Magnesium in PDB 4tnq: Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dttp Complex

The structure of Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dttp Complex, PDB code: 4tnq 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 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.159, 140.292, 97.268, 90.00, 114.56, 90.00
R / Rfree (%)	16.1 / 19.8

The binding sites of Magnesium atom in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dttp Complex (pdb code 4tnq). 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-Dttp-Dttp Complex, PDB code: 4tnq:
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-Dttp-Dttp 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-Dttp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:42.0 occ:1.00 O1B A:GTP702 1.8 39.7 1.0 O1B C:TTP701 1.8 38.8 1.0 O3G C:TTP701 1.9 39.5 1.0 O1G A:GTP702 2.0 38.7 1.0 O A:HOH803 2.0 45.9 1.0 O2A A:GTP702 2.2 35.1 1.0 PB A:GTP702 3.0 40.0 1.0 PB C:TTP701 3.1 35.9 1.0 PG C:TTP701 3.2 41.9 1.0 PG A:GTP702 3.2 41.8 1.0 PA A:GTP702 3.4 33.7 1.0 O3B A:GTP702 3.4 38.9 1.0 O3B C:TTP701 3.5 40.8 1.0 O3A A:GTP702 3.6 35.7 1.0 NZ C:LYS523 3.7 56.8 1.0 O3' A:GTP702 3.8 31.4 1.0 O2B C:TTP701 3.9 33.4 1.0 NZ D:LYS116 4.1 44.6 1.0 O2G C:TTP701 4.1 39.0 1.0 O3G A:GTP702 4.1 41.2 1.0 C5' A:GTP702 4.2 31.2 1.0 O5' A:GTP702 4.3 31.7 1.0 O3A C:TTP701 4.3 37.0 1.0 O A:HOH802 4.3 49.1 1.0 O1G C:TTP701 4.3 46.1 1.0 C3' A:GTP702 4.3 32.2 1.0 O2G A:GTP702 4.3 37.5 1.0 O2B A:GTP702 4.4 42.1 1.0 O1A A:GTP702 4.7 32.4 1.0 C4' A:GTP702 4.7 31.0 1.0 CE D:LYS116 4.7 44.1 1.0 CE C:LYS523 4.8 54.4 1.0

Magnesium binding site 2 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dttp 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-Dttp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:59.2 occ:1.00 O3G B:GTP706 1.6 56.2 1.0 O1G D:TTP703 1.9 46.6 1.0 O2B D:TTP703 2.0 46.4 1.0 O1A B:GTP706 2.2 43.6 1.0 O1B B:GTP706 2.3 54.4 1.0 PG B:GTP706 3.1 56.8 1.0 NZ C:LYS116 3.3 67.9 1.0 PG D:TTP703 3.3 49.7 1.0 PB D:TTP703 3.4 44.7 1.0 PB B:GTP706 3.5 53.5 1.0 PA B:GTP706 3.6 46.1 1.0 O3' B:GTP706 3.7 38.4 1.0 O3B D:TTP703 3.8 47.3 1.0 O3B B:GTP706 3.8 51.6 1.0 O3G D:TTP703 3.9 46.4 1.0 NZ D:LYS523 3.9 61.8 1.0 O2G B:GTP706 3.9 57.1 1.0 O1G B:GTP706 4.0 50.5 1.0 O3A B:GTP706 4.1 51.0 1.0 O3A D:TTP703 4.3 45.4 1.0 O1B D:TTP703 4.4 46.2 1.0 C3' B:GTP706 4.4 40.1 1.0 C5' B:GTP706 4.5 43.8 1.0 O2G D:TTP703 4.5 50.6 1.0 O5' B:GTP706 4.5 47.2 1.0 O2A B:GTP706 4.6 48.8 1.0 CE C:LYS116 4.6 65.0 1.0 CE D:LYS523 4.7 58.5 1.0 O2B B:GTP706 4.8 53.6 1.0 CG C:LYS116 4.8 63.1 1.0 C4' B:GTP706 4.9 41.6 1.0

