Magnesium in PDB 4tnp: Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dctp-Cctp Complex

The structure of Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dctp-Cctp Complex, PDB code: 4tnp 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 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.507, 140.753, 97.490, 90.00, 114.79, 90.00
R / Rfree (%)	19.8 / 22.2

The binding sites of Magnesium atom in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dctp-Cctp Complex (pdb code 4tnp). 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-Gtp-Dctp-Cctp Complex, PDB code: 4tnp:
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-Gtp-Dctp-Cctp 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-Gtp-Dctp-Cctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:40.2 occ:1.00 O3G D:DCP703 1.9 34.6 1.0 O1G D:GTP704 1.9 35.0 1.0 O1B D:GTP704 1.9 38.3 1.0 O D:HOH835 2.1 41.4 1.0 O1B D:DCP703 2.1 34.1 1.0 O2A D:GTP704 2.1 33.2 1.0 PB D:GTP704 3.1 36.7 1.0 PG D:GTP704 3.2 37.6 1.0 PG D:DCP703 3.2 38.5 1.0 PB D:DCP703 3.3 33.3 1.0 PA D:GTP704 3.4 33.7 1.0 O3B D:GTP704 3.5 36.8 1.0 O3B D:DCP703 3.6 34.8 1.0 NZ A:LYS116 3.7 45.9 1.0 O3A D:GTP704 3.7 37.0 1.0 NZ B:LYS523 3.8 50.5 1.0 O2G D:DCP703 4.0 38.2 1.0 O3' D:GTP704 4.1 31.6 1.0 C5' D:GTP704 4.2 33.3 1.0 O2G D:GTP704 4.2 36.2 1.0 O3G D:GTP704 4.2 39.8 1.0 O2B D:DCP703 4.3 33.2 1.0 O5' D:GTP704 4.3 34.7 1.0 O3A D:DCP703 4.4 33.5 1.0 O1G D:DCP703 4.4 37.2 1.0 O2B D:GTP704 4.5 40.7 1.0 O D:HOH820 4.5 36.1 1.0 C3' D:GTP704 4.5 32.2 1.0 O1A D:GTP704 4.7 33.3 1.0 CE A:LYS116 4.8 46.2 1.0 C4' D:GTP704 4.8 33.1 1.0 O D:HOH836 5.0 56.0 1.0

Magnesium binding site 2 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dctp-Cctp 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-Gtp-Dctp-Cctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:25.8 occ:1.00 O3G B:GTP705 1.8 28.6 1.0 O1G A:DCP704 2.0 27.4 1.0 O2B B:GTP705 2.0 24.4 1.0 O1B A:DCP704 2.0 26.8 1.0 O1A B:GTP705 2.0 24.9 1.0 O A:HOH820 2.2 29.5 1.0 PB B:GTP705 3.0 27.0 1.0 PG B:GTP705 3.1 29.6 1.0 PA B:GTP705 3.3 24.9 1.0 PB A:DCP704 3.3 26.0 1.0 PG A:DCP704 3.3 29.4 1.0 O3B B:GTP705 3.4 26.3 1.0 O3A B:GTP705 3.5 27.0 1.0 O3B A:DCP704 3.6 26.6 1.0 NZ B:LYS116 3.7 34.0 1.0 NZ A:LYS523 3.8 40.2 1.0 O2G B:GTP705 4.0 27.0 1.0 O3' B:GTP705 4.0 23.3 1.0 O1G B:GTP705 4.1 30.3 1.0 C5' B:GTP705 4.2 23.9 1.0 O2B A:DCP704 4.2 25.9 1.0 O3G A:DCP704 4.2 26.7 1.0 O5' B:GTP705 4.2 23.7 1.0 O2G A:DCP704 4.4 29.2 1.0 O1B B:GTP705 4.4 30.4 1.0 O2A B:GTP705 4.4 26.1 1.0 O3A A:DCP704 4.4 26.3 1.0 O B:HOH832 4.5 32.7 1.0 C3' B:GTP705 4.6 23.1 1.0 C4' B:GTP705 4.8 22.4 1.0 O A:HOH877 4.9 66.1 1.0 CE B:LYS116 4.9 34.5 1.0

