Calcium 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:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the SAMHD1-Dna Complex (pdb code 8d9j). 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: 8d9j:
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:110.8 occ:1.00 O A:HOH827 2.6 46.6 1.0 NE2 A:HIS233 3.2 54.1 1.0 OD1 A:ASP207 3.7 56.6 1.0 OD2 A:ASP311 3.9 53.3 1.0 CD2 A:HIS206 4.0 45.3 1.0 CE1 A:HIS233 4.0 57.9 1.0 FE A:FE701 4.2 44.8 1.0 CD2 A:HIS233 4.2 48.8 1.0 OE2 A:GLU234 4.4 75.7 1.0 CG A:GLU234 4.5 61.3 1.0 CG A:ASP311 4.6 55.3 1.0 NE2 A:HIS206 4.6 57.4 1.0 O A:HOH845 4.6 50.7 1.0 CG A:ASP207 4.6 54.8 1.0 OD1 A:ASP311 4.7 51.5 1.0 CD A:GLU234 4.8 71.9 1.0 OD2 A:ASP207 4.8 57.0 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:84.8 occ:1.00 O B:HOH826 2.7 43.2 1.0 O B:HOH809 2.8 63.3 1.0 NE2 B:HIS233 2.8 55.7 1.0 OD1 B:ASP207 3.1 50.4 1.0 CE1 B:HIS233 3.6 57.1 1.0 OD2 B:ASP311 3.7 61.0 1.0 CD2 B:HIS233 3.9 54.8 1.0 OE2 B:GLU234 4.0 59.3 1.0 FE B:FE701 4.0 44.2 1.0 CG B:ASP207 4.1 49.2 1.0 OD2 B:ASP207 4.3 44.6 1.0 CD2 B:HIS206 4.5 40.3 1.0 O B:HOH824 4.5 50.2 1.0 NE2 B:HIS210 4.6 52.0 1.0 CG B:GLU234 4.6 53.5 1.0 CD B:GLU234 4.6 63.0 1.0 CG B:ASP311 4.8 52.3 1.0 ND1 B:HIS233 4.8 52.6 1.0 CE1 B:HIS215 5.0 57.2 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:68.1 occ:1.00 O C:HOH830 2.4 57.6 1.0 OD1 C:ASP207 2.5 41.3 1.0 O C:HOH853 2.6 64.8 1.0 NE2 C:HIS233 2.9 54.1 1.0 CG C:ASP207 3.5 48.9 1.0 FE C:FE701 3.6 32.9 1.0 CD2 C:HIS206 3.6 35.0 1.0 CD2 C:HIS233 3.8 50.0 1.0 CE1 C:HIS233 3.8 52.3 1.0 OD2 C:ASP207 3.9 44.6 1.0 OD2 C:ASP311 4.1 59.2 1.0 O C:HIS206 4.2 45.6 1.0 NE2 C:HIS206 4.2 41.0 1.0 NE2 C:HIS210 4.4 40.5 1.0 CG C:HIS206 4.6 41.5 1.0 CG C:ASP311 4.6 41.2 1.0 OD1 C:ASP311 4.7 43.6 1.0 CB C:ASP207 4.8 39.7 1.0 C C:HIS206 4.8 37.0 1.0 CA C:ASP207 4.9 45.1 1.0 CG C:HIS233 5.0 51.3 1.0 O C:HOH822 5.0 67.4 1.0 ND1 C:HIS233 5.0 54.5 1.0 CG C:GLU234 5.0 51.0 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:Ca701 b:86.7 occ:1.00 OD1 D:ASP207 2.3 61.6 1.0 O D:HOH851 2.4 68.4 1.0 NE2 D:HIS233 2.4 50.1 1.0 O D:HOH828 2.5 50.5 1.0 O D:HOH836 2.5 63.0 1.0 CD2 D:HIS233 3.0 40.4 1.0 CG D:ASP207 3.4 56.3 1.0 CE1 D:HIS233 3.6 45.2 1.0 NE2 D:HIS210 3.8 41.7 1.0 FE D:FE702 3.8 45.5 1.0 OD2 D:ASP207 3.8 51.4 1.0 CD2 D:HIS206 4.1 32.2 1.0 O D:HIS206 4.1 38.0 1.0 CG D:HIS233 4.3 47.2 1.0 CD2 D:HIS210 4.4 49.1 1.0 ND1 D:HIS233 4.5 47.8 1.0 NE2 D:HIS206 4.6 44.2 1.0 O D:HOH835 4.6 59.7 1.0 CB D:ASP207 4.6 47.4 1.0 CE1 D:HIS210 4.6 45.3 1.0 CA D:ASP207 4.7 43.4 1.0 OE2 D:GLU234 4.8 68.5 1.0 CG D:GLU234 4.8 56.5 1.0 C D:HIS206 4.9 40.1 1.0 CD D:GLU234 5.0 63.7 1.0

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