Magnesium in PDB 4qg4: Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core

The structure of Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core, PDB code: 4qg4 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)	41.74 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.799, 147.120, 99.211, 90.00, 114.00, 90.00
R / Rfree (%)	22.3 / 24.5

The structure of Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core (pdb code 4qg4). 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 (H210A) Mutant Catalytic Core, PDB code: 4qg4:
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 (H210A) 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 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:35.4 occ:1.00 O1B B:DTP703 2.0 29.7 0.7 O2G B:DTP703 2.0 32.7 1.0 O1G A:GTP703 2.0 37.1 1.0 O1A A:GTP703 2.2 32.0 1.0 O1B A:GTP703 2.2 32.8 1.0 PB B:DTP703 3.3 30.7 1.0 PG B:DTP703 3.3 31.9 1.0 PB A:GTP703 3.4 37.5 1.0 PG A:GTP703 3.4 41.2 1.0 PA A:GTP703 3.5 33.8 1.0 O3B B:DTP703 3.7 30.2 0.7 O3B A:GTP703 3.8 42.3 1.0 NZ A:LYS116 3.8 38.7 1.0 O B:HOH906 3.8 42.4 1.0 O3' A:GTP703 3.9 29.3 1.0 O3A A:GTP703 3.9 34.7 1.0 NZ B:LYS523 3.9 38.7 0.9 O1G B:DTP703 3.9 29.4 1.0 O2B B:DTP703 4.2 28.4 1.0 O3G A:GTP703 4.2 43.8 1.0 O B:HOH879 4.2 43.4 1.0 C5' A:GTP703 4.2 29.3 1.0 O3A B:DTP703 4.3 29.8 0.8 O A:HOH804 4.3 29.4 1.0 O2G A:GTP703 4.3 45.3 1.0 O5' A:GTP703 4.4 34.5 1.0 O3G B:DTP703 4.4 36.7 0.9 O2B A:GTP703 4.6 33.8 1.0 O2A A:GTP703 4.6 33.0 1.0 C3' A:GTP703 4.7 30.1 1.0 CE A:LYS116 4.8 39.5 1.0 CD A:LYS116 5.0 38.5 1.0 C4' A:GTP703 5.0 26.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) 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 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:39.4 occ:1.00 O3G B:GTP702 2.0 42.4 0.9 O1B A:DTP702 2.0 36.3 0.9 O1G A:DTP702 2.0 43.5 0.9 O2B B:GTP702 2.1 36.4 0.9 O2A B:GTP702 2.3 35.0 0.9 PB B:GTP702 3.2 42.8 0.9 PG B:GTP702 3.3 45.9 0.9 PG A:DTP702 3.3 41.2 1.0 PB A:DTP702 3.3 36.9 1.0 PA B:GTP702 3.6 33.9 0.9 O3B B:GTP702 3.6 41.0 0.9 NZ B:LYS116 3.7 43.1 1.0 O3B A:DTP702 3.7 41.7 0.7 O3A B:GTP702 3.8 40.2 0.9 O2G A:DTP702 3.8 40.4 1.0 O3' B:GTP702 3.9 31.9 0.9 O2B A:DTP702 4.1 33.4 1.0 O2G B:GTP702 4.1 42.7 0.9 O B:HOH943 4.2 50.6 1.0 C5' B:GTP702 4.2 34.1 0.9 NZ A:LYS523 4.2 49.6 1.0 O1G B:GTP702 4.2 44.6 0.9 O3A A:DTP702 4.3 37.8 1.0 O5' B:GTP702 4.4 39.4 0.9 O B:HOH826 4.4 38.8 1.0 O3G A:DTP702 4.5 44.7 0.8 O1B B:GTP702 4.5 41.7 0.9 O B:HOH969 4.7 52.4 1.0 C3' B:GTP702 4.7 33.6 0.9 O1A B:GTP702 4.7 37.8 0.9 CE B:LYS116 4.9 36.5 1.0 C4' B:GTP702 5.0 35.3 0.9

Magnesium binding site 3 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) 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 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:42.7 occ:1.00 O B:HOH922 2.1 30.8 1.0 O3G B:GTP701 2.8 36.9 0.9 O C:HOH822 2.8 33.6 0.8 O2B D:DTP701 3.0 35.1 0.8 O2A B:GTP701 3.0 36.2 0.9 NZ C:LYS116 3.1 34.7 0.9 O1G D:DTP701 3.2 39.7 1.0 O3' B:GTP701 3.5 34.1 0.9 CG C:LYS116 3.6 37.7 0.9 CD C:LYS116 3.9 31.0 0.9 O2G D:DTP701 4.0 36.5 1.0 PG D:DTP701 4.1 36.5 1.0 CE C:LYS116 4.1 32.2 0.9 PB D:DTP701 4.2 33.5 1.0 PG B:GTP701 4.2 39.3 0.9 O2B B:GTP701 4.2 40.1 0.9 CB C:LYS116 4.3 33.6 0.9 C3' B:GTP701 4.5 29.4 0.9 O D:HOH852 4.5 45.5 1.0 PA B:GTP701 4.5 36.2 0.9 CA C:LYS116 4.5 35.7 0.9 O3A D:DTP701 4.6 34.5 0.8 O3B D:DTP701 4.6 37.5 0.7 O1G B:GTP701 4.6 38.3 0.9 NZ D:LYS523 4.9 40.3 0.9 O C:MET115 4.9 36.4 0.7

Magnesium binding site 4 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) 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 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:45.2 occ:1.00 O1G A:GTP701 2.7 42.1 1.0 O D:HOH816 2.9 34.4 1.0 O1A A:GTP701 2.9 35.2 1.0 O2G C:DTP701 2.9 36.1 1.0 O2B C:DTP701 2.9 36.0 1.0 NZ D:LYS116 3.1 41.8 0.9 O3' A:GTP701 3.5 33.4 1.0 CG D:LYS116 3.7 41.4 0.9 CD D:LYS116 3.9 39.6 0.9 PG C:DTP701 4.0 36.8 0.9 O1B A:GTP701 4.0 41.0 1.0 O1G C:DTP701 4.1 39.5 0.9 O C:HOH813 4.1 36.1 1.0 PB C:DTP701 4.1 32.4 1.0 CE D:LYS116 4.1 35.8 0.9 PG A:GTP701 4.2 38.9 1.0 CB D:LYS116 4.3 37.3 0.9 O3B C:DTP701 4.4 37.4 0.5 PA A:GTP701 4.4 35.4 1.0 O3A C:DTP701 4.5 35.6 0.6 C3' A:GTP701 4.5 34.1 1.0 CA D:LYS116 4.6 40.5 0.9 O3G A:GTP701 4.7 34.5 1.0 O D:HOH887 4.8 47.9 1.0 O D:MET115 4.8 43.2 0.7 NZ C:LYS523 4.8 42.5 0.9 PB A:GTP701 4.9 44.0 1.0 O3B A:GTP701 5.0 35.3 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