Iron in PDB 8qxj: Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp

The structure of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

The binding sites of Iron atom in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp (pdb code 8qxj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp, PDB code: 8qxj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:11.7 occ:1.00 O1A A:DZ4701 1.9 2.9 1.0 OD1 A:ASP311 2.0 1.9 1.0 NE2 A:HIS206 2.0 4.9 1.0 NE2 A:HIS167 2.3 7.5 1.0 OD2 A:ASP207 2.4 5.7 1.0 CD2 A:HIS206 3.0 4.9 1.0 CG A:ASP311 3.0 1.9 1.0 CE1 A:HIS206 3.1 4.9 1.0 CG A:ASP207 3.2 5.7 1.0 CD2 A:HIS167 3.3 7.5 1.0 CE1 A:HIS167 3.3 7.5 1.0 PA A:DZ4701 3.3 2.9 1.0 OD2 A:ASP311 3.4 1.9 1.0 OD1 A:ASP207 3.6 5.7 1.0 O2A A:DZ4701 3.9 2.9 1.0 MG A:MG703 4.0 7.2 1.0 N3A A:DZ4701 4.1 2.9 1.0 CG A:HIS206 4.1 4.9 1.0 NH2 A:ARG164 4.1 3.3 1.0 ND1 A:HIS206 4.1 4.9 1.0 CB A:ASP311 4.3 1.9 1.0 CB A:ASP207 4.4 5.7 1.0 CG A:HIS167 4.4 7.5 1.0 ND1 A:HIS167 4.4 7.5 1.0 O5' A:DZ4701 4.5 2.9 1.0 CG2 A:VAL171 4.7 3.9 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:8.8 occ:1.00 O1A B:DZ4702 1.9 3.3 1.0 OD1 B:ASP311 2.0 2.1 1.0 NE2 B:HIS206 2.1 3.1 1.0 NE2 B:HIS167 2.3 3.1 1.0 OD2 B:ASP207 2.7 4.0 1.0 CG B:ASP311 3.0 2.1 1.0 CD2 B:HIS206 3.1 3.1 1.0 CE1 B:HIS206 3.1 3.1 1.0 CD2 B:HIS167 3.3 3.1 1.0 CE1 B:HIS167 3.3 3.1 1.0 PA B:DZ4702 3.4 3.3 1.0 OD2 B:ASP311 3.5 2.1 1.0 CG B:ASP207 3.5 4.0 1.0 OD1 B:ASP207 3.8 4.0 1.0 O2A B:DZ4702 4.0 3.3 1.0 MG B:MG704 4.0 7.5 1.0 NH2 B:ARG164 4.1 4.5 1.0 N3A B:DZ4702 4.1 3.3 1.0 ND1 B:HIS206 4.2 3.1 1.0 CG B:HIS206 4.2 3.1 1.0 CB B:ASP311 4.3 2.1 1.0 CG B:HIS167 4.4 3.1 1.0 ND1 B:HIS167 4.4 3.1 1.0 O5' B:DZ4702 4.5 3.3 1.0 CG2 B:VAL171 4.6 3.3 1.0 CB B:ASP207 4.7 4.0 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe703 b:7.5 occ:1.00 O1A C:DZ4702 1.9 2.8 1.0 OD1 C:ASP311 2.0 2.6 1.0 NE2 C:HIS206 2.1 2.3 1.0 NE2 C:HIS167 2.3 2.4 1.0 OD2 C:ASP207 2.7 3.5 1.0 CG C:ASP311 3.0 2.6 1.0 CD2 C:HIS206 3.1 2.3 1.0 CE1 C:HIS206 3.1 2.3 1.0 CD2 C:HIS167 3.3 2.4 1.0 CE1 C:HIS167 3.3 2.4 1.0 PA C:DZ4702 3.4 2.8 1.0 OD2 C:ASP311 3.5 2.6 1.0 CG C:ASP207 3.5 3.5 1.0 OD1 C:ASP207 3.8 3.5 1.0 O2A C:DZ4702 4.0 2.8 1.0 MG C:MG704 4.0 7.4 1.0 NH2 C:ARG164 4.1 3.6 1.0 N3A C:DZ4702 4.1 2.8 1.0 ND1 C:HIS206 4.2 2.3 1.0 CG C:HIS206 4.2 2.3 1.0 CB C:ASP311 4.3 2.6 1.0 CG C:HIS167 4.4 2.4 1.0 ND1 C:HIS167 4.4 2.4 1.0 O5' C:DZ4702 4.5 2.8 1.0 CG2 C:VAL171 4.6 3.3 1.0 CB C:ASP207 4.7 3.5 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Tetrameric Human SAMHD1 with Dapnhpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe704 b:8.2 occ:1.00 O1A D:DZ4703 1.9 3.8 1.0 OD1 D:ASP311 2.0 1.3 1.0 NE2 D:HIS206 2.1 7.5 1.0 NE2 D:HIS167 2.3 7.5 1.0 OD2 D:ASP207 2.7 4.0 1.0 CG D:ASP311 3.0 1.3 1.0 CE1 D:HIS206 3.1 7.5 1.0 CD2 D:HIS206 3.1 7.5 1.0 CD2 D:HIS167 3.3 7.5 1.0 CE1 D:HIS167 3.3 7.5 1.0 PA D:DZ4703 3.4 3.8 1.0 OD2 D:ASP311 3.5 1.3 1.0 CG D:ASP207 3.5 4.0 1.0 OD1 D:ASP207 3.8 4.0 1.0 O2A D:DZ4703 4.0 3.8 1.0 MG D:MG705 4.0 8.5 1.0 N3A D:DZ4703 4.1 3.8 1.0 ND1 D:HIS206 4.2 7.5 1.0 NH1 D:ARG164 4.2 5.4 1.0 CG D:HIS206 4.2 7.5 1.0 CB D:ASP311 4.3 1.3 1.0 ND1 D:HIS167 4.4 7.5 1.0 CG D:HIS167 4.4 7.5 1.0 O5' D:DZ4703 4.5 3.8 1.0 CG2 D:VAL171 4.6 3.2 1.0 CB D:ASP207 4.7 4.0 1.0

O.J.Acton, D.Sheppard, S.Kunzelmann, S.J.Caswell, A.Nans, A.Burgess, G.Kelly, E.R.Morris, P.B.Rosenthal, I.A.Taylor. Platform-Directed Allostery and Quaternary Structure Dynamics of SAMHD1 Catalysis To Be Published.