Magnesium in PDB 7s2y: SAMHD1 Hd Domain Bound to Cndac

The structure of SAMHD1 Hd Domain Bound to Cndac, PDB code: 7s2y was solved by K.M.Digianantonio, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.03 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.84, 146.167, 99.587, 90, 114.27, 90
R / Rfree (%)	18.6 / 23.2

The binding sites of Magnesium atom in the SAMHD1 Hd Domain Bound to Cndac (pdb code 7s2y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the SAMHD1 Hd Domain Bound to Cndac, PDB code: 7s2y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


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 Cndac within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:38.1 occ:1.00 O1G B:DTP703 1.7 43.1 1.0 O1B B:DTP703 2.1 43.2 1.0 O2A D:GTP703 2.3 42.1 1.0 O3B D:GTP703 2.5 46.3 1.0 O1G D:GTP703 2.9 49.9 1.0 NZ A:LYS116 2.9 64.2 1.0 PG B:DTP703 3.1 46.1 1.0 O1B D:GTP703 3.2 42.3 1.0 PG D:GTP703 3.3 50.7 1.0 PB B:DTP703 3.3 40.8 1.0 PB D:GTP703 3.4 44.5 1.0 O3B B:DTP703 3.5 42.5 1.0 NZ B:LYS523 3.6 56.1 1.0 PA D:GTP703 3.7 46.0 1.0 O3' D:GTP703 3.8 37.5 1.0 O3A D:GTP703 3.9 44.0 1.0 O3G B:DTP703 4.0 41.3 1.0 O2G D:GTP703 4.2 47.6 1.0 O2G B:DTP703 4.3 45.5 1.0 O2B B:DTP703 4.3 45.5 1.0 CE A:LYS116 4.3 60.6 1.0 O3A B:DTP703 4.5 40.1 1.0 O3G D:GTP703 4.5 48.1 1.0 CE B:LYS523 4.6 54.0 1.0 C5' D:GTP703 4.6 41.6 1.0 O5' D:GTP703 4.6 43.0 1.0 O2B D:GTP703 4.7 45.9 1.0 C3' D:GTP703 4.7 40.7 1.0 O1A D:GTP703 4.8 41.6 1.0

Magnesium binding site 2 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


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 Cndac within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:56.7 occ:1.00 O A:HOH802 2.1 19.3 1.0 O A:HOH805 2.2 52.4 1.0 O3G A:85T701 2.4 42.3 1.0 O1B A:85T701 2.6 44.5 1.0 OD2 A:ASP309 3.0 48.7 1.0 OD1 A:ASP309 3.6 54.7 1.0 CG A:ASP309 3.7 51.9 1.0 NH1 A:ARG206 3.8 60.4 1.0 NZ A:LYS312 3.8 50.5 1.0 PG A:85T701 3.9 45.4 1.0 PB A:85T701 4.0 46.0 1.0 OG A:SER302 4.3 78.8 1.0 NH2 A:ARG206 4.4 60.9 1.0 O1G A:85T701 4.4 44.2 1.0 O3B A:85T701 4.4 48.2 1.0 CZ A:ARG206 4.6 60.4 1.0 OD2 A:ASP311 4.6 49.6 1.0 CE A:LYS312 4.8 48.8 1.0 CG A:LYS312 4.8 47.2 1.0 O3A A:85T701 4.9 51.7 1.0 O2B A:85T701 4.9 47.9 1.0 O A:GLY307 5.0 58.5 1.0 CB A:ASP311 5.0 47.3 1.0

Magnesium binding site 3 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


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 Cndac within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:46.4 occ:1.00 O B:HOH804 2.1 20.4 1.0 O B:HOH801 2.4 22.6 1.0 O1B B:85T702 2.7 43.3 1.0 O B:HOH802 2.8 46.8 1.0 OG B:SER302 2.8 64.7 1.0 NH1 B:ARG206 3.1 57.2 1.0 O3G B:85T702 3.5 44.6 1.0 NH2 B:ARG206 3.7 58.5 1.0 OD2 B:ASP309 3.7 55.5 1.0 CZ B:ARG206 3.8 56.9 1.0 PB B:85T702 4.0 47.4 1.0 CB B:SER302 4.0 60.3 1.0 CA B:SER302 4.4 56.1 1.0 O2B B:85T702 4.5 48.5 1.0 CG B:ASP309 4.5 52.5 1.0 OD1 B:ASP309 4.6 51.8 1.0 PG B:85T702 4.7 50.5 1.0 NZ B:LYS304 4.9 90.5 1.0 O3B B:85T702 4.9 49.6 1.0 O3A B:85T702 4.9 53.0 1.0 OE2 B:GLU234 4.9 61.4 1.0 C B:SER302 5.0 55.5 1.0

