Iron in PDB 8gb1: Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor

The structure of Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor, PDB code: 8gb1 was solved by M.Egleston, L.Dong, A.H.Howlader, S.Bhat, B.Orris, M.A.Bianchet, M.M.Greenberg, J.T.Stivers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.17 / 2.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.783, 144.04, 200.318, 90, 90, 90
R / Rfree (%)	19.2 / 23.6

The structure of Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Iron atom in the Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor (pdb code 8gb1). 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 SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor, PDB code: 8gb1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor


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 SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:86.4 occ:1.00 NE2 A:HIS167 1.9 54.5 1.0 OD1 A:ASP311 2.0 67.8 1.0 NE2 A:HIS206 2.1 64.6 1.0 O A:HOH881 2.2 50.9 1.0 OD2 A:ASP207 2.5 53.2 1.0 CE1 A:HIS206 2.9 46.5 1.0 CE1 A:HIS167 2.9 51.7 1.0 CG A:ASP311 2.9 54.2 1.0 HE1 A:HIS206 3.0 55.8 1.0 CD2 A:HIS167 3.0 45.0 1.0 HE1 A:HIS167 3.1 62.1 1.0 HD2 A:HIS167 3.2 54.1 1.0 CD2 A:HIS206 3.2 62.3 1.0 OD2 A:ASP311 3.3 48.7 1.0 CG A:ASP207 3.3 44.5 1.0 HD2 A:HIS206 3.5 74.8 1.0 HG21 A:VAL171 3.6 52.3 1.0 HH11 A:ARG164 3.6 48.2 1.0 OD1 A:ASP207 3.6 48.7 1.0 HD2 A:TYR315 3.7 53.8 1.0 HH12 A:ARG164 3.7 48.2 1.0 NH1 A:ARG164 4.0 40.1 1.0 ND1 A:HIS167 4.0 42.2 1.0 O A:HOH922 4.1 51.0 1.0 HE22 A:GLN149 4.1 49.2 1.0 ND1 A:HIS206 4.1 51.8 1.0 CG A:HIS167 4.1 40.3 1.0 CG A:HIS206 4.3 54.1 1.0 CB A:ASP311 4.3 52.8 1.0 CG2 A:VAL171 4.4 43.6 1.0 HB2 A:ASP207 4.4 55.0 1.0 HB2 A:ASP311 4.5 63.4 1.0 CD2 A:TYR315 4.5 44.8 1.0 HG23 A:VAL171 4.5 52.3 1.0 HB3 A:TYR315 4.5 54.1 1.0 CB A:ASP207 4.5 45.8 1.0 HA A:ASP311 4.5 62.4 1.0 O A:HOH952 4.7 53.1 1.0 HD1 A:HIS167 4.8 50.7 1.0 HD1 A:HIS206 4.8 62.2 1.0 HE2 A:TYR315 4.8 50.1 1.0 HG22 A:VAL171 4.9 52.3 1.0 NE2 A:GLN149 4.9 41.0 1.0 O A:ASP311 4.9 43.4 1.0 CA A:ASP311 4.9 52.0 1.0 HG11 A:VAL171 4.9 42.6 1.0 HB3 A:ASP311 5.0 63.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor


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 SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:58.4 occ:1.00 O B:HOH891 1.9 55.5 1.0 NE2 B:HIS206 2.0 54.6 1.0 OD1 B:ASP311 2.0 53.4 1.0 NE2 B:HIS167 2.0 50.8 1.0 OD2 B:ASP207 2.4 52.2 1.0 CG B:ASP311 2.9 47.2 1.0 CE1 B:HIS206 2.9 52.9 1.0 CE1 B:HIS167 3.0 41.2 1.0 CD2 B:HIS206 3.0 56.6 1.0 CD2 B:HIS167 3.0 47.3 1.0 HE1 B:HIS206 3.1 63.5 1.0 HE1 B:HIS167 3.1 49.5 1.0 HD2 B:HIS206 3.2 68.0 1.0 CG B:ASP207 3.2 47.5 1.0 OD2 B:ASP311 3.2 57.2 1.0 HD2 B:HIS167 3.2 56.8 1.0 HH11 B:ARG164 3.4 54.3 1.0 OD1 B:ASP207 3.4 52.5 1.0 HH12 B:ARG164 3.5 54.3 1.0 HG21 B:VAL171 3.8 57.4 1.0 NH1 B:ARG164 3.8 45.3 1.0 HD2 B:TYR315 3.8 59.9 1.0 ND1 B:HIS206 4.0 55.6 1.0 ND1 B:HIS167 4.1 41.5 1.0 CG B:HIS206 4.1 51.6 1.0 CG B:HIS167 4.2 39.2 1.0 HE22 B:GLN149 4.2 48.2 1.0 CB B:ASP311 4.2 51.6 1.0 HB2 B:ASP311 4.4 61.9 1.0 HB2 B:ASP207 4.5 56.6 1.0 HG23 B:VAL171 4.5 57.4 1.0 CB B:ASP207 4.5 47.1 1.0 CG2 B:VAL171 4.6 47.8 1.0 HA B:ASP311 4.6 59.0 1.0 CD2 B:TYR315 4.6 49.9 1.0 HB3 B:TYR315 4.6 49.0 1.0 O B:HOH949 4.7 43.8 1.0 HD1 B:HIS206 4.8 66.8 1.0 HD1 B:HIS167 4.9 49.8 1.0 CA B:ASP311 4.9 49.1 1.0 HB3 B:ASP311 4.9 61.9 1.0 HD3 B:ARG164 5.0 42.1 1.0 HE2 B:TYR315 5.0 63.3 1.0 HG11 B:VAL171 5.0 52.4 1.0 O B:ASP311 5.0 48.0 1.0 NE2 B:GLN149 5.0 40.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor


