Calcium 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:

Iron

(Fe)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:63.4 occ:1.00 O A:HOH824 2.4 33.2 1.0 O A:HOH835 2.5 35.1 1.0 NE2 A:HIS233 2.6 40.4 1.0 OD1 A:ASP207 2.7 31.5 1.0 CE1 A:HIS233 3.5 31.8 1.0 CD2 A:HIS233 3.7 26.6 1.0 CG A:ASP207 3.7 34.1 1.0 FE A:FE701 3.8 33.0 1.0 OD2 A:ASP311 3.8 51.3 1.0 CD2 A:HIS206 3.9 27.8 1.0 OD2 A:ASP207 4.1 27.8 1.0 NE2 A:HIS210 4.3 37.0 1.0 OE2 A:GLU234 4.4 52.7 1.0 O A:HOH864 4.4 34.4 1.0 NE2 A:HIS206 4.4 25.3 1.0 O A:HOH833 4.5 35.1 1.0 CG A:GLU234 4.7 37.4 1.0 ND1 A:HIS233 4.7 48.0 1.0 CD A:GLU234 4.7 44.1 1.0 O A:HIS206 4.8 31.3 1.0 CG A:HIS233 4.8 37.2 1.0 CG A:ASP311 5.0 19.9 1.0 CD2 A:HIS210 5.0 34.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:69.7 occ:1.00 O B:HOH846 2.5 34.5 1.0 NE2 B:HIS233 2.8 39.5 1.0 OD1 B:ASP207 3.2 34.6 1.0 CE1 B:HIS233 3.6 26.5 1.0 FE B:FE701 3.7 42.6 1.0 CD2 B:HIS233 3.8 35.5 1.0 CG B:ASP207 4.3 26.8 1.0 CD2 B:HIS206 4.3 27.3 1.0 OE2 B:GLU234 4.4 54.8 1.0 CG B:GLU234 4.5 28.4 1.0 O B:HOH861 4.5 36.2 1.0 OD2 B:ASP311 4.5 38.8 1.0 CD B:GLU234 4.6 49.2 1.0 OD2 B:ASP207 4.6 38.7 1.0 NE2 B:HIS210 4.7 28.5 1.0 NE2 B:HIS206 4.8 45.2 1.0 ND1 B:HIS233 4.8 39.3 1.0 CG B:HIS233 4.9 37.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:56.0 occ:1.00 O C:HOH868 2.4 45.1 1.0 O C:HOH808 2.5 40.2 1.0 OD1 C:ASP207 2.6 29.2 1.0 NE2 C:HIS233 2.9 41.3 1.0 FE C:FE701 3.2 42.4 1.0 CD2 C:HIS233 3.6 27.9 1.0 CD2 C:HIS206 3.6 34.1 1.0 CG C:ASP207 3.7 35.2 1.0 CE1 C:HIS233 4.0 34.8 1.0 NE2 C:HIS206 4.1 46.3 1.0 OD2 C:ASP311 4.1 37.0 1.0 OD2 C:ASP207 4.1 47.5 1.0 NE2 C:HIS210 4.1 30.3 1.0 O C:HOH901 4.3 46.1 1.0 O C:HIS206 4.5 24.5 1.0 OE2 C:GLU234 4.7 56.9 1.0 CG C:HIS206 4.8 33.4 1.0 CG C:ASP311 4.8 42.3 1.0 CG C:HIS233 4.9 30.6 1.0 CD2 C:HIS210 4.9 29.9 1.0 OD1 C:ASP311 4.9 43.9 1.0 CB C:ASP207 4.9 39.6 1.0 CG C:GLU234 4.9 35.4 1.0 CA C:ASP207 5.0 37.5 1.0 ND1 C:HIS233 5.0 28.9 1.0 CD C:GLU234 5.0 41.0 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of SAMHD1-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca702 b:80.2 occ:1.00 O D:HOH826 2.3 43.5 1.0 O D:HOH841 2.5 50.2 1.0 NE2 D:HIS233 2.9 51.9 1.0 OD1 D:ASP207 3.2 35.4 1.0 CE1 D:HIS233 3.7 45.1 1.0 OD2 D:ASP311 3.9 44.6 1.0 FE D:FE701 4.0 35.7 1.0 CD2 D:HIS233 4.0 45.3 1.0 CG D:ASP207 4.2 33.7 1.0 CD2 D:HIS206 4.2 31.3 1.0 OE2 D:GLU234 4.3 38.6 1.0 OD2 D:ASP207 4.5 34.2 1.0 NE2 D:HIS210 4.5 38.1 1.0 NE2 D:HIS206 4.7 28.0 1.0 O D:HOH811 4.7 41.1 1.0 CG D:ASP311 4.8 44.9 1.0 CD D:GLU234 4.9 45.5 1.0 ND1 D:HIS233 4.9 49.3 1.0 CG D:GLU234 4.9 45.3 1.0 OD1 D:ASP311 5.0 43.1 1.0 CE1 D:HIS215 5.0 42.8 1.0

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