Iron in PDB 8gb2: Crystal Structure of Apo-SAMHD1

The structure of Crystal Structure of Apo-SAMHD1, PDB code: 8gb2 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)	27.61 / 3.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.574, 81.884, 154.026, 90, 118.52, 90
R / Rfree (%)	19.7 / 25

The binding sites of Iron atom in the Crystal Structure of Apo-SAMHD1 (pdb code 8gb2). 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 Apo-SAMHD1, PDB code: 8gb2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:201.6 occ:1.00 OD2 D:ASP311 1.9 89.1 1.0 HE1 D:HIS206 2.0 101.1 1.0 NE2 D:HIS167 2.3 76.1 1.0 CE1 D:HIS206 2.4 84.1 1.0 HD2 D:HIS167 2.5 95.0 1.0 CD2 D:HIS167 2.7 79.0 1.0 OD1 D:ASP311 2.7 88.6 1.0 HD1 D:HIS206 2.8 100.1 1.0 CG D:ASP311 2.8 88.6 1.0 OD2 D:ASP207 2.8 81.6 1.0 ND1 D:HIS206 2.8 83.2 1.0 OD1 D:ASP207 2.9 82.0 1.0 CG D:ASP207 3.1 79.5 1.0 NE2 D:HIS206 3.5 94.0 1.0 CE1 D:HIS167 3.5 76.6 1.0 HH12 D:ARG164 3.8 86.7 1.0 HG21 D:VAL171 3.9 88.8 1.0 CG D:HIS206 4.0 79.1 1.0 HE1 D:HIS167 4.0 92.1 1.0 CG D:HIS167 4.0 73.0 1.0 HD2 D:TYR315 4.0 87.1 1.0 HH11 D:ARG164 4.2 86.7 1.0 NH1 D:ARG164 4.3 72.1 1.0 CD2 D:HIS206 4.3 81.2 1.0 CB D:ASP311 4.3 98.2 1.0 HB2 D:ASP207 4.4 91.1 1.0 ND1 D:HIS167 4.4 72.0 1.0 CB D:ASP207 4.4 75.7 1.0 HB3 D:TYR315 4.5 82.9 1.0 HB2 D:ASP311 4.5 118.1 1.0 CG2 D:VAL171 4.7 73.9 1.0 HG23 D:VAL171 4.7 88.8 1.0 HD3 D:ARG164 4.8 83.8 1.0 HB3 D:ASP311 4.8 118.1 1.0 HA D:ASP311 4.8 99.0 1.0 CD2 D:TYR315 4.8 72.4 1.0 HB2 D:HIS206 4.9 93.7 1.0 HE22 D:GLN149 5.0 84.9 1.0 HB3 D:ASP207 5.0 91.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:76.9 occ:1.00 OD1 A:ASP311 1.9 74.0 1.0 HE1 A:HIS167 1.9 96.3 1.0 NE2 A:HIS206 2.1 93.0 1.0 CE1 A:HIS167 2.2 80.1 1.0 HE2 A:HIS167 2.6 88.5 1.0 NE2 A:HIS167 2.6 73.6 1.0 HD2 A:HIS206 2.6 99.0 1.0 CG A:ASP311 2.6 75.0 1.0 CD2 A:HIS206 2.7 82.4 1.0 OD2 A:ASP311 2.7 75.2 1.0 OD2 A:ASP207 2.8 85.4 1.0 ND1 A:HIS167 3.2 66.5 1.0 CE1 A:HIS206 3.3 123.0 1.0 HH11 A:ARG164 3.4 75.1 1.0 CG A:ASP207 3.6 83.2 1.0 CD2 A:HIS167 3.7 62.2 1.0 HE1 A:HIS206 3.7 147.8 1.0 HH12 A:ARG164 3.7 75.1 1.0 HD2 A:TYR315 3.8 79.6 1.0 HG21 A:VAL171 3.9 74.0 1.0 OD1 A:ASP207 3.9 78.5 1.0 NH1 A:ARG164 3.9 62.4 1.0 CG A:HIS206 3.9 82.5 1.0 CG A:HIS167 4.0 61.4 1.0 CB A:ASP311 4.1 73.2 1.0 ND1 A:HIS206 4.2 111.0 1.0 HB3 A:TYR315 4.3 74.5 1.0 HD2 A:HIS167 4.4 74.8 1.0 HB2 A:ASP311 4.4 88.0 1.0 HG23 A:VAL171 4.5 74.0 1.0 HB2 A:ASP207 4.5 95.2 1.0 HA A:ASP311 4.5 82.4 1.0 CD2 A:TYR315 4.5 66.2 1.0 CG2 A:VAL171 4.6 61.5 1.0 O A:ASP311 4.7 65.9 1.0 HB3 A:ASP311 4.7 88.0 1.0 CB A:ASP207 4.7 79.1 1.0 CA A:ASP311 4.8 68.5 1.0 HE1 A:HIS210 4.9 76.1 1.0 HD3 A:ARG164 4.9 73.7 1.0 HE22 A:GLN149 5.0 69.