Magnesium in PDB 6dw7: SAMHD1 Without Catalytic Nucleotides

The structure of SAMHD1 Without Catalytic Nucleotides, PDB code: 6dw7 was solved by K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl, O.T.Keppler, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.546, 146.372, 98.929, 90.00, 113.67, 90.00
R / Rfree (%)	21.2 / 25

The structure of SAMHD1 Without Catalytic Nucleotides also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Magnesium atom in the SAMHD1 Without Catalytic Nucleotides (pdb code 6dw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the SAMHD1 Without Catalytic Nucleotides, PDB code: 6dw7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:47.0 occ:1.00 O1G A:GTP703 1.9 52.8 1.0 O1B B:DTP703 2.0 34.8 1.0 O1A A:GTP703 2.0 38.0 1.0 O3G B:DTP703 2.1 35.7 1.0 O1B A:GTP703 2.6 36.1 1.0 CD A:LYS116 3.2 36.7 1.0 PG A:GTP703 3.3 45.2 1.0 PB B:DTP703 3.3 34.7 1.0 O3' A:GTP703 3.4 29.0 1.0 PG B:DTP703 3.5 36.4 1.0 PA A:GTP703 3.5 39.0 1.0 PB A:GTP703 3.6 40.6 1.0 O3B A:GTP703 3.7 44.2 1.0 O3B B:DTP703 3.7 38.4 1.0 O3A A:GTP703 4.0 42.1 1.0 O2G A:GTP703 4.1 40.8 1.0 CG A:LYS116 4.1 42.9 1.0 NZ B:LYS523 4.2 58.5 1.0 C3' A:GTP703 4.2 36.1 1.0 O1G B:DTP703 4.2 35.5 1.0 O3A B:DTP703 4.3 36.4 1.0 O3G A:GTP703 4.3 44.6 1.0 CE A:LYS116 4.3 33.6 1.0 C5' A:GTP703 4.4 39.6 1.0 O2B B:DTP703 4.4 36.3 1.0 O2A A:GTP703 4.5 34.0 1.0 O5' A:GTP703 4.5 40.9 1.0 CE B:LYS523 4.6 60.0 1.0 O2G B:DTP703 4.6 32.8 1.0 O B:HOH811 4.7 31.1 1.0 C4' A:GTP703 4.8 35.2 1.0

Magnesium binding site 2 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:48.3 occ:1.00 O2G B:GTP702 1.7 57.6 1.0 O2A B:GTP702 2.1 43.6 1.0 O2B B:GTP702 2.1 30.3 1.0 O1G A:DTP701 2.1 34.7 1.0 O1B A:DTP701 2.1 38.6 1.0 PG B:GTP702 3.0 49.0 1.0 PB B:GTP702 3.2 37.4 1.0 PG A:DTP701 3.3 42.8 1.0 PB A:DTP701 3.3 35.2 1.0 O B:HOH813 3.4 52.1 1.0 O3B B:GTP702 3.4 41.6 1.0 PA B:GTP702 3.4 36.7 1.0 O3B A:DTP701 3.6 37.5 1.0 O3A B:GTP702 3.8 39.0 1.0 O3G A:DTP701 3.8 41.3 1.0 O3G B:GTP702 3.9 48.2 1.0 O1G B:GTP702 4.0 46.9 1.0 NZ A:LYS523 4.1 57.7 1.0 CE B:LYS116 4.1 52.0 1.0 O2B A:DTP701 4.1 34.1 1.0 O3' B:GTP702 4.2 39.0 1.0 C5' B:GTP702 4.4 36.3 1.0 O5' B:GTP702 4.4 35.5 1.0 CE A:LYS523 4.5 60.0 1.0 O1A B:GTP702 4.5 41.8 1.0 O3A A:DTP701 4.5 36.7 1.0 NZ B:LYS116 4.5 52.1 1.0 O2G A:DTP701 4.6 44.1 1.0 O1B B:GTP702 4.6 34.4 1.0 CD B:LYS116 4.9 49.7 1.0 C3' B:GTP702 4.9 37.4 1.0

