Iron in PDB 5ao2: Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) R164A Variant Bound to Dgtp

The structure of Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) R164A Variant Bound to Dgtp, PDB code: 5ao2 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)	29.564 / 2.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.706, 199.320, 81.804, 90.00, 100.79, 90.00
R / Rfree (%)	15.62 / 23.44

The binding sites of Iron atom in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) R164A Variant Bound to Dgtp (pdb code 5ao2). 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) R164A Variant Bound to Dgtp, PDB code: 5ao2:
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) R164A Variant Bound to Dgtp


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) R164A Variant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:58.4 occ:1.00 OD2 A:ASP207 1.9 62.6 1.0 OD1 A:ASP311 1.9 63.5 1.0 NE2 A:HIS167 2.1 30.0 1.0 NE2 A:HIS206 2.1 54.8 1.0 O A:HOH2001 2.7 46.0 1.0 CG A:ASP311 2.8 68.2 1.0 CD2 A:HIS167 3.0 42.4 1.0 CG A:ASP207 3.0 71.0 1.0 CD2 A:HIS206 3.1 47.3 1.0 OD2 A:ASP311 3.1 81.9 1.0 CE1 A:HIS167 3.1 33.3 1.0 CE1 A:HIS206 3.2 41.5 1.0 OD1 A:ASP207 3.7 71.0 1.0 CG A:HIS167 4.2 32.0 1.0 ND1 A:HIS167 4.2 36.5 1.0 CB A:ASP207 4.2 38.6 1.0 CG A:HIS206 4.2 33.6 1.0 ND1 A:HIS206 4.2 36.2 1.0 CB A:ASP311 4.2 49.3 1.0 CD2 A:TYR315 4.6 54.6 1.0 CG2 A:VAL171 4.7 54.3 1.0 CA A:ASP311 4.8 43.6 1.0 O A:ASP311 4.9 43.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) R164A Variant Bound to Dgtp


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) R164A Variant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:63.5 occ:1.00 OD2 B:ASP207 1.9 52.3 1.0 O B:HOH2001 1.9 57.4 1.0 OD1 B:ASP311 2.0 33.5 1.0 NE2 B:HIS206 2.0 53.1 1.0 NE2 B:HIS167 2.1 45.0 1.0 CE1 B:HIS206 2.9 49.5 1.0 CD2 B:HIS167 2.9 42.7 1.0 CG B:ASP311 3.0 46.2 1.0 CG B:ASP207 3.0 58.5 1.0 CD2 B:HIS206 3.1 41.6 1.0 CE1 B:HIS167 3.2 34.4 1.0 OD2 B:ASP311 3.3 73.8 1.0 OD1 B:ASP207 3.5 49.7 1.0 ND1 B:HIS206 4.0 38.7 1.0 CG B:HIS167 4.1 23.5 1.0 CG B:HIS206 4.1 32.1 1.0 ND1 B:HIS167 4.2 28.9 1.0 CB B:ASP207 4.2 51.2 1.0 CB B:ASP311 4.3 37.2 1.0 CG2 B:VAL171 4.5 37.4 1.0 CD2 B:TYR315 4.8 62.0 1.0 CA B:ASP311 4.9 43.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) R164A Variant Bound to Dgtp


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) R164A Variant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1001 b:60.3 occ:1.00 OD1 C:ASP311 2.0 48.2 1.0 NE2 C:HIS206 2.1 54.0 1.0 OD2 C:ASP207 2.1 60.3 1.0 NE2 C:HIS167 2.2 35.8 1.0 CG C:ASP311 2.8 49.4 1.0 OD2 C:ASP311 3.0 54.5 1.0 CD2 C:HIS206 3.1 52.0 1.0 CG C:ASP207 3.1 67.2 1.0 CE1 C:HIS167 3.2 44.4 1.0 CD2 C:HIS167 3.2 42.3 1.0 CE1 C:HIS206 3.2 51.5 1.0 OD1 C:ASP207 3.5 82.5 1.0 CG C:HIS206 4.2 44.5 1.0 CB C:ASP311 4.3 45.9 1.0 ND1 C:HIS206 4.3 46.2 1.0 ND1 C:HIS167 4.3 37.1 1.0 CG C:HIS167 4.3 29.6 1.0 CB C:ASP207 4.4 68.8 1.0 CD2 C:TYR315 4.5 52.2 1.0 CG2 C:VAL171 4.7 46.1 1.0 CE2 C:TYR315 4.8 82.4 1.0 CA C:ASP311 4.9 41.2 1.0 O C:ASP311 4.9 48.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-583) R164A Variant Bound to Dgtp


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) R164A Variant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1001 b:69.3 occ:1.00 OD1 D:ASP311 1.9 59.5 1.0 OD2 D:ASP207 2.1 64.3 1.0 NE2 D:HIS206 2.1 52.8 1.0 NE2 D:HIS167 2.3 40.8 1.0 CG D:ASP311 2.8 56.8 1.0 OD2 D:ASP311 2.9 56.5 1.0 CE1 D:HIS206 3.0 60.7 1.0 CG D:ASP207 3.1 68.4 1.0 CD2 D:HIS206 3.1 46.9 1.0 CE1 D:HIS167 3.2 39.4 1.0 CD2 D:HIS167 3.3 46.8 1.0 OD1 D:ASP207 3.5 80.6 1.0 ND1 D:HIS206 4.2 56.5 1.0 CB D:ASP311 4.2 49.1 1.0 CG D:HIS206 4.2 44.5 1.0 CB D:ASP207 4.4 52.8 1.0 ND1 D:HIS167 4.4 39.7 1.0 CG D:HIS167 4.5 41.2 1.0 CD2 D:TYR315 4.5 50.4 1.0 CG2 D:VAL171 4.7 51.7 1.0 CA D:ASP311 4.8 49.4 1.0 O D:ASP311 4.9 69.5 1.0 CE2 D:TYR315 5.0 58.2 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