Magnesium in PDB 6cm2: SAMHD1 Hd Domain Bound to Decitabine Triphosphate

The structure of SAMHD1 Hd Domain Bound to Decitabine Triphosphate, PDB code: 6cm2 was solved by T.Oellerich, C.Schneider, D.Thomas, K.M.Knecht, O.Buzovetsky, L.Kaderali, C.Schliemann, H.Bohnenberger, L.Angenendt, W.Hartmann, E.Wardelmann, T.Rothenburger, S.Mohr, S.Scheich, F.Comoglio, A.Wilke, P.Strobel, H.Serve, M.Michaelis, N.Ferreiros, G.Geisslinger, Y.Xiong, O.T.Keppler, J.Cinatl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.492, 146.536, 98.552, 90.00, 114.61, 90.00
R / Rfree (%)	17.4 / 22.5

The binding sites of Magnesium atom in the SAMHD1 Hd Domain Bound to Decitabine Triphosphate (pdb code 6cm2). 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 Hd Domain Bound to Decitabine Triphosphate, PDB code: 6cm2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the SAMHD1 Hd Domain Bound to Decitabine Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SAMHD1 Hd Domain Bound to Decitabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:25.5 occ:1.00 O3G B:GTP705 1.9 37.5 1.0 O2B B:GTP705 2.0 29.3 1.0 O B:HOH838 2.0 24.6 1.0 O2G D:F6G703 2.1 30.5 1.0 O2A B:GTP705 2.1 22.8 1.0 O2B D:F6G703 2.1 29.7 1.0 PB B:GTP705 3.1 32.5 1.0 PG B:GTP705 3.2 32.9 1.0 PA B:GTP705 3.3 26.2 1.0 PB D:F6G703 3.4 27.1 1.0 PG D:F6G703 3.4 30.5 1.0 O3B B:GTP705 3.5 30.2 1.0 NZ C:LYS116 3.6 41.8 1.0 O3A B:GTP705 3.7 27.9 1.0 O3B D:F6G703 3.7 30.2 1.0 O3' B:GTP705 3.8 26.4 1.0 NZ D:LYS523 4.0 32.4 1.0 C5' B:GTP705 4.1 25.9 1.0 O2G B:GTP705 4.1 40.6 1.0 O1B D:F6G703 4.2 25.9 1.0 O5' B:GTP705 4.2 26.9 1.0 O1G D:F6G703 4.2 28.0 1.0 O1G B:GTP705 4.2 35.2 1.0 O B:HOH833 4.3 28.1 1.0 O3A D:F6G703 4.4 30.5 1.0 O1B B:GTP705 4.5 34.3 1.0 O3G D:F6G703 4.5 31.9 1.0 C3' B:GTP705 4.5 23.6 1.0 O1A B:GTP705 4.6 30.8 1.0 C4' B:GTP705 4.8 24.5 1.0 CE C:LYS116 4.9 40.9 1.0

Magnesium binding site 2 out of 4 in the SAMHD1 Hd Domain Bound to Decitabine Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SAMHD1 Hd Domain Bound to Decitabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:22.3 occ:1.00 O A:HOH866 2.0 19.4 1.0 O1G A:GTP704 2.0 29.5 1.0 O1B A:GTP704 2.1 24.8 1.0 O1G C:F6G703 2.1 21.7 1.0 O2B C:F6G703 2.1 25.1 1.0 O1A A:GTP704 2.2 23.2 1.0 PB A:GTP704 3.2 29.9 1.0 PG A:GTP704 3.2 30.4 1.0 PG C:F6G703 3.3 24.2 1.0 PB C:F6G703 3.4 22.3 1.0 O3B A:GTP704 3.4 28.8 1.0 PA A:GTP704 3.5 23.9 1.0 NZ D:LYS116 3.5 33.2 1.0 O3B C:F6G703 3.7 24.2 1.0 O3A A:GTP704 3.8 27.2 1.0 NZ C:LYS523 3.8 37.8 1.0 O3' A:GTP704 4.0 17.8 1.0 O2G C:F6G703 4.1 20.9 1.0 O3G A:GTP704 4.1 29.4 1.0 O2G A:GTP704 4.1 35.8 1.0 O1B C:F6G703 4.2 22.2 1.0 O A:HOH833 4.2 20.0 1.0 C5' A:GTP704 4.3 22.6 1.0 O5' A:GTP704 4.3 24.6 1.0 O3A C:F6G703 4.4 24.1 1.0 O3G C:F6G703 4.4 25.2 1.0 CE C:LYS523 4.6 32.2 1.0 O2B A:GTP704 4.6 26.4 1.0 O2A A:GTP704 4.6 24.4 1.0 C3' A:GTP704 4.6 19.5 1.0 CE D:LYS116 4.7 34.8 1.0

