Magnesium in PDB 4to6: Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp- Dttp/Dgtp Complex

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp- Dttp/Dgtp Complex, PDB code: 4to6 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 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.587, 140.808, 96.900, 90.00, 114.94, 90.00
R / Rfree (%)	22.5 / 24.4

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp- Dttp/Dgtp Complex (pdb code 4to6). 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-Dgtp-Datp- Dttp/Dgtp Complex, PDB code: 4to6:
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-Dgtp-Datp- Dttp/Dgtp 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-Datp- Dttp/Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:59.0 occ:1.00 O3G D:DGT704 1.7 50.9 1.0 O2A D:DGT704 1.9 40.9 1.0 O2G B:DTP704 1.9 46.4 1.0 O B:HOH803 2.0 45.5 1.0 O1B B:DTP704 2.0 41.8 1.0 O1B D:DGT704 2.2 44.6 1.0 PG D:DGT704 3.1 50.6 1.0 PG B:DTP704 3.2 48.4 1.0 PB D:DGT704 3.3 46.1 1.0 PA D:DGT704 3.3 42.3 1.0 PB B:DTP704 3.4 41.4 1.0 NZ A:LYS116 3.4 54.8 1.0 O3B D:DGT704 3.5 48.1 1.0 O3A D:DGT704 3.7 44.5 1.0 O3B B:DTP704 3.8 43.8 1.0 O1G B:DTP704 3.8 44.4 1.0 O3' D:DGT704 3.8 41.3 1.0 NZ B:LYS523 3.8 66.2 1.0 O2G D:DGT704 3.9 48.1 1.0 C5' D:DGT704 4.0 42.0 1.0 O1G D:DGT704 4.1 51.5 1.0 O5' D:DGT704 4.2 41.6 1.0 O3A B:DTP704 4.3 40.5 1.0 C3' D:DGT704 4.3 40.9 1.0 O D:HOH806 4.3 35.8 1.0 O3G B:DTP704 4.4 49.1 1.0 O2B B:DTP704 4.4 40.6 1.0 O1A D:DGT704 4.5 39.4 1.0 C4' D:DGT704 4.5 41.4 1.0 CE A:LYS116 4.6 53.9 1.0 O2B D:DGT704 4.6 48.8 1.0 CE B:LYS523 4.8 65.5 1.0 CD A:LYS116 4.9 54.7 1.0

Magnesium binding site 2 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp- Dttp/Dgtp 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-Datp- Dttp/Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:55.3 occ:1.00 O1A C:DGT704 1.8 54.8 1.0 O3G A:DTP703 1.8 56.5 1.0 O2B A:DTP703 1.9 52.5 1.0 O A:HOH808 2.0 51.4 1.0 O2B C:DGT704 2.0 61.7 1.0 O3G C:DGT704 2.1 69.6 1.0 PG C:DGT704 3.1 68.3 1.0 PA C:DGT704 3.1 55.6 1.0 PB C:DGT704 3.1 63.1 1.0 PG A:DTP703 3.2 56.5 1.0 PB A:DTP703 3.2 50.5 1.0 O1G C:DGT704 3.3 71.6 1.0 NZ B:LYS116 3.4 71.6 1.0 O3A C:DGT704 3.5 59.1 1.0 O3B C:DGT704 3.5 65.5 1.0 NZ A:LYS523 3.7 70.5 1.0 O3B A:DTP703 3.7 52.1 1.0 O1G A:DTP703 3.9 56.9 1.0 C5' C:DGT704 4.0 54.7 1.0 O5' C:DGT704 4.0 55.8 1.0 O3' C:DGT704 4.1 54.1 1.0 O1B A:DTP703 4.2 49.0 1.0 O2A C:DGT704 4.2 56.4 1.0 O3A A:DTP703 4.3 48.6 1.0 C3' C:DGT704 4.4 53.6 1.0 O2G A:DTP703 4.4 56.6 1.0 O C:HOH805 4.4 47.1 1.0 O2G C:DGT704 4.4 69.0 1.0 O1B C:DGT704 4.5 64.7 1.0 C4' C:DGT704 4.6 53.3 1.0 CE B:LYS116 4.6 70.1 1.0 O A:HOH809 4.7 52.7 1.0 CE A:LYS523 4.8 68.7 1.0 CD B:LYS116 4.9 68.7 1.0

