Iron in PDB 6tx0: Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg, PDB code: 6tx0 was solved by E.R.Morris, S.Kunzelmann, S.J.Caswell, L.H.Arnold, A.G.Purkiss, G.Kelly, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.31 / 2.01
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.924, 105.924, 198.073, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.8

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Iron atom in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg (pdb code 6tx0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg, PDB code: 6tx0:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg


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 Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:22.4 occ:1.00 OD1 A:ASP311 2.0 28.9 1.0 OD2 A:ASP207 2.1 23.0 1.0 O1A A:DZ4705 2.1 24.8 1.0 O A:HOH808 2.1 18.5 1.0 NE2 A:HIS206 2.2 24.3 1.0 NE2 A:HIS167 2.2 20.2 1.0 CG A:ASP207 3.0 27.5 1.0 CG A:ASP311 3.1 29.3 1.0 CD2 A:HIS206 3.1 24.6 1.0 CE1 A:HIS206 3.2 25.2 1.0 CD2 A:HIS167 3.2 20.6 1.0 CE1 A:HIS167 3.2 20.0 1.0 PA A:DZ4705 3.3 26.4 1.0 OD1 A:ASP207 3.5 29.2 1.0 OD2 A:ASP311 3.6 35.2 1.0 O2A A:DZ4705 3.8 25.9 1.0 MG A:MG702 3.9 29.1 1.0 NH2 A:ARG164 3.9 24.3 1.0 N3A A:DZ4705 4.0 25.1 1.0 ND1 A:HIS206 4.3 24.7 1.0 CG A:HIS206 4.3 25.9 1.0 CB A:ASP207 4.3 26.7 1.0 ND1 A:HIS167 4.3 19.3 1.0 CG A:HIS167 4.4 20.4 1.0 CB A:ASP311 4.4 25.4 1.0 O5' A:DZ4705 4.6 24.7 1.0 CG2 A:VAL171 4.7 22.2 1.0 NE2 A:GLN149 5.0 23.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg


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 Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:28.7 occ:1.00 OD1 B:ASP311 2.0 30.1 1.0 OD2 B:ASP207 2.1 27.8 1.0 O1A B:DZ4706 2.1 26.7 1.0 NE2 B:HIS206 2.2 35.8 1.0 NE2 B:HIS167 2.3 23.2 1.0 O B:HOH812 2.3 32.5 1.0 CG B:ASP207 3.0 30.2 1.0 CG B:ASP311 3.0 29.0 1.0 CD2 B:HIS206 3.1 34.9 1.0 CE1 B:HIS206 3.2 33.4 1.0 PA B:DZ4706 3.2 28.5 1.0 CE1 B:HIS167 3.3 23.7 1.0 CD2 B:HIS167 3.3 23.0 1.0 OD2 B:ASP311 3.4 27.1 1.0 OD1 B:ASP207 3.4 33.5 1.0 O2A B:DZ4706 3.7 28.7 1.0 NH1 B:ARG164 3.9 25.6 1.0 N3A B:DZ4706 3.9 27.5 1.0 MG B:MG703 3.9 36.0 1.0 CB B:ASP207 4.3 29.8 1.0 CG B:HIS206 4.3 35.0 1.0 ND1 B:HIS206 4.3 33.4 1.0 CB B:ASP311 4.3 28.3 1.0 ND1 B:HIS167 4.4 23.3 1.0 CG B:HIS167 4.5 24.6 1.0 O5' B:DZ4706 4.5 25.8 1.0 CG2 B:VAL171 4.8 27.4 1.0 O B:HOH818 4.9 39.3 1.0 O B:HOH822 5.0 37.2 1.0 CA B:ASP311 5.0 28.9 1.0

E.R.Morris, S.Kunzelmann, S.J.Caswell, L.H.Arnold, A.G.Purkiss, G.Kelly, I.A.Taylor. Crystal Structures of SAMHD1 Inhibitor Complexes Reveal the Mechanism of Water-Mediated Dntp Hydrolysis Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-16983-2