Iron 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:

Magnesium

(Mg)

4 atoms

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

Iron 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 Iron with other atoms in the Fe 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 A:Fe1584 b:48.8 occ:1.00 O1B A:DG31585 2.0 47.5 1.0 OD1 A:ASP311 2.2 49.7 1.0 NE2 A:HIS206 2.2 37.4 1.0 OD2 A:ASP207 2.2 51.7 1.0 NE2 A:HIS167 2.3 39.7 1.0 O3G A:DG31585 2.4 0.0 1.0 CG A:ASP311 3.0 45.4 1.0 CD2 A:HIS206 3.1 38.5 1.0 CG A:ASP207 3.2 48.0 1.0 CD2 A:HIS167 3.2 36.2 1.0 OD2 A:ASP311 3.3 44.6 1.0 CE1 A:HIS206 3.3 37.8 1.0 CE1 A:HIS167 3.3 38.7 1.0 PB A:DG31585 3.4 47.6 1.0 OD1 A:ASP207 3.5 46.7 1.0 PG A:DG31585 3.7 0.3 1.0 O3B A:DG31585 3.8 81.5 1.0 NH1 A:ARG164 3.9 34.5 1.0 O3A A:DG31585 4.2 70.4 1.0 CG A:HIS206 4.3 40.8 1.0 ND1 A:HIS206 4.3 40.4 1.0 CB A:ASP311 4.3 43.7 1.0 ND1 A:HIS167 4.4 38.2 1.0 CG A:HIS167 4.4 38.8 1.0 CB A:ASP207 4.4 46.7 1.0 O2B A:DG31585 4.5 49.4 1.0 CD2 A:TYR315 4.6 34.9 1.0 O2G A:DG31585 4.6 0.4 1.0 O1G A:DG31585 4.7 0.1 1.0 CG2 A:VAL171 4.7 42.5 1.0 CA A:ASP311 4.9 45.2 1.0 NE2 A:GLN149 5.0 33.6 1.0 CE2 A:TYR315 5.0 38.0 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe1586 b:42.2 occ:1.00 O1B B:DG31587 2.0 49.8 1.0 OD2 B:ASP207 2.1 49.4 1.0 NE2 B:HIS167 2.2 54.3 1.0 OD1 B:ASP311 2.2 43.7 1.0 NE2 B:HIS206 2.2 43.9 1.0 O2G B:DG31587 2.6 0.8 1.0 CG B:ASP311 3.0 40.7 1.0 CE1 B:HIS167 3.1 44.9 1.0 CD2 B:HIS167 3.2 42.1 1.0 CG B:ASP207 3.2 41.1 1.0 CE1 B:HIS206 3.2 42.1 1.0 CD2 B:HIS206 3.2 40.2 1.0 OD2 B:ASP311 3.2 40.4 1.0 PB B:DG31587 3.4 51.9 1.0 OD1 B:ASP207 3.5 44.8 1.0 PG B:DG31587 3.8 0.3 1.0 NH1 B:ARG164 3.9 22.1 1.0 O3B B:DG31587 3.9 0.7 1.0 O3A B:DG31587 4.2 0.6 1.0 ND1 B:HIS167 4.2 36.7 1.0 CG B:HIS167 4.3 35.4 1.0 CB B:ASP311 4.3 36.4 1.0 ND1 B:HIS206 4.3 40.5 1.0 CG B:HIS206 4.3 40.4 1.0 CB B:ASP207 4.4 35.5 1.0 CD2 B:TYR315 4.5 37.6 1.0 O2B B:DG31587 4.5 55.6 1.0 O1G B:DG31587 4.6 0.5 1.0 CG2 B:VAL171 4.7 30.3 1.0 O B:ASP311 4.9 43.2 1.0 CA B:ASP311 5.0 36.2 1.0 O3G B:DG31587 5.0 0.4 1.0 CE2 B:TYR315 5.0 36.6 1.0

Iron 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 Iron with other atoms in the Fe 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 C:Fe1584 b:51.2 occ:1.00 O1B C:DG31585 2.0 52.9 1.0 NE2 C:HIS206 2.2 50.3 1.0 OD1 C:ASP311 2.3 48.5 1.0 NE2 C:HIS167 2.3 40.0 1.0 O3G C:DG31585 2.4 0.1 1.0 OD2 C:ASP207 2.5 48.1 1.0 CD2 C:HIS206 3.0 50.5 1.0 CG C:ASP311 3.1 48.5 1.0 CG C:ASP207 3.1 48.7 1.0 CD2 C:HIS167 3.2 40.1 1.0 OD2 C:ASP311 3.2 48.6 1.0 CE1 C:HIS167 3.3 41.1 1.0 OD1 C:ASP207 3.3 49.4 1.0 CE1 C:HIS206 3.3 48.3 1.0 PB C:DG31585 3.4 48.1 1.0 PG C:DG31585 3.7 0.8 1.0 O3B C:DG31585 3.8 82.4 1.0 NH1 C:ARG164 3.9 39.5 1.0 O3A C:DG31585 4.1 0.1 1.0 CG C:HIS206 4.2 49.5 1.0 CG C:HIS167 4.3 44.0 1.0 ND1 C:HIS206 4.3 48.2 1.0 ND1 C:HIS167 4.3 45.0 1.0 CB C:ASP311 4.4 48.5 1.0 O2G C:DG31585 4.4 0.2 1.0 CB C:ASP207 4.5 45.6 1.0 O2B C:DG31585 4.5 48.0 1.0 CD2 C:TYR315 4.7 49.7 1.0 CG2 C:VAL171 4.7 34.9 1.0 O1G C:DG31585 4.8 0.2 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe1585 b:39.5 occ:1.00 O1B D:DG31586 1.9 52.3 1.0 NE2 D:HIS206 2.1 38.8 1.0 NE2 D:HIS167 2.3 38.4 1.0 OD1 D:ASP311 2.3 50.9 1.0 OD2 D:ASP207 2.4 40.4 1.0 O1G D:DG31586 2.7 95.8 1.0 CG D:ASP311 3.0 49.1 1.0 CE1 D:HIS206 3.0 40.4 1.0 CD2 D:HIS167 3.1 35.4 1.0 CD2 D:HIS206 3.1 40.6 1.0 OD2 D:ASP311 3.1 52.1 1.0 CG D:ASP207 3.1 40.6 1.0 CE1 D:HIS167 3.3 37.5 1.0 PB D:DG31586 3.4 48.6 1.0 OD1 D:ASP207 3.4 41.5 1.0 NH1 D:ARG164 3.8 33.0 1.0 PG D:DG31586 3.8 97.1 1.0 O3B D:DG31586 4.0 0.1 1.0 ND1 D:HIS206 4.2 42.9 1.0 CG D:HIS206 4.2 42.4 1.0 O2B D:DG31586 4.3 50.4 1.0 CG D:HIS167 4.3 35.5 1.0 O3A D:DG31586 4.3 0.9 1.0 O2G D:DG31586 4.3 95.9 1.0 CB D:ASP311 4.4 42.2 1.0 ND1 D:HIS167 4.4 36.1 1.0 CB D:ASP207 4.5 41.0 1.0 CG2 D:VAL171 4.6 38.7 1.0 CD2 D:TYR315 4.6 34.5 1.0 O D:ASP311 5.0 37.9 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