Magnesium in PDB 7ltt: SAMHD1(113-626) H206R D207N R366C

The structure of SAMHD1(113-626) H206R D207N R366C, PDB code: 7ltt was solved by J.T.Temple, N.E.Bowen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.38 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.926, 140.105, 97.193, 90, 114.18, 90
R / Rfree (%)	17.8 / 21.2

The binding sites of Magnesium atom in the SAMHD1(113-626) H206R D207N R366C (pdb code 7ltt). 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(113-626) H206R D207N R366C, PDB code: 7ltt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the SAMHD1(113-626) H206R D207N R366C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:28.2 occ:1.00 O3G A:DGT704 1.9 27.2 1.0 O3G B:DGT703 2.0 27.1 1.0 O2B A:DGT704 2.0 28.9 1.0 O1B B:DGT703 2.1 26.7 1.0 O A:HOH858 2.1 27.1 1.0 O2A A:DGT704 2.1 26.5 1.0 PB A:DGT704 3.1 30.6 1.0 PG A:DGT704 3.1 30.8 1.0 O3B A:DGT704 3.3 29.6 1.0 PB B:DGT703 3.3 26.7 1.0 PG B:DGT703 3.3 30.6 1.0 PA A:DGT704 3.4 27.0 1.0 O3A A:DGT704 3.6 29.0 1.0 O3B B:DGT703 3.7 28.2 1.0 NZ A:LYS116 3.8 40.6 1.0 O1G A:DGT704 4.0 34.8 1.0 O3' A:DGT704 4.0 25.9 1.0 NZ B:LYS523 4.0 49.6 1.0 O2G A:DGT704 4.1 32.8 1.0 O1G B:DGT703 4.1 29.6 1.0 O2B B:DGT703 4.2 26.4 1.0 O B:HOH862 4.2 46.8 1.0 O A:HOH890 4.3 55.1 1.0 C5' A:DGT704 4.3 26.0 1.0 O5' A:DGT704 4.3 25.0 1.0 O2G B:DGT703 4.4 31.3 1.0 O1B A:DGT704 4.5 31.9 1.0 O3A B:DGT703 4.5 26.4 1.0 C3' A:DGT704 4.6 26.1 1.0 O1A A:DGT704 4.6 28.6 1.0 O A:HOH840 4.7 29.3 1.0 O B:HOH802 4.8 68.8 1.0 C4' A:DGT704 5.0 26.4 1.0 CE A:LYS116 5.0 40.8 1.0

Magnesium binding site 2 out of 4 in the SAMHD1(113-626) H206R D207N R366C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:33.8 occ:1.00 O3G A:DGT702 1.9 33.1 1.0 O1B B:DGT702 2.0 34.5 1.0 O B:HOH853 2.0 32.7 1.0 O1B A:DGT702 2.0 30.5 1.0 O2G B:DGT702 2.1 36.6 1.0 O2A B:DGT702 2.1 32.9 1.0 PB B:DGT702 3.2 39.4 1.0 PG B:DGT702 3.2 38.8 1.0 PB A:DGT702 3.3 31.0 1.0 PG A:DGT702 3.3 34.8 1.0 PA B:DGT702 3.4 35.4 1.0 O3B B:DGT702 3.4 36.4 1.0 O3B A:DGT702 3.6 35.5 1.0 O3A B:DGT702 3.6 36.0 1.0 NZ B:LYS116 3.7 45.3 1.0 O3' B:DGT702 3.9 33.4 1.0 O1G A:DGT702 4.0 33.3 1.0 O3G B:DGT702 4.1 38.8 1.0 C5' B:DGT702 4.2 34.2 1.0 O2B A:DGT702 4.2 30.6 1.0 NZ A:LYS523 4.2 54.4 1.0 O B:HOH842 4.2 48.7 1.0 O5' B:DGT702 4.2 35.7 1.0 O1G B:DGT702 4.3 43.2 1.0 O3A A:DGT702 4.4 32.6 1.0 O B:HOH814 4.4 26.9 1.0 O2G A:DGT702 4.5 36.0 1.0 C3' B:DGT702 4.5 31.9 1.0 O2B B:DGT702 4.5 36.7 1.0 O1A B:DGT702 4.6 35.3 1.0 C4' B:DGT702 4.8 33.1 1.0 CE B:LYS116 4.9 44.0 1.0