Magnesium binding site 4 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


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 Cndac within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:31.2 occ:1.00 O1G A:DTP702 1.9 43.1 1.0 O2A C:GTP702 2.1 43.5 1.0 O1B A:DTP702 2.2 44.8 1.0 O3B C:GTP702 2.4 45.2 1.0 O1B C:GTP702 2.7 44.8 1.0 NZ B:LYS116 2.9 65.2 1.0 PB C:GTP702 3.1 43.7 1.0 PG C:GTP702 3.3 46.8 1.0 PG A:DTP702 3.3 44.2 1.0 O1G C:GTP702 3.3 45.9 1.0 PB A:DTP702 3.4 43.0 1.0 PA C:GTP702 3.4 45.1 1.0 O3B A:DTP702 3.6 44.5 1.0 O3A C:GTP702 3.6 44.3 1.0 NZ A:LYS523 3.7 66.3 1.0 O2G C:GTP702 3.8 43.1 1.0 O3' C:GTP702 3.9 37.5 1.0 O3G A:DTP702 4.2 42.7 1.0 CE B:LYS116 4.2 64.5 1.0 O2B A:DTP702 4.3 42.5 1.0 C5' C:GTP702 4.3 40.5 1.0 O5' C:GTP702 4.3 41.8 1.0 O2G A:DTP702 4.4 47.1 1.0 O3G C:GTP702 4.4 50.3 1.0 CE A:LYS523 4.5 64.1 1.0 O2B C:GTP702 4.5 43.7 1.0 C3' C:GTP702 4.5 38.5 1.0 O3A A:DTP702 4.5 43.8 1.0 O1A C:GTP702 4.6 42.5 1.0 C4' C:GTP702 4.9 39.0 1.0

Magnesium binding site 5 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of SAMHD1 Hd Domain Bound to Cndac within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg704 b:27.6 occ:1.00 O1B D:DTP702 2.1 51.4 1.0 O2A B:GTP701 2.2 50.5 1.0 O1G D:DTP702 2.3 41.2 1.0 O2G B:GTP701 2.5 55.5 1.0 O3B B:GTP701 2.7 48.7 1.0 NZ C:LYS116 3.2 68.0 1.0 PG B:GTP701 3.3 51.0 1.0 PB D:DTP702 3.4 50.8 1.0 O3' B:GTP701 3.5 51.1 1.0 PG D:DTP702 3.5 45.0 1.0 PA B:GTP701 3.7 49.8 1.0 O3B D:DTP702 3.8 46.6 1.0 O1B B:GTP701 3.9 54.8 1.0 PB B:GTP701 3.9 51.0 1.0 O3G D:DTP702 4.0 43.8 1.0 O3G B:GTP701 4.0 44.2 1.0 NZ D:LYS523 4.0 61.4 1.0 O3A B:GTP701 4.3 48.1 1.0 C3' B:GTP701 4.3 48.8 1.0 CE C:LYS116 4.4 66.7 1.0 O3A D:DTP702 4.4 48.3 1.0 CG C:LYS116 4.4 67.9 1.0 O1A B:GTP701 4.5 49.1 1.0 O2B D:DTP702 4.5 51.4 1.0 O1G B:GTP701 4.5 44.6 1.0 CD C:LYS116 4.6 66.5 1.0 C5' B:GTP701 4.6 50.8 1.0 O5' B:GTP701 4.7 50.6 1.0 O2G D:DTP702 4.9 41.9 1.0 C4' B:GTP701 5.0 50.4 1.0

