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

The structure of Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Datp Complex, PDB code: 4tnr 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 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.916, 141.697, 97.524, 90.00, 115.40, 90.00
R / Rfree (%)	22.4 / 24.2

The binding sites of Magnesium atom in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Datp Complex (pdb code 4tnr). 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-Datp-Datp Complex, PDB code: 4tnr:
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-Datp-Datp 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-Datp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:72.2 occ:1.00 O1B C:DTP704 1.9 73.1 1.0 O3G C:DTP704 1.9 78.2 1.0 O3G A:GTP703 2.1 86.9 1.0 O C:HOH802 2.1 0.2 1.0 O2B A:GTP703 2.2 83.5 1.0 O1A A:GTP703 2.3 78.9 1.0 NZ D:LYS116 3.2 98.3 1.0 PG C:DTP704 3.2 76.0 1.0 PB C:DTP704 3.3 71.4 1.0 PB A:GTP703 3.3 86.6 1.0 PG A:GTP703 3.4 89.9 1.0 PA A:GTP703 3.7 80.2 1.0 O3B A:GTP703 3.7 89.1 1.0 O3B C:DTP704 3.7 73.1 1.0 O2G C:DTP704 3.7 73.4 1.0 O3' A:GTP703 3.8 69.9 1.0 NZ C:LYS523 3.9 94.8 1.0 O3A A:GTP703 3.9 83.7 1.0 O3A C:DTP704 4.2 67.1 1.0 O1G A:GTP703 4.3 89.5 1.0 O2B C:DTP704 4.3 72.3 1.0 O2G A:GTP703 4.3 94.0 1.0 C5' A:GTP703 4.4 74.4 1.0 CE D:LYS116 4.4 97.1 1.0 O1G C:DTP704 4.5 79.0 1.0 O5' A:GTP703 4.5 76.8 1.0 C3' A:GTP703 4.6 69.4 1.0 O1B A:GTP703 4.7 90.1 1.0 CD D:LYS116 4.8 94.0 1.0 CE C:LYS523 4.9 94.3 1.0 O2A A:GTP703 4.9 81.7 1.0 C4' A:GTP703 4.9 69.9 1.0

Magnesium binding site 2 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Datp 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-Datp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:46.0 occ:1.00 O2A C:GTP703 1.9 47.2 1.0 O1G D:DTP703 1.9 62.0 1.0 O3G C:GTP703 2.1 52.3 1.0 O1B D:DTP703 2.1 58.7 1.0 O2B C:GTP703 2.2 50.6 1.0 NZ C:LYS116 3.0 67.5 1.0 PA C:GTP703 3.3 47.8 1.0 PG C:GTP703 3.3 53.9 1.0 PB C:GTP703 3.3 52.1 1.0 PG D:DTP703 3.3 61.4 1.0 PB D:DTP703 3.4 57.4 1.0 O3B C:GTP703 3.7 54.3 1.0 O3B D:DTP703 3.8 58.2 1.0 O3A C:GTP703 3.8 50.2 1.0 O1G C:GTP703 3.8 52.4 1.0 NZ D:LYS523 3.9 78.4 1.0 O3' C:GTP703 4.0 43.8 1.0 CE C:LYS116 4.2 66.0 1.0 O1A C:GTP703 4.3 47.8 1.0 O3G D:DTP703 4.3 61.2 1.0 O5' C:GTP703 4.3 46.4 1.0 O3A D:DTP703 4.4 54.4 1.0 C5' C:GTP703 4.4 45.9 1.0 O2G D:DTP703 4.4 63.3 1.0 O2B D:DTP703 4.4 58.2 1.0 O2G C:GTP703 4.5 57.6 1.0 C3' C:GTP703 4.5 43.3 1.0 CD C:LYS116 4.6 64.8 1.0 O1B C:GTP703 4.6 54.4 1.0 O D:HOH806 4.7 85.4 1.0 CE D:LYS523 4.8 78.4 1.0 C4' C:GTP703 4.9 43.5 1.0

