Iron in PDB 8d9j: SAMHD1-Dna Complex

The structure of SAMHD1-Dna Complex, PDB code: 8d9j 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)	39.05 / 2.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.43, 179.678, 79.891, 90, 109, 90
R / Rfree (%)	18.2 / 24.2

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 8d9j). 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: 8d9j:
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:44.8 occ:1.00 OD1 A:ASP311 2.1 51.5 1.0 OD2 A:ASP207 2.2 57.0 1.0 NE2 A:HIS206 2.2 57.4 1.0 NE2 A:HIS167 2.2 51.0 1.0 O A:HOH845 2.5 50.7 1.0 CE1 A:HIS167 2.9 40.4 1.0 CG A:ASP311 3.0 55.3 1.0 O A:HOH827 3.0 46.6 1.0 CG A:ASP207 3.2 54.8 1.0 CE1 A:HIS206 3.2 55.8 1.0 CD2 A:HIS206 3.2 45.3 1.0 OD2 A:ASP311 3.2 53.3 1.0 CD2 A:HIS167 3.3 52.0 1.0 OD1 A:ASP207 3.6 56.6 1.0 NH1 A:ARG164 3.9 50.7 1.0 ND1 A:HIS167 4.1 32.8 1.0 CA A:CA702 4.2 110.8 1.0 CG A:HIS167 4.3 35.0 1.0 ND1 A:HIS206 4.3 44.6 1.0 CG A:HIS206 4.4 45.9 1.0 CB A:ASP311 4.4 49.5 1.0 CB A:ASP207 4.4 47.9 1.0 O A:HOH817 4.5 59.4 1.0 CD2 A:TYR315 4.7 54.6 1.0 O A:ASP311 4.9 44.0 1.0 CG2 A:VAL171 4.9 41.8 1.0 CE2 A:TYR315 5.0 54.0 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:44.2 occ:1.00 OD2 B:ASP207 2.0 44.6 1.0 NE2 B:HIS167 2.1 27.0 1.0 OD1 B:ASP311 2.4 59.7 1.0 NE2 B:HIS206 2.5 44.6 1.0 OD2 B:ASP311 2.6 61.0 1.0 CE1 B:HIS167 2.8 25.9 1.0 CG B:ASP311 2.8 52.3 1.0 CG B:ASP207 3.1 49.2 1.0 CD2 B:HIS167 3.3 38.8 1.0 CD2 B:HIS206 3.3 40.3 1.0 O B:HOH826 3.5 43.2 1.0 CE1 B:HIS206 3.5 40.0 1.0 OD1 B:ASP207 3.5 50.4 1.0 NH1 B:ARG164 3.7 42.5 1.0 ND1 B:HIS167 4.0 17.5 1.0 O B:HOH829 4.0 57.2 1.0 CA B:CA702 4.0 84.8 1.0 CG B:HIS167 4.2 31.0 1.0 CB B:ASP311 4.3 48.2 1.0 CB B:ASP207 4.4 44.0 1.0 CD2 B:TYR315 4.4 45.2 1.0 CG B:HIS206 4.4 38.9 1.0 ND1 B:HIS206 4.5 49.8 1.0 CE2 B:TYR315 4.8 60.4 1.0 O B:HOH809 4.9 63.3 1.0 CG2 B:VAL171 4.9 36.1 1.0 CA B:ASP311 4.9 49.5 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:32.9 occ:1.00 OD1 C:ASP311 2.1 43.6 1.0 NE2 C:HIS167 2.2 23.5 1.0 OD2 C:ASP207 2.3 44.6 1.0 NE2 C:HIS206 2.3 41.0 1.0 CG C:ASP311 3.0 41.2 1.0 CD2 C:HIS206 3.1 35.0 1.0 CD2 C:HIS167 3.1 30.2 1.0 CG C:ASP207 3.2 48.9 1.0 CE1 C:HIS167 3.2 29.4 1.0 OD2 C:ASP311 3.3 59.2 1.0 CE1 C:HIS206 3.3 35.4 1.0 NH1 C:ARG164 3.4 35.8 1.0 OD1 C:ASP207 3.5 41.3 1.0 O C:HOH840 3.6 49.5 1.0 CA C:CA702 3.6 68.1 1.0 O C:HOH830 4.1 57.6 1.0 CB C:ASP311 4.2 49.3 1.0 CG C:HIS206 4.3 41.5 1.0 ND1 C:HIS167 4.3 30.3 1.0 CG C:HIS167 4.3 28.8 1.0 ND1 C:HIS206 4.3 45.5 1.0 CB C:ASP207 4.4 39.7 1.0 CZ C:ARG164 4.7 42.7 1.0 CD2 C:TYR315 4.9 45.3 1.0 CG2 C:VAL171 4.9 34.8 1.0 CA C:ASP311 4.9 48.0 1.0 O C:ASP311 5.0 43.4 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:Fe702 b:45.5 occ:1.00 O D:HOH835 2.1 59.7 1.0 OD2 D:ASP207 2.1 51.4 1.0 OD1 D:ASP311 2.2 51.1 1.0 NE2 D:HIS167 2.2 37.0 1.0 NE2 D:HIS206 2.3 44.2 1.0 O D:HOH828 2.5 50.5 1.0 CD2 D:HIS206 3.1 32.2 1.0 CE1 D:HIS167 3.1 37.5 1.0 CG D:ASP207 3.1 56.3 1.0 CG D:ASP311 3.1 49.6 1.0 CD2 D:HIS167 3.2 43.4 1.0 CE1 D:HIS206 3.4 41.1 1.0 OD1 D:ASP207 3.4 61.6 1.0 OD2 D:ASP311 3.5 48.1 1.0 CA D:CA701 3.8 86.7 1.0 NH1 D:ARG164 3.9 45.1 1.0 O D:HOH836 3.9 63.0 1.0 ND1 D:HIS167 4.2 39.8 1.0 CG D:HIS206 4.3 38.1 1.0 CG D:HIS167 4.3 32.2 1.0 ND1 D:HIS206 4.4 31.0 1.0 CB D:ASP207 4.4 47.4 1.0 CB D:ASP311 4.5 49.3 1.0 CD2 D:TYR315 4.7 63.2 1.0 O D:HOH851 4.7 68.4 1.0 O D:ASP311 4.9 44.7 1.0 CE2 D:TYR315 4.9 65.3 1.0 CG2 D:VAL171 5.0 35.1 1.0

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