Iron in PDB 8d94: SAMHD1-Dna Complex

The structure of SAMHD1-Dna Complex, PDB code: 8d94 was solved by T.J.Hollis, S.M.Batalis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.98 / 2.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.116, 179.936, 79.792, 90, 108.95, 90
R / Rfree (%)	19 / 24.3

The structure of SAMHD1-Dna Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Iron atom in the SAMHD1-Dna Complex (pdb code 8d94). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the SAMHD1-Dna Complex, PDB code: 8d94:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the SAMHD1-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:33.0 occ:1.00 NE2 A:HIS167 2.1 24.2 1.0 NE2 A:HIS206 2.3 25.3 1.0 OD2 A:ASP207 2.4 27.8 1.0 O A:HOH833 2.6 35.1 1.0 OD1 A:ASP311 2.6 45.2 1.0 OD2 A:ASP311 2.7 51.3 1.0 CE1 A:HIS167 2.8 32.2 1.0 CG A:ASP311 3.0 19.9 1.0 CG A:ASP207 3.1 34.1 1.0 CD2 A:HIS206 3.1 27.8 1.0 CD2 A:HIS167 3.3 46.4 1.0 CE1 A:HIS206 3.3 30.0 1.0 OD1 A:ASP207 3.4 31.5 1.0 NH1 A:ARG164 3.7 29.5 1.0 O A:HOH824 3.8 33.2 1.0 CA A:CA702 3.8 63.4 1.0 ND1 A:HIS167 4.0 27.4 1.0 CG A:HIS167 4.2 27.1 1.0 CB A:ASP207 4.3 22.2 1.0 CD2 A:TYR315 4.3 44.7 1.0 CG A:HIS206 4.3 33.6 1.0 ND1 A:HIS206 4.4 38.3 1.0 CB A:ASP311 4.4 35.8 1.0 CE2 A:TYR315 4.5 48.3 1.0 CG2 A:VAL171 4.8 22.4 1.0 O A:HOH835 5.0 35.1 1.0

Iron binding site 2 out of 4 in the SAMHD1-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:42.6 occ:1.00 OD1 B:ASP311 2.6 49.1 1.0 OD2 B:ASP207 2.6 38.7 1.0 O B:HOH861 2.7 36.2 1.0 NE2 B:HIS206 2.7 45.2 1.0 NE2 B:HIS167 2.7 32.1 1.0 OD2 B:ASP311 3.2 38.8 1.0 CG B:ASP311 3.2 32.1 1.0 CG B:ASP207 3.3 26.8 1.0 O B:HOH846 3.3 34.5 1.0 OD1 B:ASP207 3.3 34.6 1.0 CD2 B:HIS206 3.5 27.3 1.0 CE1 B:HIS167 3.5 47.5 1.0 CD2 B:HIS167 3.6 37.0 1.0 NH1 B:ARG164 3.7 28.4 1.0 CE1 B:HIS206 3.7 39.2 1.0 CA B:CA702 3.7 69.7 1.0 ND1 B:HIS167 4.6 34.9 1.0 CB B:ASP207 4.6 31.0 1.0 CB B:ASP311 4.7 40.4 1.0 CD2 B:TYR315 4.7 43.6 1.0 CG B:HIS206 4.7 37.2 1.0 CG B:HIS167 4.7 32.1 1.0 ND1 B:HIS206 4.7 36.1 1.0 O B:HOH865 4.7 53.8 1.0 CZ B:ARG164 4.9 31.2 1.0

Iron binding site 3 out of 4 in the SAMHD1-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe701 b:42.4 occ:1.00 OD1 C:ASP311 2.6 43.9 1.0 OD2 C:ASP207 2.6 47.5 1.0 O C:HOH901 2.7 46.1 1.0 NE2 C:HIS206 2.7 46.3 1.0 NE2 C:HIS167 2.8 31.5 1.0 O C:HOH868 3.1 45.1 1.0 CA C:CA702 3.2 56.0 1.0 OD2 C:ASP311 3.2 37.0 1.0 CG C:ASP311 3.2 42.3 1.0 OD1 C:ASP207 3.2 29.2 1.0 CG C:ASP207 3.2 35.2 1.0 CD2 C:HIS206 3.4 34.1 1.0 CE1 C:HIS167 3.6 29.6 1.0 NH1 C:ARG164 3.6 30.5 1.0 CE1 C:HIS206 3.8 37.8 1.0 CD2 C:HIS167 3.8 26.6 1.0 CD2 C:TYR315 4.4 46.6 1.0 CE2 C:TYR315 4.4 47.6 1.0 CB C:ASP207 4.7 39.6 1.0 CB C:ASP311 4.7 47.1 1.0 CG C:HIS206 4.7 33.4 1.0 ND1 C:HIS167 4.8 23.0 1.0 ND1 C:HIS206 4.8 39.9 1.0 O C:HOH808 4.9 40.2 1.0 CG C:HIS167 4.9 23.1 1.0 CZ C:ARG164 4.9 39.0 1.0

Iron binding site 4 out of 4 in the SAMHD1-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:35.7 occ:1.00 OD1 D:ASP311 2.2 43.1 1.0 NE2 D:HIS167 2.3 27.9 1.0 OD2 D:ASP207 2.4 34.2 1.0 NE2 D:HIS206 2.4 28.0 1.0 O D:HOH811 2.9 41.1 1.0 CG D:ASP311 3.1 44.9 1.0 CG D:ASP207 3.1 33.7 1.0 CD2 D:HIS167 3.2 27.4 1.0 CE1 D:HIS167 3.3 33.2 1.0 CD2 D:HIS206 3.3 31.3 1.0 CE1 D:HIS206 3.3 34.4 1.0 OD2 D:ASP311 3.4 44.6 1.0 OD1 D:ASP207 3.4 35.4 1.0 NH1 D:ARG164 3.6 35.9 1.0 CA D:CA702 4.0 80.2 1.0 O D:HOH826 4.1 43.5 1.0 CG D:HIS167 4.3 30.1 1.0 ND1 D:HIS167 4.4 19.9 1.0 CB D:ASP207 4.4 28.5 1.0 ND1 D:HIS206 4.4 46.7 1.0 CG D:HIS206 4.4 33.8 1.0 CD2 D:TYR315 4.4 39.8 1.0 CB D:ASP311 4.4 30.4 1.0 CG2 D:VAL171 4.7 26.1 1.0 CE2 D:TYR315 4.8 35.2 1.0 O D:ASP311 4.9 30.5 1.0 CZ D:ARG164 4.9 37.0 1.0 O D:HOH841 5.0 50.2 1.0

T.J.Hollis, S.M.Batalis. SAMHD1-Dna Complex To Be Published.