Magnesium binding site 3 out of 4 in the SAMHD1(113-626) H206R D207N R366C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:25.8 occ:1.00 O3G A:DGT701 2.0 30.1 1.0 O2B A:DGT701 2.0 26.3 1.0 O A:HOH862 2.1 23.7 1.0 O2B C:DGT701 2.1 24.6 1.0 O2A A:DGT701 2.1 25.3 1.0 O2G C:DGT701 2.3 25.9 1.0 PB A:DGT701 3.2 30.3 1.0 PG A:DGT701 3.3 31.0 1.0 PB C:DGT701 3.3 25.4 1.0 PA A:DGT701 3.4 25.9 1.0 O3B A:DGT701 3.4 29.1 1.0 PG C:DGT701 3.5 27.7 1.0 O3A A:DGT701 3.6 28.4 1.0 O3B C:DGT701 3.7 24.5 1.0 NZ D:LYS116 3.8 31.8 1.0 O3' A:DGT701 3.8 24.1 1.0 O C:HOH884 3.9 54.2 1.0 NZ C:LYS523 4.0 56.8 1.0 O1B C:DGT701 4.1 24.1 1.0 O3G C:DGT701 4.2 26.4 1.0 O1G A:DGT701 4.2 31.8 1.0 C5' A:DGT701 4.2 24.5 1.0 O5' A:DGT701 4.2 24.4 1.0 O2G A:DGT701 4.3 33.0 1.0 C3' A:DGT701 4.5 23.4 1.0 O A:HOH864 4.5 23.9 1.0 O1B A:DGT701 4.5 30.7 1.0 O3A C:DGT701 4.5 24.7 1.0 O A:HOH914 4.5 62.8 1.0 O1A A:DGT701 4.6 27.4 1.0 O1G C:DGT701 4.7 27.4 1.0 C4' A:DGT701 4.8 23.1 1.0 CE C:LYS523 4.9 56.1 1.0 CE D:LYS116 4.9 32.1 1.0

Magnesium binding site 4 out of 4 in the SAMHD1(113-626) H206R D207N R366C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:41.5 occ:1.00 O1G C:DGT704 1.9 44.7 1.0 O2B D:DGT800 2.0 37.3 1.0 O2G D:DGT800 2.0 41.0 1.0 O C:HOH866 2.1 35.4 1.0 O1B C:DGT704 2.1 42.0 1.0 O1A C:DGT704 2.1 39.1 1.0 PB C:DGT704 3.2 49.3 1.0 PG C:DGT704 3.2 47.1 1.0 PB D:DGT800 3.3 36.0 1.0 PG D:DGT800 3.3 42.3 1.0 O3B C:DGT704 3.4 43.8 1.0 PA C:DGT704 3.5 42.2 1.0 NZ C:LYS116 3.5 53.3 1.0 O3B D:DGT800 3.5 41.7 1.0 O3A C:DGT704 3.6 43.5 1.0 NZ D:LYS523 3.8 56.6 1.0 O3' C:DGT704 4.0 37.7 1.0 O3G D:DGT800 4.1 45.8 1.0 O2G C:DGT704 4.2 50.0 1.0 O3G C:DGT704 4.2 43.4 1.0 O1B D:DGT800 4.2 35.0 1.0 C5' C:DGT704 4.3 40.3 1.0 O5' C:DGT704 4.4 41.3 1.0 O1G D:DGT800 4.4 44.9 1.0 O3A D:DGT800 4.4 37.6 1.0 O C:HOH904 4.5 54.8 1.0 O2B C:DGT704 4.5 46.8 1.0 O C:HOH844 4.6 36.7 1.0 C3' C:DGT704 4.6 35.9 1.0 O2A C:DGT704 4.6 40.3 1.0 CE C:LYS116 4.9 51.1 1.0 C4' C:DGT704 4.9 37.4 1.0 NZ B:LYS377 5.0 78.1 1.0 CE D:LYS523 5.0 57.8 1.0

N.E.Bowen, J.Temple, C.Shepard, A.Oo, F.Arizaga, P.Kapoor-Vazirani, M.Persaud, C.H.Yu, D.H.Kim, R.F.Schinazi, D.N.Ivanov, F.Diaz-Griffero, D.S.Yu, Y.Xiong, B.Kim. Structural and Functional Characterization Explains Loss of Dntpase Activity of the Cancer-Specific R366C/H Mutant SAMHD1 Proteins. J.Biol.Chem. V. 297 01170 2021.
ISSN: ESSN 1083-351X
PubMed: 34492268
DOI: 10.1016/J.JBC.2021.101170