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 SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe702 b:64.1 occ:1.00 NE2 C:HIS206 2.0 71.5 1.0 NE2 C:HIS167 2.1 58.8 1.0 OD1 C:ASP311 2.1 81.5 1.0 O C:HOH831 2.1 60.1 1.0 OD2 C:ASP207 2.9 59.5 1.0 CE1 C:HIS206 2.9 65.0 1.0 CG C:ASP311 2.9 75.2 1.0 HE1 C:HIS206 3.0 78.0 1.0 CE1 C:HIS167 3.1 54.0 1.0 CD2 C:HIS206 3.1 78.0 1.0 OD2 C:ASP311 3.1 67.8 1.0 CD2 C:HIS167 3.1 64.4 1.0 HE1 C:HIS167 3.2 64.8 1.0 OD1 C:ASP207 3.3 48.5 1.0 CG C:ASP207 3.3 44.3 1.0 HD2 C:HIS206 3.3 93.6 1.0 HD2 C:HIS167 3.3 77.2 1.0 HH11 C:ARG164 3.5 62.4 1.0 HG21 C:VAL171 3.6 78.3 1.0 HH12 C:ARG164 3.6 62.4 1.0 HD2 C:TYR315 3.9 61.4 1.0 NH1 C:ARG164 3.9 52.0 1.0 ND1 C:HIS206 4.0 63.0 1.0 CG C:HIS206 4.1 64.9 1.0 O C:HOH894 4.2 68.7 1.0 ND1 C:HIS167 4.2 53.1 1.0 HE22 C:GLN149 4.2 55.7 1.0 CG C:HIS167 4.2 49.5 1.0 CB C:ASP311 4.3 68.8 1.0 HB2 C:ASP207 4.4 69.0 1.0 HB2 C:ASP311 4.5 82.5 1.0 CG2 C:VAL171 4.5 65.3 1.0 CB C:ASP207 4.5 57.5 1.0 HG23 C:VAL171 4.6 78.3 1.0 CD2 C:TYR315 4.6 51.2 1.0 HB3 C:TYR315 4.6 54.8 1.0 HA C:ASP311 4.7 82.1 1.0 HD1 C:HIS206 4.8 75.6 1.0 HG11 C:VAL171 4.9 72.5 1.0 HB3 C:ASP311 4.9 82.5 1.0 HG22 C:VAL171 4.9 78.3 1.0 HD1 C:HIS167 5.0 63.8 1.0 CA C:ASP311 5.0 68.4 1.0 HE2 C:TYR315 5.0 61.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor


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 SAMHD1 Dimer Bound to Deoxyguanosine Linked Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe702 b:60.6 occ:1.00 OD1 D:ASP311 2.0 59.2 1.0 NE2 D:HIS206 2.0 57.0 1.0 NE2 D:HIS167 2.1 53.3 1.0 OD2 D:ASP207 2.4 55.2 1.0 CG D:ASP311 2.7 53.4 1.0 OD2 D:ASP311 2.9 52.5 1.0 CE1 D:HIS206 2.9 58.1 1.0 HE1 D:HIS206 3.0 69.7 1.0 CE1 D:HIS167 3.1 53.5 1.0 CD2 D:HIS206 3.1 55.8 1.0 CD2 D:HIS167 3.2 54.1 1.0 CG D:ASP207 3.2 49.9 1.0 HE1 D:HIS167 3.2 64.2 1.0 HD2 D:HIS167 3.4 64.9 1.0 HD2 D:HIS206 3.4 67.0 1.0 HH11 D:ARG164 3.4 60.4 1.0 HH12 D:ARG164 3.4 60.4 1.0 OD1 D:ASP207 3.5 46.7 1.0 HD2 D:TYR315 3.7 67.2 1.0 NH1 D:ARG164 3.7 50.3 1.0 HG21 D:VAL171 3.8 53.4 1.0 ND1 D:HIS206 4.0 51.3 1.0 HE22 D:GLN149 4.1 55.8 1.0 CB D:ASP311 4.2 47.5 1.0 CG D:HIS206 4.2 53.4 1.0 ND1 D:HIS167 4.2 49.9 1.0 CG D:HIS167 4.3 48.6 1.0 O D:HOH906 4.3 56.9 1.0 HB2 D:ASP311 4.4 57.1 1.0 HB2 D:ASP207 4.5 67.8 1.0 CB D:ASP207 4.5 56.5 1.0 HA D:ASP311 4.5 72.9 1.0 CD2 D:TYR315 4.6 56.0 1.0 HG23 D:VAL171 4.6 53.4 1.0 CG2 D:VAL171 4.6 44.5 1.0 HE1 D:HIS210 4.6 59.1 1.0 HE2 D:TYR315 4.7 60.9 1.0 HB3 D:ASP311 4.8 57.1 1.0 HB3 D:TYR315 4.8 54.7 1.0 HD1 D:HIS206 4.8 61.5 1.0 CA D:ASP311 4.8 60.7 1.0 HD3 D:ARG164 4.9 54.2 1.0 NE2 D:GLN149 4.9 46.5 1.0 HD1 D:HIS167 5.0 59.9 1.0

M.Egleston, L.Dong, A.H.Howlader, S.Bhat, B.Orris, M.A.Bianchet, M.M.Greenberg, J.T.Stivers. Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 Dntpase Activity and Nucleic Acid Binding. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37233733
DOI: 10.1021/ACSCHEMBIO.3C00118