Iron in PDB 5ao3: Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-626) Bound to Gtp

The structure of Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-626) Bound to Gtp, PDB code: 5ao3 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)	29.657 / 3.004
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.919, 95.733, 97.592, 91.37, 108.97, 115.33
R / Rfree (%)	17.71 / 24.73

The binding sites of Iron atom in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-626) Bound to Gtp (pdb code 5ao3). 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 115-626) Bound to Gtp, PDB code: 5ao3:
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 115-626) Bound to Gtp


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 115-626) Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1584 b:30.9 occ:1.00 NE2 A:HIS167 2.0 38.6 1.0 NE2 A:HIS206 2.0 39.0 1.0 O1 A:SO41588 2.1 93.7 1.0 OD2 A:ASP311 2.1 67.4 1.0 CE1 A:HIS167 2.9 41.1 1.0 OD2 A:ASP207 2.9 77.7 1.0 CG A:ASP311 2.9 62.5 1.0 CE1 A:HIS206 3.0 45.2 1.0 OD1 A:ASP311 3.0 78.0 1.0 CD2 A:HIS206 3.0 21.8 1.0 CD2 A:HIS167 3.1 39.8 1.0 S A:SO41588 3.2 93.7 1.0 CG A:ASP207 3.5 65.2 1.0 O2 A:SO41588 3.5 93.7 1.0 OD1 A:ASP207 3.6 59.6 1.0 O3 A:SO41588 3.6 93.7 1.0 NH1 A:ARG164 3.8 31.9 1.0 ND1 A:HIS167 4.0 38.0 1.0 ND1 A:HIS206 4.1 35.9 1.0 CG A:HIS206 4.2 23.1 1.0 CG A:HIS167 4.2 31.5 1.0 CB A:ASP311 4.4 48.7 1.0 CG2 A:VAL171 4.4 16.7 1.0 O4 A:SO41588 4.5 93.7 1.0 CD2 A:TYR315 4.6 34.1 1.0 CB A:ASP207 4.8 49.0 1.0 O A:ASP311 4.9 51.5 1.0 CE2 A:TYR315 4.9 26.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-626) Bound to Gtp


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 115-626) Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1584 b:32.7 occ:1.00 O4 B:SO41588 1.7 97.1 1.0 NE2 B:HIS206 2.1 49.3 1.0 NE2 B:HIS167 2.1 49.5 1.0 OD1 B:ASP311 2.2 57.2 1.0 OD2 B:ASP207 2.5 92.5 1.0 CE1 B:HIS206 2.9 44.8 1.0 CG B:ASP311 3.0 59.2 1.0 S B:SO41588 3.1 97.1 1.0 CD2 B:HIS167 3.1 43.0 1.0 CE1 B:HIS167 3.1 46.4 1.0 OD2 B:ASP311 3.2 65.5 1.0 CD2 B:HIS206 3.2 52.9 1.0 CG B:ASP207 3.4 75.2 1.0 O3 B:SO41588 3.5 97.1 1.0 O2 B:SO41588 3.8 97.1 1.0 OD1 B:ASP207 3.9 61.9 1.0 O1 B:SO41588 4.1 97.1 1.0 ND1 B:HIS206 4.1 48.4 1.0 NH1 B:ARG164 4.1 36.7 1.0 ND1 B:HIS167 4.2 43.5 1.0 CG B:HIS167 4.2 39.6 1.0 CG B:HIS206 4.3 45.5 1.0 CG2 B:VAL171 4.4 43.4 1.0 CB B:ASP311 4.4 36.3 1.0 CB B:ASP207 4.6 69.7 1.0 CD2 B:TYR315 4.6 41.4 1.0 O B:ASP311 5.0 38.2 1.0 CA B:ASP311 5.0 33.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-626) Bound to Gtp


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 115-626) Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1584 b:36.6 occ:1.00 O1 C:SO41587 1.8 0.0 1.0 NE2 C:HIS206 2.2 28.0 1.0 NE2 C:HIS167 2.2 45.0 1.0 OD1 C:ASP311 2.3 36.1 1.0 OD2 C:ASP207 2.5 65.1 1.0 CG C:ASP311 3.0 39.8 1.0 OD2 C:ASP311 3.0 50.5 1.0 CD2 C:HIS167 3.1 51.3 1.0 CD2 C:HIS206 3.1 33.8 1.0 CE1 C:HIS206 3.2 43.9 1.0 S C:SO41587 3.2 0.0 1.0 CE1 C:HIS167 3.2 43.4 1.0 CG C:ASP207 3.3 58.3 1.0 OD1 C:ASP207 3.5 46.6 1.0 O4 C:SO41587 3.5 0.0 1.0 NH1 C:ARG164 3.9 46.3 1.0 O3 C:SO41587 4.0 0.0 1.0 O2 C:SO41587 4.2 0.0 1.0 ND1 C:HIS206 4.3 52.9 1.0 CG C:HIS206 4.3 41.9 1.0 CG C:HIS167 4.3 50.2 1.0 ND1 C:HIS167 4.3 43.9 1.0 CB C:ASP311 4.4 35.0 1.0 CB C:ASP207 4.6 60.0 1.0 CG2 C:VAL171 4.6 34.9 1.0 CD2 C:TYR315 4.8 28.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human SAMHD1 (Amino Acid Residues 115-626) Bound to Gtp


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 115-626) Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1584 b:30.4 occ:1.00 O3 D:SO41588 1.9 0.8 1.0 NE2 D:HIS206 2.1 33.8 1.0 NE2 D:HIS167 2.2 37.9 1.0 OD1 D:ASP311 2.4 34.1 1.0 OD2 D:ASP207 2.8 68.2 1.0 S D:SO41588 3.0 0.8 1.0 CE1 D:HIS167 3.0 42.7 1.0 CE1 D:HIS206 3.0 45.3 1.0 CG D:ASP311 3.0 40.9 1.0 OD2 D:ASP311 3.1 47.0 1.0 CD2 D:HIS206 3.1 26.7 1.0 O1 D:SO41588 3.2 0.8 1.0 CD2 D:HIS167 3.3 42.7 1.0 O4 D:SO41588 3.4 0.8 1.0 CG D:ASP207 3.5 67.2 1.0 OD1 D:ASP207 3.6 66.3 1.0 NH1 D:ARG164 4.0 43.9 1.0 ND1 D:HIS206 4.1 36.7 1.0 ND1 D:HIS167 4.2 40.5 1.0 CG D:HIS206 4.2 32.9 1.0 O2 D:SO41588 4.2 0.8 1.0 CG D:HIS167 4.3 38.4 1.0 CB D:ASP311 4.5 45.1 1.0 CD2 D:TYR315 4.5 31.4 1.0 CG2 D:VAL171 4.5 35.0 1.0 CB D:ASP207 4.8 66.2 1.0 O D:ASP311 4.9 60.9 1.0 CE2 D:TYR315 5.0 37.3 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