Magnesium in PDB 4qg2: Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core

The structure of Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qg2 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)	43.07 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.230, 147.005, 99.292, 90.00, 114.60, 90.00
R / Rfree (%)	23.7 / 27.1

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core (pdb code 4qg2). 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/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core, PDB code: 4qg2:
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/Atp-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/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:40.9 occ:1.00 O1B D:GTP702 2.0 33.1 1.0 O2G B:DTP703 2.1 72.0 1.0 O3B B:DTP703 2.1 49.7 1.0 O1G D:GTP702 2.3 44.2 1.0 PG B:DTP703 2.5 40.4 1.0 O1A D:GTP702 2.7 32.0 1.0 O2B B:DTP703 2.9 38.5 1.0 PB B:DTP703 3.1 38.1 1.0 O3G B:DTP703 3.3 57.6 1.0 PB D:GTP702 3.3 54.6 1.0 PG D:GTP702 3.6 48.3 1.0 O1G B:DTP703 3.8 42.9 1.0 O3B D:GTP702 3.9 61.0 1.0 PA D:GTP702 3.9 43.9 1.0 NZ B:LYS523 4.0 56.7 0.9 O3A D:GTP702 4.1 43.8 1.0 O3A B:DTP703 4.1 51.7 0.5 O3' D:GTP702 4.1 46.6 1.0 O1B B:DTP703 4.2 65.2 0.7 NZ A:LYS116 4.3 53.3 1.0 O3G D:GTP702 4.3 51.1 1.0 O2B D:GTP702 4.4 37.6 1.0 O A:HOH807 4.6 40.3 1.0 O2G D:GTP702 4.6 80.0 1.0 C5' D:GTP702 4.7 46.2 1.0 O B:HOH808 4.7 48.3 1.0 O5' D:GTP702 4.8 53.4 1.0 C3' D:GTP702 5.0 51.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-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/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:58.1 occ:1.00 O1B A:DTP702 1.9 49.9 0.8 O3G B:GTP702 1.9 68.2 1.0 O1G A:DTP702 2.0 41.9 1.0 O2B B:GTP702 2.1 48.4 1.0 O A:HOH813 2.2 53.5 1.0 O2A B:GTP702 2.3 40.6 1.0 PG B:GTP702 3.2 62.6 1.0 PB A:DTP702 3.2 49.5 1.0 PG A:DTP702 3.2 51.8 1.0 PB B:GTP702 3.2 58.1 1.0 PA B:GTP702 3.6 51.5 1.0 O3B B:GTP702 3.6 61.0 1.0 O3B A:DTP702 3.6 58.9 0.3 O3A B:GTP702 3.8 56.0 1.0 O2G B:GTP702 3.9 62.9 1.0 O2G A:DTP702 3.9 60.2 0.9 O2B A:DTP702 4.0 52.0 1.0 O3' B:GTP702 4.0 41.3 1.0 C5' B:GTP702 4.2 51.8 1.0 O1G B:GTP702 4.2 60.5 1.0 O3A A:DTP702 4.3 53.7 0.6 NZ B:LYS116 4.3 61.8 0.9 O B:HOH807 4.3 52.7 1.0 O3G A:DTP702 4.4 62.8 1.0 NZ A:LYS523 4.4 73.1 1.0 O5' B:GTP702 4.4 49.1 1.0 O1B B:GTP702 4.5 60.7 1.0 O1A B:GTP702 4.7 49.1 1.0 C3' B:GTP702 4.7 52.8 1.0 CE A:LYS523 4.8 71.0 1.0 C4' B:GTP702 5.0 56.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-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/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:56.8 occ:1.00 O2B D:DTP701 2.2 55.4 0.4 O2A B:GTP701 2.2 43.3 0.9 O3G B:GTP701 2.4 59.8 0.9 O1G D:DTP701 2.6 52.2 1.0 NZ C:LYS116 3.2 56.1 1.0 O2B B:GTP701 3.2 40.6 0.9 O3' B:GTP701 3.5 49.6 0.9 PB D:DTP701 3.6 45.4 1.0 PG D:DTP701 3.7 55.8 0.8 PA B:GTP701 3.7 51.3 0.9 PG B:GTP701 3.7 55.1 0.9 O2G D:DTP701 3.9 53.0 1.0 CD C:LYS116 4.1 54.4 1.0 O3B D:DTP701 4.1 54.7 0.6 O1G B:GTP701 4.1 58.8 0.9 CE C:LYS116 4.1 49.6 1.0 PB B:GTP701 4.2 50.4 0.9 CG C:LYS116 4.2 59.0 1.0 O3A D:DTP701 4.3 54.0 0.8 C3' B:GTP701 4.4 55.6 0.9 O3B B:GTP701 4.4 53.1 0.9 O3A B:GTP701 4.4 43.1 0.9 NZ D:LYS523 4.5 62.1 0.8 O5' B:GTP701 4.5 62.3 0.9 O1A B:GTP701 4.6 63.3 0.9 O1B D:DTP701 4.6 49.6 0.8 C5' B:GTP701 4.6 50.1 0.9 O2G B:GTP701 4.8 66.6 0.9 CB C:LYS116 4.9 60.8 1.0 O3G D:DTP701 4.9 50.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-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/Atp-Bound SAMHD1 (RN206) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:56.1 occ:1.00 O2B C:DTP701 1.9 45.2 1.0 O1G A:GTP701 2.0 47.8 0.9 O1A A:GTP701 2.1 54.7 0.9 O2G C:DTP701 2.2 46.3 0.9 O1B A:GTP701 2.3 49.2 0.9 PB C:DTP701 3.3 47.5 0.9 PG A:GTP701 3.4 56.7 0.9 PG C:DTP701 3.4 48.4 0.8 PB A:GTP701 3.4 60.6 0.9 PA A:GTP701 3.5 57.7 0.9 NZ D:LYS116 3.6 51.0 1.0 O3B C:DTP701 3.8 58.6 0.5 NZ C:LYS523 3.8 61.1 0.8 O3B A:GTP701 3.8 67.0 0.9 O3' A:GTP701 3.8 56.9 0.9 O3A A:GTP701 3.9 59.2 0.9 O1G C:DTP701 3.9 55.9 1.0 O3G A:GTP701 4.1 50.9 0.9 O3A C:DTP701 4.2 50.7 0.6 C5' A:GTP701 4.2 47.5 0.9 O1B C:DTP701 4.3 60.1 1.0 O2G A:GTP701 4.3 63.2 0.9 O5' A:GTP701 4.4 55.1 0.9 C3' A:GTP701 4.5 58.1 0.9 O2A A:GTP701 4.5 53.0 0.9 O3G C:DTP701 4.6 57.2 0.9 CE D:LYS116 4.6 51.7 1.0 O2B A:GTP701 4.7 58.5 0.9 CD D:LYS116 4.7 64.3 1.0 CE C:LYS523 4.8 69.5 0.8 C4' A:GTP701 4.9 56.1 0.9 CG D:LYS116 5.0 72.7 1.0

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