Iron in PDB 6yom: Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg, PDB code: 6yom 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)	92.72 / 3.25
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.298, 105.298, 195.629, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.6

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

Magnesium	(Mg)	4 atoms
Manganese	(Mn)	2 atoms

The binding sites of Iron atom in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg (pdb code 6yom). 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, Datp, Dcmpnpp, Mn and Mg, PDB code: 6yom:
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, Datp, Dcmpnpp, Mn 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, Datp, Dcmpnpp, Mn and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:53.3 occ:1.00 O2A A:0KX705 2.0 58.9 1.0 OD1 A:ASP311 2.1 61.8 1.0 NE2 A:HIS206 2.1 65.5 1.0 OD2 A:ASP207 2.2 52.2 1.0 NE2 A:HIS167 2.4 47.0 1.0 CG A:ASP311 2.9 65.9 1.0 CG A:ASP207 3.0 53.7 1.0 CD2 A:HIS206 3.0 64.4 1.0 PA A:0KX705 3.0 60.6 1.0 OD2 A:ASP311 3.2 71.9 1.0 CE1 A:HIS206 3.2 62.0 1.0 CE1 A:HIS167 3.3 50.9 1.0 OD1 A:ASP207 3.3 52.0 1.0 CD2 A:HIS167 3.4 46.6 1.0 O1A A:0KX705 3.5 62.2 1.0 N3A A:0KX705 3.6 62.5 1.0 MN A:MN702 3.6 57.8 1.0 NH2 A:ARG164 4.1 53.6 1.0 CG A:HIS206 4.2 59.7 1.0 CB A:ASP311 4.2 64.0 1.0 CB A:ASP207 4.2 57.2 1.0 ND1 A:HIS206 4.2 60.3 1.0 O5' A:0KX705 4.4 57.6 1.0 ND1 A:HIS167 4.4 48.3 1.0 CG A:HIS167 4.5 48.9 1.0 CG2 A:VAL171 4.7 51.6 1.0 CA A:ASP311 4.9 58.4 1.0 C5' A:0KX705 5.0 59.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn 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, Datp, Dcmpnpp, Mn and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:60.6 occ:1.00 O2A B:0KX706 2.0 64.0 1.0 OD2 B:ASP207 2.1 62.8 1.0 NE2 B:HIS206 2.2 68.3 1.0 OD1 B:ASP311 2.2 64.5 1.0 NE2 B:HIS167 2.4 59.1 1.0 CG B:ASP207 3.0 63.9 1.0 CG B:ASP311 3.0 68.1 1.0 CD2 B:HIS206 3.0 68.4 1.0 PA B:0KX706 3.0 66.6 1.0 OD2 B:ASP311 3.2 77.8 1.0 CE1 B:HIS206 3.2 68.8 1.0 OD1 B:ASP207 3.3 66.1 1.0 CE1 B:HIS167 3.3 58.3 1.0 MN B:MN703 3.4 61.7 1.0 CD2 B:HIS167 3.4 61.6 1.0 O1A B:0KX706 3.5 68.8 1.0 N3A B:0KX706 3.5 69.4 1.0 NH1 B:ARG164 4.0 64.4 1.0 CB B:ASP207 4.2 63.7 1.0 CG B:HIS206 4.2 67.9 1.0 ND1 B:HIS206 4.3 66.7 1.0 CB B:ASP311 4.3 65.0 1.0 ND1 B:HIS167 4.5 59.4 1.0 O5' B:0KX706 4.5 61.5 1.0 CG B:HIS167 4.5 61.5 1.0 CG2 B:VAL171 4.8 60.6 1.0 CA B:ASP311 5.0 61.5 1.0 PB B:0KX706 5.0 70.3 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