Magnesium in PDB 5ao1: Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp

The structure of Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp, PDB code: 5ao1 was solved by D.Schwefel, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.228 / 2.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.121, 187.356, 81.373, 90.00, 100.54, 90.00
R / Rfree (%)	17.09 / 22.01

The structure of Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp (pdb code 5ao1). 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 Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp, PDB code: 5ao1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp


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 Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1585 b:84.7 occ:1.00 O1B B:DG31584 2.4 0.7 1.0 O3G B:DG31584 2.8 0.1 1.0 O1A B:DG31584 3.8 85.3 1.0 PB B:DG31584 3.9 0.1 1.0 PG B:DG31584 4.1 0.9 1.0 O3B B:DG31584 4.4 0.1 1.0 O2B B:DG31584 4.8 1.0 1.0 O1G B:DG31584 4.8 0.3 1.0 C5' B:DG31584 4.9 60.7 1.0 O3A B:DG31584 4.9 67.2 1.0 PA B:DG31584 4.9 83.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp


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 Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1590 b:74.5 occ:1.00 O3A B:DG31588 2.5 93.3 1.0 O A:HOH2046 2.7 59.3 1.0 O1B B:DG31588 3.3 98.8 1.0 PB B:DG31588 3.5 99.2 1.0 O2A B:DG31588 3.5 60.9 1.0 PA B:DG31588 3.6 61.9 1.0 CD1 A:LEU453 3.7 45.8 1.0 CG2 A:VAL378 3.8 43.5 1.0 O2G B:DG31588 4.0 0.3 1.0 O3B B:DG31588 4.3 0.0 1.0 CG1 A:VAL378 4.3 36.8 1.0 CG A:LEU453 4.5 47.3 1.0 O5' B:DG31588 4.5 72.7 1.0 CB A:LEU453 4.6 47.0 1.0 O1A B:DG31588 4.7 64.4 1.0 CB A:VAL378 4.7 40.6 1.0 O2B B:DG31588 4.8 99.2 1.0 PG B:DG31588 4.9 0.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp


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 Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1584 b:85.4 occ:1.00 O1G D:DG31583 2.4 0.3 1.0 O3A D:DG31583 2.6 0.9 1.0 O1B D:DG31583 2.8 94.8 1.0 PB D:DG31583 3.2 94.0 1.0 O5' D:DG31583 3.4 59.6 1.0 PG D:DG31583 3.5 0.9 1.0 PA D:DG31583 3.7 58.4 1.0 O3B D:DG31583 3.7 0.9 1.0 O3G D:DG31583 4.0 0.7 1.0 C3' D:DG31583 4.2 57.2 1.0 CD C:LYS116 4.3 65.6 1.0 C5' D:DG31583 4.3 57.2 1.0 CE C:LYS116 4.5 66.1 1.0 O1A D:DG31583 4.6 60.2 1.0 O2B D:DG31583 4.7 92.6 1.0 C4' D:DG31583 4.7 56.4 1.0 O2A D:DG31583 4.7 63.1 1.0 O D:HOH2040 4.7 72.2 1.0 O2G D:DG31583 4.9 0.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp


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 Human SAMHD1 (Amino Acid Residues 115-583) Bound to Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1590 b:84.2 occ:1.00 O3A D:DG31587 1.9 0.9 1.0 O2B D:DG31587 2.3 1.0 1.0 O2G D:DG31587 2.4 0.7 1.0 PB D:DG31587 2.6 0.2 1.0 O5' D:DG31587 3.0 71.2 1.0 PA D:DG31587 3.0 65.9 1.0 O3B D:DG31587 3.4 0.8 1.0 PG D:DG31587 3.5 0.4 1.0 O2A D:DG31587 3.6 65.7 1.0 O1B D:DG31587 3.8 0.2 1.0 O1A D:DG31587 4.2 69.8 1.0 C5' D:DG31587 4.4 69.6 1.0 C3' D:DG31587 4.5 66.5 1.0 CD D:LYS116 4.5 73.9 1.0 O1G D:DG31587 4.5 0.2 1.0 CE D:LYS116 4.5 82.0 1.0 O3G D:DG31587 4.5 0.4 1.0 C4' D:DG31587 4.8 67.5 1.0 CG2 C:VAL378 5.0 55.1 1.0

L.H.Arnold, H.C.T.Groom, S.Kunzelmann, D.Schwefel, S.J.Caswell, P.Ordonez, M.C.Mann, S.Rueschenbaum, D.C.Goldstone, S.Pennell, S.A.Howell, J.P.Stoye, M.Webb, I.A.Taylor, K.N.Bishop. Phospho-Dependent Regulation of SAMHD1 Oligomerisation Couples Catalysis and Restriction. Plos Pathog. V. 11 5194 2015.
ISSN: ISSN 1553-7366
PubMed: 26431200
DOI: 10.1371/JOURNAL.PPAT.1005194