Magnesium binding site 3 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dttp 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-Dttp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:40.8 occ:1.00 O3G B:GTP702 1.7 50.0 1.0 O3G A:TTP703 1.9 39.7 1.0 O1B A:TTP703 1.9 36.5 1.0 O2B B:GTP702 2.0 39.7 1.0 O2A B:GTP702 2.1 35.0 1.0 O A:HOH804 2.2 50.0 1.0 PB B:GTP702 3.1 39.1 1.0 PG B:GTP702 3.1 46.4 1.0 PB A:TTP703 3.2 40.6 1.0 PG A:TTP703 3.2 39.0 1.0 PA B:GTP702 3.4 35.9 1.0 O3B B:GTP702 3.4 42.4 1.0 NZ A:LYS523 3.6 55.5 1.0 O3B A:TTP703 3.6 40.9 1.0 O3A B:GTP702 3.6 39.0 1.0 O3' B:GTP702 4.0 38.7 1.0 CE B:LYS116 4.0 59.9 1.0 O2G B:GTP702 4.0 49.9 1.0 O1G B:GTP702 4.0 47.1 1.0 O1G A:TTP703 4.1 35.1 1.0 O2B A:TTP703 4.2 40.5 1.0 O2G A:TTP703 4.2 39.5 1.0 O B:HOH822 4.2 70.6 1.0 O B:HOH802 4.3 65.3 1.0 C5' B:GTP702 4.3 35.4 1.0 O5' B:GTP702 4.3 37.3 1.0 O3A A:TTP703 4.3 38.3 1.0 O1B B:GTP702 4.4 46.4 1.0 NZ B:LYS116 4.5 62.2 1.0 C3' B:GTP702 4.5 37.7 1.0 O1A B:GTP702 4.5 36.9 1.0 CE A:LYS523 4.7 53.0 1.0 C4' B:GTP702 4.8 36.4 1.0 CD B:LYS116 5.0 60.0 1.0

Magnesium binding site 4 out of 4 in the Structural Basis of Cellular Dntp Regulation, SAMHD1-Gtp-Dttp-Dttp 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-Dttp-Dttp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:49.3 occ:1.00 O3G B:TTP703 1.6 41.7 1.0 O2G D:GTP702 1.9 39.9 1.0 O1B D:GTP702 1.9 43.7 1.0 O2B B:TTP703 2.0 36.3 1.0 O D:HOH808 2.2 46.7 1.0 O2A D:GTP702 2.3 33.2 1.0 PG B:TTP703 3.0 38.5 1.0 PB B:TTP703 3.2 35.4 1.0 PG D:GTP702 3.2 42.1 1.0 PB D:GTP702 3.2 42.7 1.0 O3B B:TTP703 3.5 37.6 1.0 NZ B:LYS523 3.5 60.7 1.0 O3B D:GTP702 3.6 40.5 1.0 PA D:GTP702 3.7 36.7 1.0 O1G B:TTP703 3.7 36.1 1.0 O3G D:GTP702 3.8 49.4 1.0 NZ A:LYS116 3.8 47.8 1.0 O3A D:GTP702 3.9 36.1 1.0 O2G B:TTP703 4.1 39.8 1.0 O3' D:GTP702 4.1 34.0 1.0 O1B B:TTP703 4.1 36.7 1.0 O3A B:TTP703 4.3 33.7 1.0 CE B:LYS523 4.3 60.4 1.0 O D:HOH809 4.4 49.4 1.0 O1G D:GTP702 4.4 42.3 1.0 O2B D:GTP702 4.4 42.7 1.0 C5' D:GTP702 4.5 33.2 1.0 O5' D:GTP702 4.7 33.3 1.0 NZ D:LYS377 4.7 74.6 1.0 C3' D:GTP702 4.7 34.3 1.0 O1A D:GTP702 4.8 33.5 1.0 O B:HOH842 4.9 60.3 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