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:111.8 occ:1.00 HE2 B:HIS167 1.5 132.2 1.0 OD1 B:ASP311 1.8 110.6 1.0 NE2 B:HIS167 2.1 110.0 1.0 NE2 B:HIS206 2.5 123.9 1.0 HD2 B:HIS167 2.6 125.9 1.0 HD2 B:HIS206 2.6 138.2 1.0 CD2 B:HIS167 2.6 104.7 1.0 OD2 B:ASP207 2.7 126.8 1.0 CD2 B:HIS206 2.7 115.0 1.0 CG B:ASP311 2.9 108.2 1.0 HH12 B:ARG164 3.1 135.4 1.0 CE1 B:HIS167 3.3 105.8 1.0 OD2 B:ASP311 3.3 110.3 1.0 HH11 B:ARG164 3.5 135.4 1.0 CE1 B:HIS206 3.6 137.6 1.0 CG B:ASP207 3.6 130.0 1.0 NH1 B:ARG164 3.7 112.7 1.0 HE1 B:HIS167 3.7 127.2 1.0 CG B:HIS167 3.9 102.2 1.0 CG B:HIS206 3.9 116.0 1.0 OD1 B:ASP207 4.0 124.2 1.0 HE1 B:HIS206 4.1 165.3 1.0 ND1 B:HIS167 4.1 100.0 1.0 CB B:ASP311 4.1 105.5 1.0 HB2 B:ASP311 4.2 126.8 1.0 HD2 B:TYR315 4.2 137.7 1.0 HG21 B:VAL171 4.2 115.7 1.0 ND1 B:HIS206 4.3 129.9 1.0 HG22 B:VAL171 4.3 115.7 1.0 HE22 B:GLN149 4.4 131.5 1.0 HB3 B:TYR315 4.4 132.0 1.0 HB2 B:ASP207 4.5 142.5 1.0 HA B:ASP311 4.6 126.3 1.0 HD3 B:ARG164 4.6 135.3 1.0 CB B:ASP207 4.7 118.6 1.0 CG2 B:VAL171 4.8 96.2 1.0 HB3 B:HIS206 4.8 134.8 1.0 HB3 B:ASP311 4.8 126.8 1.0 CA B:ASP311 4.9 105.1 1.0 CZ B:ARG164 4.9 115.7 1.0 CD2 B:TYR315 5.0 114.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe701 b:163.1 occ:1.00 HE1 C:HIS167 1.9 172.7 1.0 OD1 C:ASP311 1.9 153.1 1.0 OD2 C:ASP311 2.1 154.6 1.0 CG C:ASP311 2.3 151.6 1.0 ND1 C:HIS206 2.4 173.0 1.0 CE1 C:HIS167 2.6 143.8 1.0 HB2 C:HIS206 2.8 213.3 1.0 OD2 C:ASP207 2.8 227.8 1.0 HD1 C:HIS167 2.9 175.0 1.0 ND1 C:HIS167 3.1 145.7 1.0 HH11 C:ARG164 3.3 190.0 1.0 CG C:HIS206 3.3 178.7 1.0 HH12 C:ARG164 3.4 190.0 1.0 CE1 C:HIS206 3.4 171.1 1.0 CB C:HIS206 3.5 177.6 1.0 HE1 C:HIS206 3.6 205.6 1.0 NH1 C:ARG164 3.7 158.2 1.0 CG C:ASP207 3.7 230.9 1.0 NE2 C:HIS167 3.8 140.2 1.0 HG21 C:VAL171 3.9 186.5 1.0 CB C:ASP311 3.9 147.4 1.0 HB3 C:HIS206 3.9 213.3 1.0 OD1 C:ASP207 4.2 235.9 1.0 HA C:ASP311 4.2 174.0 1.0 HB2 C:ASP311 4.3 177.1 1.0 HG23 C:VAL171 4.3 186.5 1.0 HB3 C:ASP311 4.3 177.1 1.0 CG C:HIS167 4.4 142.9 1.0 HB2 C:TYR315 4.4 171.6 1.0 CD2 C:HIS206 4.5 179.9 1.0 NE2 C:HIS206 4.5 175.1 1.0 CG2 C:VAL171 4.5 155.2 1.0 CA C:ASP311 4.6 144.8 1.0 CD2 C:HIS167 4.7 139.9 1.0 CA C:HIS206 4.7 179.3 1.0 HB2 C:ASP207 4.7 272.1 1.0 C C:HIS206 4.7 188.8 1.0 HG11 C:VAL171 4.8 202.2 1.0 CB C:ASP207 4.9 226.6 1.0 CZ C:ARG164 4.9 145.0 1.0 N C:ASP207 5.0 232.9 1.0 HD3 C:ARG164 5.0 176.9 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