Magnesium binding site 3 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp- Dttp/Dgtp 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-Datp- Dttp/Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:47.4 occ:1.00 O1G B:DGT702 1.6 50.0 1.0 O D:HOH805 1.8 31.0 1.0 O3G D:DTP702 1.9 41.4 1.0 O1B D:DTP702 2.0 39.9 1.0 O2A B:DGT702 2.0 44.4 1.0 O2B B:DGT702 2.1 39.8 1.0 PG B:DGT702 3.0 49.2 1.0 PG D:DTP702 3.3 42.6 1.0 PB B:DGT702 3.3 42.1 1.0 PB D:DTP702 3.3 38.7 1.0 PA B:DGT702 3.4 46.3 1.0 NZ C:LYS116 3.5 57.9 1.0 O3B B:DGT702 3.6 44.5 1.0 O3' B:DGT702 3.7 43.0 1.0 O3B D:DTP702 3.7 40.6 1.0 NZ D:LYS523 3.7 64.3 1.0 O3A B:DGT702 3.8 43.7 1.0 O3G B:DGT702 3.9 46.4 1.0 O2G B:DGT702 3.9 48.2 1.0 O2G D:DTP702 4.0 40.8 1.0 C5' B:DGT702 4.2 44.0 1.0 O2B D:DTP702 4.2 38.4 1.0 O5' B:DGT702 4.3 44.4 1.0 O3A D:DTP702 4.3 40.9 1.0 C3' B:DGT702 4.3 43.4 1.0 O1G D:DTP702 4.4 44.0 1.0 O B:HOH801 4.4 49.3 1.0 O1A B:DGT702 4.5 49.3 1.0 O1B B:DGT702 4.6 42.1 1.0 CE C:LYS116 4.7 57.0 1.0 CE D:LYS523 4.8 61.2 1.0 C4' B:DGT702 4.8 43.9 1.0 CD C:LYS116 5.0 57.2 1.0

Magnesium binding site 4 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Dgtp-Datp- Dttp/Dgtp 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-Datp- Dttp/Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:50.2 occ:1.00 O2G A:DGT702 1.6 52.6 1.0 O C:HOH802 1.8 47.6 1.0 O3G C:DTP701 1.9 38.1 1.0 O1B A:DGT702 1.9 46.4 1.0 O1A A:DGT702 2.0 43.7 1.0 O2B C:DTP701 2.0 38.6 1.0 PG A:DGT702 3.0 49.9 1.0 PB A:DGT702 3.1 50.6 1.0 PG C:DTP701 3.4 41.2 1.0 PA A:DGT702 3.4 44.4 1.0 PB C:DTP701 3.4 38.8 1.0 O3B A:DGT702 3.4 49.7 1.0 NZ D:LYS116 3.5 67.6 1.0 NZ C:LYS523 3.6 65.6 1.0 O3A A:DGT702 3.7 45.1 1.0 O1G A:DGT702 3.8 46.9 1.0 O3B C:DTP701 3.9 41.5 1.0 O3' A:DGT702 3.9 42.8 1.0 O3G A:DGT702 4.0 49.8 1.0 O2G C:DTP701 4.1 39.8 1.0 C5' A:DGT702 4.3 43.5 1.0 C3' A:DGT702 4.3 41.9 1.0 O3A C:DTP701 4.3 38.4 1.0 O5' A:DGT702 4.3 47.2 1.0 O2B A:DGT702 4.4 46.7 1.0 O1B C:DTP701 4.4 37.0 1.0 O1G C:DTP701 4.5 39.8 1.0 O2A A:DGT702 4.6 43.3 1.0 CE C:LYS523 4.7 67.5 1.0 CE D:LYS116 4.8 66.7 1.0 C4' A:DGT702 4.9 42.8 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