Magnesium in PDB 4rxq: The Structure of Gtp-Dutp-Bound SAMHD1

The structure of The Structure of Gtp-Dutp-Bound SAMHD1, PDB code: 4rxq 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 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.800, 108.915, 92.217, 90.00, 122.73, 90.00
R / Rfree (%)	19.7 / 22.9

The binding sites of Magnesium atom in the The Structure of Gtp-Dutp-Bound SAMHD1 (pdb code 4rxq). 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-Dutp-Bound SAMHD1, PDB code: 4rxq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Structure of Gtp-Dutp-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-Dutp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:26.4 occ:1.00 O2G B:DUT703 1.9 26.1 1.0 O1B A:GTP804 2.0 30.8 1.0 O1G A:GTP804 2.0 32.1 1.0 O2A A:GTP804 2.1 25.8 1.0 O1B B:DUT703 2.1 28.8 1.0 O A:HOH935 2.1 26.2 1.0 PB A:GTP804 3.1 28.6 1.0 PB B:DUT703 3.2 26.7 1.0 PG A:GTP804 3.3 30.2 1.0 PG B:DUT703 3.3 28.2 1.0 PA A:GTP804 3.4 27.3 1.0 O3B A:GTP804 3.5 32.3 1.0 NZ A:LYS116 3.6 31.2 1.0 O3A A:GTP804 3.6 25.3 1.0 O3B B:DUT703 3.7 29.8 1.0 O3' A:GTP804 4.0 27.9 1.0 O1G B:DUT703 4.0 28.2 1.0 O3G A:GTP804 4.1 31.8 1.0 O2B B:DUT703 4.1 31.0 1.0 C5' A:GTP804 4.1 24.1 1.0 O2G A:GTP804 4.2 30.9 1.0 O B:HOH930 4.3 38.7 1.0 O5' A:GTP804 4.3 26.0 1.0 O A:HOH919 4.3 24.5 1.0 O3A B:DUT703 4.4 30.0 1.0 O3G B:DUT703 4.4 27.2 1.0 O2B A:GTP804 4.5 30.8 1.0 C3' A:GTP804 4.6 25.6 1.0 O1A A:GTP804 4.6 24.4 1.0 CE A:LYS116 4.8 30.6 1.0 C4' A:GTP804 4.9 25.1 1.0

Magnesium binding site 2 out of 2 in the The Structure of Gtp-Dutp-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-Dutp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:28.6 occ:1.00 O1B A:GTP801 1.9 33.0 1.0 O2A A:GTP801 2.0 31.7 1.0 O1G A:GTP801 2.0 35.4 1.0 O A:HOH1164 2.1 26.3 1.0 O2G A:DUT803 2.1 29.6 1.0 O1B A:DUT803 2.1 32.0 1.0 PB A:GTP801 3.0 32.2 1.0 PG A:GTP801 3.2 34.8 1.0 PB A:DUT803 3.2 28.9 1.0 PA A:GTP801 3.3 32.8 1.0 O3B A:GTP801 3.3 34.3 1.0 PG A:DUT803 3.4 29.9 1.0 NZ B:LYS116 3.4 42.4 1.0 O3A A:GTP801 3.5 29.3 1.0 O3B A:DUT803 3.7 32.0 1.0 O3' A:GTP801 3.9 30.0 1.0 O3G A:GTP801 4.0 34.9 1.0 O A:HOH1058 4.1 42.9 1.0 O2B A:DUT803 4.1 30.7 1.0 C5' A:GTP801 4.1 28.4 1.0 O2G A:GTP801 4.1 34.3 1.0 O5' A:GTP801 4.2 29.9 1.0 O1G A:DUT803 4.2 32.0 1.0 O A:HOH1007 4.3 54.4 1.0 O2B A:GTP801 4.3 30.5 1.0 O3A A:DUT803 4.4 33.0 1.0 O A:HOH945 4.4 26.4 1.0 O1A A:GTP801 4.5 28.9 1.0 C3' A:GTP801 4.5 29.2 1.0 O3G A:DUT803 4.6 29.7 1.0 CE B:LYS116 4.7 41.4 1.0 C4' A:GTP801 4.8 28.4 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