 28.6 1.0 CE A:LYS116 5.0 96.2 1.0

Magnesium binding site 2 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp-Dgtp 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-Datp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:45.5 occ:1.00 O3G D:DTP703 1.7 28.5 1.0 O2G B:DGT703 1.8 34.0 1.0 O B:HOH801 1.9 67.5 1.0 O1B D:DTP703 2.0 27.8 1.0 O2A B:DGT703 2.0 32.2 1.0 O1B B:DGT703 2.2 29.2 1.0 PG D:DTP703 3.0 28.2 1.0 PB D:DTP703 3.2 27.5 1.0 PG B:DGT703 3.2 31.5 1.0 PB B:DGT703 3.3 28.6 1.0 PA B:DGT703 3.4 34.0 1.0 O3B D:DTP703 3.4 28.4 1.0 NZ C:LYS116 3.5 82.4 1.0 O2G D:DTP703 3.5 23.7 1.0 O3B B:DGT703 3.6 30.0 1.0 O3' B:DGT703 3.6 32.3 1.0 O3A B:DGT703 3.8 30.1 1.0 NZ D:LYS523 3.9 80.2 1.0 O3G B:DGT703 3.9 30.5 1.0 C5' B:DGT703 4.2 35.1 1.0 O3A D:DTP703 4.2 28.9 1.0 O1G D:DTP703 4.3 25.1 1.0 O1G B:DGT703 4.3 29.6 1.0 C3' B:DGT703 4.3 31.0 1.0 O2B D:DTP703 4.3 29.2 1.0 O5' B:DGT703 4.3 36.2 1.0 O1A B:DGT703 4.6 32.5 1.0 O2B B:DGT703 4.6 32.3 1.0 CE C:LYS116 4.7 79.4 1.0 C4' B:DGT703 4.7 33.5 1.0 CD C:LYS116 4.9 78.2 1.0

Magnesium binding site 3 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp-Dgtp 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-Datp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:32.1 occ:1.00 O2G C:DGT703 1.7 26.4 1.0 O A:HOH801 1.8 62.1 1.0 O3G A:DTP702 2.0 27.8 1.0 O1B A:DTP702 2.0 24.7 1.0 O2A C:DGT703 2.1 27.4 1.0 O1B C:DGT703 2.3 25.0 1.0 PG C:DGT703 3.1 27.8 1.0 PG A:DTP702 3.3 27.3 1.0 PB A:DTP702 3.3 24.5 1.0 NZ B:LYS116 3.4 60.5 1.0 PB C:DGT703 3.4 25.4 1.0 PA C:DGT703 3.5 27.4 1.0 O3B C:DGT703 3.7 26.0 1.0 O3B A:DTP702 3.7 25.4 1.0 NZ A:LYS523 3.8 71.0 1.0 O3' C:DGT703 3.8 29.0 1.0 O2G A:DTP702 3.9 27.7 1.0 O3A C:DGT703 4.0 25.3 1.0 O3G C:DGT703 4.0 26.4 1.0 O1G C:DGT703 4.1 28.2 1.0 O C:HOH801 4.2 40.1 1.0 O3A A:DTP702 4.3 24.3 1.0 O2B A:DTP702 4.3 24.8 1.0 O1G A:DTP702 4.4 26.9 1.0 C5' C:DGT703 4.4 27.2 1.0 O5' C:DGT703 4.5 27.6 1.0 C3' C:DGT703 4.5 28.9 1.0 CE B:LYS116 4.5 60.2 1.0 O1A C:DGT703 4.5 28.9 1.0 O2B C:DGT703 4.7 26.3 1.0 O A:HOH802 4.7 34.4 1.0 CD B:LYS116 4.8 61.1 1.0 CE A:LYS523 4.9 71.5 1.0 CG B:LYS116 4.9 62.4 1.0 C4' C:DGT703 4.9 28.1 1.0

Magnesium binding site 4 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp-Dgtp 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-Datp-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:30.3 occ:1.00 O2G D:DGT702 1.8 28.8 1.0 O1B D:DGT702 2.0 29.5 1.0 O D:HOH804 2.0 34.2 1.0 O2A D:DGT702 2.0 26.9 1.0 O1B C:DTP701 2.0 25.3 1.0 O3G C:DTP701 2.0 25.1 1.0 PG D:DGT702 3.1 27.4 1.0 PB D:DGT702 3.1 28.4 1.0 PB C:DTP701 3.4 24.9 1.0 PA D:DGT702 3.4 28.3 1.0 NZ D:LYS116 3.4 58.0 1.0 PG C:DTP701 3.4 27.6 1.0 O3B D:DGT702 3.5 29.0 1.0 O3A D:DGT702 3.7 27.5 1.0 NZ C:LYS523 3.8 66.6 1.0 O3B C:DTP701 3.8 25.1 1.0 O3' D:DGT702 3.8 35.2 1.0 O1G D:DGT702 4.0 28.1 1.0 O3G D:DGT702 4.1 27.0 1.0 C5' D:DGT702 4.1 30.6 1.0 O5' D:DGT702 4.3 30.2 1.0 O2B C:DTP701 4.3 27.9 1.0 C3' D:DGT702 4.3 31.7 1.0 O1G C:DTP701 4.4 28.4 1.0 O3A C:DTP701 4.4 24.8 1.0 O2G C:DTP701 4.4 30.4 1.0 O2B D:DGT702 4.5 30.8 1.0 O1A D:DGT702 4.5 29.4 1.0 CE D:LYS116 4.6 57.9 1.0 C4' D:DGT702 4.7 30.8 1.0 CD D:LYS116 4.8 58.6 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