Magnesium binding site 3 out of 4 in the SAMHD1 Hd Domain Bound to Decitabine Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SAMHD1 Hd Domain Bound to Decitabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:23.9 occ:1.00 O D:HOH842 2.0 26.9 1.0 O1B D:GTP702 2.0 27.8 1.0 O1B B:F6G701 2.0 23.4 1.0 O1G D:GTP702 2.1 27.5 1.0 O1G B:F6G701 2.2 22.7 1.0 O1A D:GTP702 2.2 22.9 1.0 PB D:GTP702 3.0 29.6 1.0 PG D:GTP702 3.2 30.2 1.0 PB B:F6G701 3.2 23.2 1.0 PA D:GTP702 3.3 24.4 1.0 O3B D:GTP702 3.4 28.8 1.0 PG B:F6G701 3.4 25.3 1.0 O3A D:GTP702 3.5 25.3 1.0 O3B B:F6G701 3.6 27.4 1.0 NZ B:LYS523 3.7 30.7 1.0 O3' D:GTP702 3.8 22.1 1.0 NZ A:LYS116 3.9 35.8 1.0 O2B B:F6G701 4.0 24.6 1.0 C5' D:GTP702 4.2 22.9 1.0 O3G D:GTP702 4.2 31.0 1.0 O2G D:GTP702 4.2 27.9 1.0 O2G B:F6G701 4.2 23.3 1.0 O5' D:GTP702 4.3 21.6 1.0 O3A B:F6G701 4.4 24.6 1.0 O D:HOH831 4.4 47.1 1.0 O2B D:GTP702 4.4 30.3 1.0 O3G B:F6G701 4.5 27.1 1.0 O D:HOH874 4.5 24.7 1.0 CE B:LYS523 4.6 33.8 1.0 C3' D:GTP702 4.6 23.4 1.0 O2A D:GTP702 4.6 25.8 1.0 C4' D:GTP702 4.9 23.5 1.0

Magnesium binding site 4 out of 4 in the SAMHD1 Hd Domain Bound to Decitabine Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SAMHD1 Hd Domain Bound to Decitabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:31.9 occ:1.00 O1B A:F6G701 2.0 33.1 1.0 O2G A:F6G701 2.0 32.9 1.0 O2B B:GTP703 2.1 32.1 1.0 O3G B:GTP703 2.1 37.3 1.0 O B:HOH824 2.1 26.4 1.0 O2A B:GTP703 2.2 24.9 1.0 PB A:F6G701 3.1 28.9 1.0 PB B:GTP703 3.1 33.6 1.0 PG A:F6G701 3.2 31.9 1.0 PG B:GTP703 3.3 34.0 1.0 O3B A:F6G701 3.4 32.8 1.0 PA B:GTP703 3.4 26.8 1.0 O3B B:GTP703 3.4 30.7 1.0 O3A B:GTP703 3.7 28.0 1.0 O2B A:F6G701 3.9 27.4 1.0 NZ A:LYS523 3.9 41.5 1.0 NZ B:LYS116 3.9 37.5 1.0 O3' B:GTP703 3.9 24.4 1.0 O1G A:F6G701 4.1 30.8 1.0 C5' B:GTP703 4.1 24.4 1.0 O2G B:GTP703 4.1 34.9 1.0 O5' B:GTP703 4.2 26.4 1.0 O A:HOH819 4.2 44.5 1.0 O3A A:F6G701 4.3 34.0 1.0 O1G B:GTP703 4.3 31.3 1.0 O3G A:F6G701 4.3 35.6 1.0 O B:HOH848 4.4 25.6 1.0 O1B B:GTP703 4.5 32.8 1.0 O A:HOH896 4.5 46.9 1.0 C3' B:GTP703 4.6 24.2 1.0 O1A B:GTP703 4.7 27.4 1.0 CE A:LYS523 4.8 39.4 1.0 C4' B:GTP703 4.8 23.5 1.0

T.Oellerich, C.Schneider, D.Thomas, K.M.Knecht, O.Buzovetsky, L.Kaderali, C.Schliemann, H.Bohnenberger, L.Angenendt, W.Hartmann, E.Wardelmann, T.Rothenburger, S.Mohr, S.Scheich, F.Comoglio, A.Wilke, P.Strobel, H.Serve, M.Michaelis, N.Ferreiros, G.Geisslinger, Y.Xiong, O.T.Keppler, J.Cinatl. SAMHD1 Is A Resistance Factor and Predictive Biomarker For Decitabine in Acute Myeloid Leukemia To Be Published.