Magnesium in PDB 4qg1: Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core

The structure of Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qg1 was solved by L.M.I.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.99 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.695, 146.724, 99.256, 90.00, 114.76, 90.00
R / Rfree (%)	21.4 / 26.4

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core (pdb code 4qg1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qg1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:37.9 occ:0.64 O1B B:DTP703 1.9 48.2 0.5 O3G D:GTP703 2.0 49.3 0.8 O1B D:GTP703 2.0 38.4 0.8 O2G B:DTP703 2.0 32.4 0.7 O2A D:GTP703 2.4 37.4 0.8 PB D:GTP703 3.2 51.6 0.8 PB B:DTP703 3.3 60.5 1.0 PG D:GTP703 3.3 51.1 0.8 PG B:DTP703 3.3 42.1 0.7 PA D:GTP703 3.6 51.8 0.8 O3B D:GTP703 3.6 51.5 0.8 NZ B:LYS523 3.7 47.2 0.8 O3B B:DTP703 3.7 46.9 0.3 NZ A:LYS116 3.8 45.1 0.8 O3A D:GTP703 3.9 45.6 0.8 O2B B:DTP703 4.0 59.1 1.0 O1G B:DTP703 4.0 41.0 0.7 O3' D:GTP703 4.1 39.2 0.8 O1G D:GTP703 4.1 54.7 0.8 C5' D:GTP703 4.2 44.3 0.8 O2G D:GTP703 4.3 59.3 0.8 O3A B:DTP703 4.4 57.2 0.5 O5' D:GTP703 4.4 52.1 0.8 O2B D:GTP703 4.4 38.2 0.8 O3G B:DTP703 4.4 41.7 0.7 O A:HOH801 4.5 44.0 0.9 CE B:LYS523 4.5 51.9 0.8 O1A D:GTP703 4.8 39.6 0.8 C3' D:GTP703 4.8 45.8 0.8 O B:HOH822 4.9 46.9 0.9 CE A:LYS116 4.9 48.7 0.8 O A:HOH834 4.9 62.4 0.9

Magnesium binding site 2 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:56.6 occ:0.84 O3G C:GTP702 1.9 67.8 0.8 O1B A:DTP702 1.9 53.8 0.6 O1B C:GTP702 1.9 52.9 0.8 O2A C:GTP702 2.1 42.7 0.8 O2G A:DTP702 2.1 51.9 0.9 PB C:GTP702 3.1 62.9 0.8 PG C:GTP702 3.2 60.8 0.8 PB A:DTP702 3.3 53.3 0.9 PA C:GTP702 3.4 54.5 0.8 PG A:DTP702 3.5 58.0 0.8 O3B C:GTP702 3.5 61.4 0.8 O3A C:GTP702 3.6 56.8 0.8 O3B A:DTP702 3.8 58.0 0.5 NZ A:LYS523 3.9 66.0 0.9 O2G C:GTP702 3.9 68.8 0.8 NZ B:LYS116 3.9 60.8 0.8 C5' C:GTP702 4.0 53.0 0.8 O2B A:DTP702 4.0 56.1 1.0 O3' C:GTP702 4.0 50.7 0.8 O5' C:GTP702 4.2 56.0 0.8 O1G C:GTP702 4.2 60.0 0.8 O1G A:DTP702 4.2 60.1 0.7 O2B C:GTP702 4.3 61.4 0.8 O C:HOH807 4.4 50.3 0.8 O3A A:DTP702 4.4 56.8 0.5 O1A C:GTP702 4.5 52.6 0.8 O3G A:DTP702 4.5 59.3 0.6 C3' C:GTP702 4.7 51.0 0.8 CE A:LYS523 4.8 71.6 0.9 C4' C:GTP702 4.9 55.9 0.8

Magnesium binding site 3 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:62.8 occ:0.95 O1B D:DTP702 2.0 56.1 0.8 O3G B:GTP701 2.2 64.0 0.8 O2G D:DTP702 2.2 56.0 1.0 O2A B:GTP701 2.4 43.7 0.8 O1B B:GTP701 3.0 55.3 0.8 PB D:DTP702 3.4 48.2 0.8 PG D:DTP702 3.4 52.7 0.7 NZ C:LYS116 3.5 48.6 0.8 O3' B:GTP701 3.6 48.2 0.8 PG B:GTP701 3.6 55.3 0.8 O3B D:DTP702 3.8 56.1 0.8 O1G D:DTP702 3.8 52.1 0.9 PA B:GTP701 3.8 49.2 0.8 PB B:GTP701 4.0 57.4 0.8 O1G B:GTP701 4.1 54.4 0.8 O3A D:DTP702 4.2 54.5 0.6 O3B B:GTP701 4.3 58.8 0.8 C5' B:GTP701 4.3 47.5 0.8 O2B D:DTP702 4.4 50.9 0.8 O3A B:GTP701 4.4 51.8 0.8 C3' B:GTP701 4.4 50.2 0.8 CE C:LYS116 4.5 48.0 0.8 O D:HOH840 4.5 52.4 0.8 CD C:LYS116 4.6 57.1 0.8 O5' B:GTP701 4.6 56.0 0.8 O3G D:DTP702 4.6 56.0 0.9 O2G B:GTP701 4.6 63.9 0.8 CG C:LYS116 4.8 58.1 0.8 O1A B:GTP701 4.8 48.7 0.8 C4' B:GTP701 4.9 49.2 0.8

Magnesium binding site 4 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Tetrameric Gtp/Datp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg705 b:60.1 occ:0.90 O1B C:DTP701 2.0 53.3 0.9 O3G D:GTP701 2.1 62.1 0.8 O2G C:DTP701 2.1 59.5 0.9 O2A D:GTP701 2.2 52.8 0.8 O1B D:GTP701 2.4 55.9 0.8 PB C:DTP701 3.3 53.0 0.9 PG D:GTP701 3.4 59.4 0.8 PG C:DTP701 3.4 56.6 0.8 NZ D:LYS116 3.5 59.3 0.8 PB D:GTP701 3.5 58.0 0.8 PA D:GTP701 3.6 55.4 0.8 O3B C:DTP701 3.7 57.0 0.3 O3' D:GTP701 3.8 49.9 0.8 O3B D:GTP701 3.9 61.3 0.8 O1G D:GTP701 4.0 57.0 0.8 NZ C:LYS523 4.0 64.1 0.8 O3A D:GTP701 4.0 56.7 0.8 O1G C:DTP701 4.1 60.5 0.7 O D:HOH820 4.1 55.9 0.8 O2B C:DTP701 4.2 55.7 0.9 C5' D:GTP701 4.2 49.1 0.8 O3A C:DTP701 4.4 56.4 0.5 O5' D:GTP701 4.4 54.8 0.8 O3G C:DTP701 4.5 58.5 0.9 O2G D:GTP701 4.5 69.7 0.8 CE D:LYS116 4.6 53.5 0.8 C3' D:GTP701 4.6 51.7 0.8 O1A D:GTP701 4.6 53.5 0.8 CE C:LYS523 4.7 65.9 0.8 O2B D:GTP701 4.8 57.7 0.8 CD D:LYS116 4.8 57.4 0.8 O C:HOH805 4.8 56.5 0.8 C4' D:GTP701 4.9 51.7 0.8

L.M.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn. Structural Basis of Allosteric Activation of Sterile Alpha Motif and Histidine-Aspartate Domain Containing Protein 1 (SAMHD1) By Nucleoside Triphosphates. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25288794
DOI: 10.1074/JBC.M114.591958