Magnesium in PDB 4rxr: The Structure of Gtp-Dctp-Bound SAMHD1

The structure of The Structure of Gtp-Dctp-Bound SAMHD1, PDB code: 4rxr was solved by C.F.Zhu, W.Wei, X.Peng, Y.H.Dong, Y.Gong, X.F.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.894, 108.260, 92.663, 90.00, 122.92, 90.00
R / Rfree (%)	17.9 / 21.3

The binding sites of Magnesium atom in the The Structure of Gtp-Dctp-Bound SAMHD1 (pdb code 4rxr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of Gtp-Dctp-Bound SAMHD1, PDB code: 4rxr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Structure of Gtp-Dctp-Bound SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Gtp-Dctp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:38.8 occ:1.00 O1G B:GTP801 1.9 38.6 1.0 O1B B:GTP801 2.0 36.0 1.0 O1G B:DCP802 2.0 33.9 1.0 O B:HOH924 2.1 37.4 1.0 O1B B:DCP802 2.1 39.6 1.0 O2A B:GTP801 2.2 33.9 1.0 PB B:GTP801 3.1 38.2 1.0 PG B:GTP801 3.2 39.1 1.0 PB B:DCP802 3.3 37.6 1.0 PG B:DCP802 3.3 38.3 1.0 O3B B:GTP801 3.4 39.5 1.0 PA B:GTP801 3.4 37.0 1.0 NZ A:LYS116 3.6 42.4 1.0 O3B B:DCP802 3.6 41.3 1.0 O3A B:GTP801 3.6 36.8 1.0 O3' B:GTP801 3.9 36.1 1.0 O3G B:DCP802 4.0 37.7 1.0 O3G B:GTP801 4.1 39.1 1.0 O2B B:DCP802 4.1 41.4 1.0 O B:HOH1032 4.2 54.7 1.0 O2G B:GTP801 4.2 37.2 1.0 C5' B:GTP801 4.2 34.7 1.0 O5' B:GTP801 4.3 35.3 1.0 O3A B:DCP802 4.4 39.2 1.0 O2G B:DCP802 4.4 40.2 1.0 O2B B:GTP801 4.5 40.2 1.0 O B:HOH939 4.5 37.3 1.0 C3' B:GTP801 4.6 35.1 1.0 O1A B:GTP801 4.7 34.4 1.0 CE A:LYS116 4.8 40.7 1.0 C4' B:GTP801 4.9 35.6 1.0

Magnesium binding site 2 out of 2 in the The Structure of Gtp-Dctp-Bound SAMHD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Gtp-Dctp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg805 b:37.7 occ:1.00 O1B B:GTP803 1.9 39.4 1.0 O1G B:GTP803 2.0 41.8 1.0 O1B A:DCP703 2.0 39.3 1.0 O2A B:GTP803 2.1 37.9 1.0 O B:HOH933 2.1 37.3 1.0 O1G A:DCP703 2.1 36.5 1.0 PB B:GTP803 3.0 41.5 1.0 PG B:GTP803 3.2 44.3 1.0 PB A:DCP703 3.2 37.0 1.0 PA B:GTP803 3.3 39.6 1.0 O3B B:GTP803 3.4 40.1 1.0 PG A:DCP703 3.4 38.5 1.0 NZ B:LYS116 3.5 51.0 1.0 O3A B:GTP803 3.6 36.8 1.0 O3B A:DCP703 3.7 40.7 1.0 O3' B:GTP803 3.8 38.1 1.0 O3G B:GTP803 4.1 43.0 1.0 O3G A:DCP703 4.1 39.2 1.0 O2B A:DCP703 4.1 39.8 1.0 O A:HOH915 4.1 50.1 1.0 O2G B:GTP803 4.2 41.6 1.0 C5' B:GTP803 4.2 36.6 1.0 O5' B:GTP803 4.3 35.8 1.0 O B:HOH1038 4.3 52.5 1.0 O3A A:DCP703 4.3 41.3 1.0 O2B B:GTP803 4.4 36.9 1.0 O B:HOH946 4.5 38.7 1.0 O1A B:GTP803 4.5 38.7 1.0 C3' B:GTP803 4.6 36.9 1.0 O2G A:DCP703 4.6 40.8 1.0 CE B:LYS116 4.8 52.4 1.0 C4' B:GTP803 4.9 37.0 1.0

C.F.Zhu, W.Wei, X.Peng, Y.H.Dong, Y.Gong, X.F.Yu. The Mechanism of Substrate-Controlled Allosteric Regulation of SAMHD1 Activated By Gtp Acta Crystallogr.,Sect.D 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714027527