Magnesium binding site 3 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dctp-Cctp 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-Gtp-Dctp-Cctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:30.9 occ:1.00 O1G B:GTP703 1.7 30.6 1.0 O1B B:GTP703 1.9 27.5 1.0 O2G B:DCP702 1.9 26.5 1.0 O1A B:GTP703 2.0 24.4 1.0 O B:HOH828 2.1 25.8 1.0 O1B B:DCP702 2.1 27.4 1.0 PB B:GTP703 3.0 28.0 1.0 PG B:GTP703 3.0 31.8 1.0 PA B:GTP703 3.3 25.6 1.0 PG B:DCP702 3.3 28.5 1.0 PB B:DCP702 3.3 26.2 1.0 O3B B:GTP703 3.3 28.6 1.0 O3A B:GTP703 3.5 27.4 1.0 O3B B:DCP702 3.7 26.3 1.0 NZ C:LYS116 3.8 43.1 1.0 O3G B:GTP703 3.8 34.8 1.0 NZ D:LYS523 3.9 43.7 1.0 O3' B:GTP703 4.1 23.0 1.0 O2G B:GTP703 4.1 28.8 1.0 O3G B:DCP702 4.1 28.0 1.0 O2B B:DCP702 4.2 25.8 1.0 C5' B:GTP703 4.2 24.9 1.0 O B:HOH866 4.2 59.6 1.0 O5' B:GTP703 4.3 25.3 1.0 O2B B:GTP703 4.3 28.5 1.0 O B:HOH863 4.4 48.1 1.0 O B:HOH834 4.4 32.1 1.0 O3A B:DCP702 4.5 25.1 1.0 O2A B:GTP703 4.5 24.1 1.0 O1G B:DCP702 4.5 28.9 1.0 C3' B:GTP703 4.6 24.1 1.0 C4' B:GTP703 4.9 23.7 1.0 CE C:LYS116 5.0 41.1 1.0

Magnesium binding site 4 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dctp-Cctp 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-Gtp-Dctp-Cctp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:30.2 occ:1.00 O2B A:GTP703 1.7 30.2 1.0 O3G A:GTP703 1.8 30.4 1.0 O1B A:DCP702 1.9 26.6 1.0 O A:HOH832 1.9 36.6 1.0 O1G A:DCP702 2.0 28.9 1.0 O1A A:GTP703 2.1 28.0 1.0 PB A:GTP703 3.0 31.3 1.0 PG A:GTP703 3.2 31.6 1.0 PB A:DCP702 3.2 26.2 1.0 PA A:GTP703 3.3 30.0 1.0 PG A:DCP702 3.4 28.1 1.0 O3B A:GTP703 3.4 30.6 1.0 O3A A:GTP703 3.6 31.5 1.0 NZ D:LYS116 3.6 41.5 1.0 O3B A:DCP702 3.7 28.0 1.0 NZ C:LYS523 3.9 44.9 1.0 O3' A:GTP703 4.0 28.6 1.0 C5' A:GTP703 4.1 28.9 1.0 O2G A:GTP703 4.1 32.8 1.0 O A:HOH842 4.1 51.1 1.0 O1G A:GTP703 4.1 34.1 1.0 O2B A:DCP702 4.2 26.2 1.0 O5' A:GTP703 4.2 30.5 1.0 O3G A:DCP702 4.3 27.4 1.0 O1B A:GTP703 4.3 32.0 1.0 O3A A:DCP702 4.3 26.3 1.0 O A:HOH822 4.4 37.3 1.0 C3' A:GTP703 4.5 28.8 1.0 O2G A:DCP702 4.5 29.9 1.0 O2A A:GTP703 4.5 33.4 1.0 C4' A:GTP703 4.7 28.6 1.0 CE D:LYS116 4.8 40.1 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