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

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mn, PDB code: 6txf 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)	71.51 / 2.25
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.978, 104.978, 195.516, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.9

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

Manganese

(Mn)

6 atoms

The binding sites of Iron atom in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mn (pdb code 6txf). 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 Mn, PDB code: 6txf:
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 Mn


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 Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:26.2 occ:1.00 O A:HOH814 2.0 26.4 1.0 OD2 A:ASP207 2.0 27.6 1.0 OD1 A:ASP311 2.1 30.8 1.0 NE2 A:HIS206 2.1 29.5 1.0 O1A A:DZ4705 2.2 28.0 1.0 NE2 A:HIS167 2.3 21.5 1.0 CG A:ASP207 3.0 30.4 1.0 CG A:ASP311 3.0 29.2 1.0 CD2 A:HIS206 3.1 29.4 1.0 CE1 A:HIS206 3.2 28.9 1.0 CD2 A:HIS167 3.2 22.2 1.0 PA A:DZ4705 3.2 31.8 1.0 OD2 A:ASP311 3.3 29.2 1.0 CE1 A:HIS167 3.3 22.6 1.0 OD1 A:ASP207 3.4 31.0 1.0 O2A A:DZ4705 3.6 29.2 1.0 MN A:MN702 3.7 30.9 1.0 NH2 A:ARG164 3.8 30.0 1.0 N3A A:DZ4705 3.9 30.5 1.0 CG A:HIS206 4.2 29.8 1.0 ND1 A:HIS206 4.3 28.6 1.0 CB A:ASP207 4.3 30.0 1.0 CB A:ASP311 4.4 26.8 1.0 CG A:HIS167 4.4 22.8 1.0 ND1 A:HIS167 4.4 21.8 1.0 O5' A:DZ4705 4.6 31.0 1.0 CG2 A:VAL171 4.7 25.5 1.0 O A:HOH822 4.9 30.4 1.0 O A:HOH846 4.9 34.2 1.0 O A:HOH821 5.0 27.2 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 Mn


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 Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:34.4 occ:1.00 OD1 B:ASP311 2.0 31.1 1.0 OD2 B:ASP207 2.1 32.6 1.0 NE2 B:HIS206 2.1 36.2 1.0 O1A B:DZ4706 2.2 34.5 1.0 NE2 B:HIS167 2.2 31.1 1.0 O B:HOH824 2.7 37.9 1.0 CG B:ASP207 3.0 37.3 1.0 CG B:ASP311 3.0 32.6 1.0 CD2 B:HIS206 3.0 35.2 1.0 CE1 B:HIS206 3.1 35.5 1.0 CD2 B:HIS167 3.1 32.0 1.0 CE1 B:HIS167 3.2 31.5 1.0 PA B:DZ4706 3.3 31.8 1.0 OD1 B:ASP207 3.4 38.4 1.0 OD2 B:ASP311 3.5 31.4 1.0 MN B:MN703 3.6 41.6 1.0 O2A B:DZ4706 3.8 39.8 1.0 NH1 B:ARG164 3.9 36.4 1.0 N3A B:DZ4706 4.0 33.0 1.0 ND1 B:HIS206 4.2 35.2 1.0 CG B:HIS206 4.2 37.5 1.0 CB B:ASP207 4.2 36.8 1.0 CG B:HIS167 4.3 32.6 1.0 CB B:ASP311 4.3 31.7 1.0 ND1 B:HIS167 4.4 31.3 1.0 CG2 B:VAL171 4.6 35.1 1.0 O5' B:DZ4706 4.7 31.5 1.0 O B:HOH833 4.8 28.8 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