Magnesium binding site 3 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Datp 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-Datp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:88.8 occ:1.00 O3G B:GTP703 1.7 88.6 1.0 O A:HOH802 2.0 1.0 1.0 O2B B:GTP703 2.0 82.4 1.0 O1A B:GTP703 2.1 80.6 1.0 O2G A:DTP702 2.3 90.9 1.0 O1B A:DTP702 2.5 84.4 1.0 PG B:GTP703 3.1 91.2 1.0 NZ B:LYS116 3.1 90.3 1.0 PB B:GTP703 3.1 84.1 1.0 PA B:GTP703 3.3 79.6 1.0 O3B B:GTP703 3.4 88.2 1.0 PG A:DTP702 3.4 89.2 1.0 O3B A:DTP702 3.5 84.9 1.0 O3A B:GTP703 3.6 81.2 1.0 PB A:DTP702 3.6 82.4 1.0 O1G A:DTP702 3.9 90.9 1.0 O1G B:GTP703 4.0 94.5 1.0 O2G B:GTP703 4.0 92.7 1.0 O3' B:GTP703 4.0 71.4 1.0 NZ A:LYS523 4.0 0.9 1.0 C5' B:GTP703 4.2 73.3 1.0 O5' B:GTP703 4.2 76.0 1.0 CE B:LYS116 4.3 89.4 1.0 O1B B:GTP703 4.4 85.7 1.0 O2A B:GTP703 4.5 80.4 1.0 O3A A:DTP702 4.6 77.6 1.0 O2B A:DTP702 4.7 83.1 1.0 O3G A:DTP702 4.7 89.6 1.0 C3' B:GTP703 4.7 70.5 1.0 CD B:LYS116 4.7 87.0 1.0 C4' B:GTP703 4.9 69.9 1.0

Magnesium binding site 4 out of 4 in the Structure Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Datp-Datp 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-Datp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:46.1 occ:1.00 O2B D:GTP702 1.9 42.5 1.0 O3G B:DTP701 1.9 46.9 1.0 O1B B:DTP701 2.0 45.3 1.0 O3G D:GTP702 2.1 45.2 1.0 O B:HOH801 2.1 60.3 1.0 O2A D:GTP702 2.2 41.2 1.0 PG B:DTP701 3.2 45.6 1.0 PB B:DTP701 3.2 44.1 1.0 NZ A:LYS116 3.2 62.4 1.0 PB D:GTP702 3.2 43.1 1.0 PG D:GTP702 3.3 45.5 1.0 O B:HOH802 3.4 88.2 1.0 PA D:GTP702 3.6 41.2 1.0 O3' D:GTP702 3.6 38.8 1.0 O3B B:DTP701 3.6 44.3 1.0 O3B D:GTP702 3.7 44.7 1.0 NZ B:LYS523 3.8 54.9 1.0 O2G D:GTP702 3.8 45.8 1.0 O3A D:GTP702 4.0 41.6 1.0 O1G B:DTP701 4.1 45.6 1.0 O2B B:DTP701 4.1 43.8 1.0 O2G B:DTP701 4.2 45.6 1.0 O3A B:DTP701 4.3 43.5 1.0 C3' D:GTP702 4.4 39.0 1.0 CE A:LYS116 4.5 62.6 1.0 O1B D:GTP702 4.5 43.7 1.0 O1G D:GTP702 4.5 46.7 1.0 O5' D:GTP702 4.5 40.5 1.0 C5' D:GTP702 4.6 38.8 1.0 O A:HOH801 4.6 70.0 1.0 O1A D:GTP702 4.6 42.5 1.0 CE B:LYS523 4.7 55.6 1.0 CD A:LYS116 4.8 61.9 1.0 C4' D:GTP702 4.9 38.1 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