Magnesium binding site 3 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:36.0 occ:1.00 O1G D:GTP701 1.8 65.6 1.0 O3G C:DTP701 2.0 37.9 1.0 O2B C:DTP701 2.0 32.7 1.0 O3A D:GTP701 2.3 44.8 1.0 O1B D:GTP701 2.8 40.4 1.0 PG D:GTP701 3.2 52.0 1.0 PB D:GTP701 3.2 42.0 1.0 PB C:DTP701 3.3 37.4 1.0 PG C:DTP701 3.3 40.2 1.0 O1A D:GTP701 3.4 44.4 1.0 PA D:GTP701 3.5 44.3 1.0 O3' D:GTP701 3.6 39.7 1.0 O3B D:GTP701 3.6 42.4 1.0 NZ D:LYS116 3.6 58.1 1.0 O3B C:DTP701 3.7 37.7 1.0 C5' D:GTP701 4.0 37.9 1.0 O2G D:GTP701 4.0 44.3 1.0 O1G C:DTP701 4.1 36.2 1.0 NZ C:LYS523 4.1 45.3 1.0 O3G D:GTP701 4.2 54.2 1.0 O5' D:GTP701 4.2 45.3 1.0 O3A C:DTP701 4.2 33.6 1.0 C3' D:GTP701 4.3 43.8 1.0 O1B C:DTP701 4.3 37.0 1.0 O2G C:DTP701 4.5 37.5 1.0 O2B D:GTP701 4.6 36.7 1.0 CE C:LYS523 4.6 49.2 1.0 C4' D:GTP701 4.6 41.9 1.0 O2A D:GTP701 4.7 54.0 1.0 CE D:LYS116 4.8 54.7 1.0

Magnesium binding site 4 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:43.4 occ:1.00 O2G C:GTP704 1.7 56.9 1.0 O2A C:GTP704 2.0 42.6 1.0 O2B D:DTP702 2.1 51.5 1.0 O1G D:DTP702 2.1 41.9 1.0 O2B C:GTP704 2.6 47.5 1.0 PG C:GTP704 3.1 51.3 1.0 NZ C:LYS116 3.3 56.7 1.0 PB D:DTP702 3.4 42.5 1.0 PG D:DTP702 3.4 45.0 1.0 PA C:GTP704 3.5 46.2 1.0 PB C:GTP704 3.6 47.8 1.0 O3B C:GTP704 3.6 44.5 1.0 O3B D:DTP702 3.8 46.3 1.0 O1G C:GTP704 3.8 43.9 1.0 NZ D:LYS523 3.8 67.3 1.0 O3' C:GTP704 3.9 34.4 1.0 O3A C:GTP704 4.0 44.3 1.0 O3G D:DTP702 4.0 40.8 1.0 O3G C:GTP704 4.1 56.2 1.0 O3A D:DTP702 4.4 44.2 1.0 O1A C:GTP704 4.4 48.2 1.0 O1B D:DTP702 4.5 40.3 1.0 C5' C:GTP704 4.5 47.0 1.0 C3' C:GTP704 4.5 38.9 1.0 O5' C:GTP704 4.6 48.0 1.0 CE C:LYS116 4.6 54.0 1.0 CE D:LYS523 4.6 68.7 1.0 O2G D:DTP702 4.7 45.1 1.0 CG C:LYS116 4.8 52.1 1.0 CD C:LYS116 4.9 45.5 1.0 O1B C:GTP704 5.0 41.4 1.0

K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl Jr., O.T.Keppler, Y.Xiong. The Structural Basis For Cancer Drug Interactions with the Catalytic and Allosteric Sites of SAMHD1. Proc. Natl. Acad. Sci. V. 115 10022 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30305425
DOI: 10.1073/PNAS.1805593115