Magnesium binding site 6 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of SAMHD1 Hd Domain Bound to Cndac within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg705 b:30.8 occ:1.00 O1G C:DTP701 1.9 41.3 1.0 O3B D:GTP701 1.9 47.5 1.0 O1B C:DTP701 2.3 42.5 1.0 O2A D:GTP701 2.3 43.5 1.0 O C:HOH805 2.5 26.5 1.0 O1B D:GTP701 2.8 44.9 1.0 PB D:GTP701 3.0 43.3 1.0 O2G D:GTP701 3.0 47.0 1.0 PG D:GTP701 3.0 50.4 1.0 NZ C:LYS523 3.1 55.1 1.0 PG C:DTP701 3.2 42.2 1.0 NZ D:LYS116 3.4 67.9 1.0 PB C:DTP701 3.5 44.4 1.0 PA D:GTP701 3.6 45.3 1.0 O3G C:DTP701 3.6 40.0 1.0 O3A D:GTP701 3.6 43.1 1.0 O1G D:GTP701 3.7 47.7 1.0 O3B C:DTP701 3.8 43.8 1.0 O3G D:GTP701 4.1 53.7 1.0 O2B D:GTP701 4.2 43.8 1.0 CE C:LYS523 4.4 56.3 1.0 O3' D:GTP701 4.4 48.4 1.0 O2G C:DTP701 4.4 44.0 1.0 O2B C:DTP701 4.4 42.3 1.0 C5' D:GTP701 4.6 47.9 1.0 O5' D:GTP701 4.6 47.6 1.0 O3A C:DTP701 4.7 42.5 1.0 O1A D:GTP701 4.7 45.6 1.0 C3' D:GTP701 4.8 48.0 1.0 CE D:LYS116 4.8 64.7 1.0 O C:HOH804 4.9 36.1 1.0 O D:HOH805 5.0 31.2 1.0

Magnesium binding site 7 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of SAMHD1 Hd Domain Bound to Cndac within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg706 b:37.3 occ:1.00 O C:HOH801 2.3 33.4 1.0 O1B C:85T703 2.3 49.5 1.0 O2G C:85T703 2.6 45.9 1.0 O C:HOH809 3.0 50.8 1.0 O3G C:85T703 3.2 46.9 1.0 PG C:85T703 3.4 46.1 1.0 OD2 C:ASP309 3.6 50.7 1.0 NZ C:LYS312 3.6 57.3 1.0 PB C:85T703 3.6 50.7 1.0 O3B C:85T703 4.1 47.9 1.0 O2B C:85T703 4.2 53.9 1.0 OG C:SER302 4.4 70.4 1.0 CG C:ASP309 4.4 50.4 1.0 OD1 C:ASP309 4.5 52.1 1.0 NH1 C:ARG206 4.5 43.4 1.0 O1G C:85T703 4.7 47.9 1.0 NH2 C:ARG206 4.7 43.3 1.0 CE C:LYS312 4.8 55.3 1.0 O3A C:85T703 4.9 49.7 1.0

Magnesium binding site 8 out of 8 in the SAMHD1 Hd Domain Bound to Cndac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of SAMHD1 Hd Domain Bound to Cndac within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg705 b:33.8 occ:1.00 O D:HOH801 2.0 65.5 1.0 O D:HOH807 2.4 39.9 1.0 O3G D:85T704 2.4 54.0 1.0 O2B D:85T704 2.5 50.3 1.0 NZ D:LYS312 3.3 48.1 1.0 OD2 D:ASP309 3.3 56.1 1.0 O2G D:85T704 3.4 54.8 1.0 PG D:85T704 3.4 52.7 1.0 PB D:85T704 3.8 52.4 1.0 OD1 D:ASP309 4.1 56.3 1.0 CG D:ASP309 4.2 54.5 1.0 O3B D:85T704 4.2 51.1 1.0 O1B D:85T704 4.5 52.5 1.0 CE D:LYS312 4.5 43.7 1.0 NH1 D:ARG206 4.6 40.9 1.0 O1G D:85T704 4.6 59.7 1.0 OG D:SER302 4.9 61.9 1.0 O D:GLY307 4.9 52.7 1.0 NH2 D:ARG206 5.0 39.7 1.0

T.Rothenburger, D.Thomas, Y.Schreiber, P.R.Wratil, T.Pflantz, K.Knecht, K.Digianantonio, J.Temple, C.Schneider, H.M.Baldauf, K.M.Mclaughlin, F.Rothweiler, B.Bilen, S.Farmand, D.Bojkova, R.Costa, N.Ferreiros, G.Geisslinger, T.Oellerich, Y.Xiong, O.T.Keppler, M.N.Wass, M.Michaelis, J.Cinatl Jr.. Differences Between Intrinsic and Acquired Nucleoside Analogue Resistance in Acute Myeloid Leukaemia Cells. J Exp Clin Cancer Res V. 40 317 2021.
ISSN: ISSN 1756-9966
PubMed: 34641952
DOI: 10.1186/S13046-021-02093-4