Magnesium in PDB 4rxp: The Structure of Gtp-Datp-Bound SAMHD1

The structure of The Structure of Gtp-Datp-Bound SAMHD1, PDB code: 4rxp 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 (°)	151.154, 108.094, 92.425, 90.00, 122.98, 90.00
R / Rfree (%)	18 / 20.8

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

Magnesium binding site 1 out of 2 in the The Structure of Gtp-Datp-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-Datp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:22.8 occ:1.00 O1G A:GTP703 1.9 26.3 1.0 O1G B:DTP804 2.0 20.8 1.0 O1B A:GTP703 2.0 25.1 1.0 O A:HOH834 2.0 23.2 1.0 O2A A:GTP703 2.1 22.7 1.0 O2B B:DTP804 2.1 23.3 1.0 PB A:GTP703 3.1 27.3 1.0 PG A:GTP703 3.2 28.8 1.0 PG B:DTP804 3.3 25.9 1.0 PB B:DTP804 3.3 23.8 1.0 O3B A:GTP703 3.4 27.7 1.0 PA A:GTP703 3.4 24.3 1.0 NZ A:LYS116 3.6 32.7 1.0 O3A A:GTP703 3.6 24.9 1.0 O3B B:DTP804 3.7 26.6 1.0 O3' A:GTP703 4.0 23.7 1.0 O3G A:GTP703 4.1 30.7 1.0 O2G B:DTP804 4.1 23.8 1.0 O2G A:GTP703 4.2 27.0 1.0 O1B B:DTP804 4.2 25.6 1.0 C5' A:GTP703 4.3 24.3 1.0 O B:HOH1029 4.3 39.2 1.0 O5' A:GTP703 4.3 25.0 1.0 O3G B:DTP804 4.4 26.7 1.0 O2B A:GTP703 4.5 26.9 1.0 O3A B:DTP804 4.5 25.5 1.0 O A:HOH819 4.5 22.3 1.0 O1A A:GTP703 4.6 24.7 1.0 C3' A:GTP703 4.7 23.9 1.0 CE A:LYS116 4.8 33.0 1.0 C4' A:GTP703 5.0 24.6 1.0

Magnesium binding site 2 out of 2 in the The Structure of Gtp-Datp-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-Datp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:25.1 occ:1.00 O1G B:GTP801 2.0 30.0 1.0 O2B A:DTP702 2.0 25.2 1.0 O1B B:GTP801 2.0 27.7 1.0 O1G A:DTP702 2.0 23.2 1.0 O2A B:GTP801 2.1 27.7 1.0 O B:HOH1142 2.1 23.4 1.0 PB B:GTP801 3.1 28.9 1.0 PG B:GTP801 3.2 33.7 1.0 PB A:DTP702 3.3 23.5 1.0 PG A:DTP702 3.3 24.8 1.0 PA B:GTP801 3.3 28.6 1.0 O3B B:GTP801 3.4 28.4 1.0 NZ B:LYS116 3.6 41.6 1.0 O3A B:GTP801 3.6 26.7 1.0 O3B A:DTP702 3.7 26.7 1.0 O3' B:GTP801 3.9 26.6 1.0 O A:HOH945 4.0 33.8 1.0 O3G B:GTP801 4.0 32.2 1.0 O2G A:DTP702 4.1 24.9 1.0 O2G B:GTP801 4.2 31.1 1.0 O1B A:DTP702 4.2 24.2 1.0 C5' B:GTP801 4.2 26.8 1.0 O5' B:GTP801 4.3 26.3 1.0 O B:HOH1000 4.3 33.4 1.0 O3A A:DTP702 4.4 25.8 1.0 O2B B:GTP801 4.5 27.4 1.0 O3G A:DTP702 4.5 25.7 1.0 O1A B:GTP801 4.5 27.2 1.0 O B:HOH939 4.5 23.6 1.0 C3' B:GTP801 4.6 26.9 1.0 CE B:LYS116 4.8 42.5 1.0 C4' B:GTP801 4.9 26.3 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