Iron in PDB 6xu1: Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg, PDB code: 6xu1 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)	107.30 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	137.369, 171.860, 179.572, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.2

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg also contains other interesting chemical elements:

Magnesium

(Mg)

25 atoms

The binding sites of Iron atom in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg (pdb code 6xu1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg, PDB code: 6xu1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, 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 H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:15.0 occ:1.00 OD1 A:ASP311 2.0 13.7 1.0 NE2 A:HIS206 2.2 13.5 1.0 O1A A:DZ4705 2.2 13.6 1.0 OD2 A:ASP207 2.2 12.3 1.0 O A:HOH866 2.2 15.7 1.0 NE2 A:HIS167 2.2 11.0 1.0 CG A:ASP207 3.0 13.2 1.0 CG A:ASP311 3.1 13.9 1.0 CD2 A:HIS206 3.1 13.4 1.0 CD2 A:HIS167 3.2 11.6 1.0 CE1 A:HIS206 3.2 13.3 1.0 CE1 A:HIS167 3.2 11.6 1.0 PA A:DZ4705 3.3 14.4 1.0 OD1 A:ASP207 3.4 13.5 1.0 OD2 A:ASP311 3.5 14.1 1.0 MG A:MG702 3.7 8.2 1.0 O2A A:DZ4705 3.8 15.1 1.0 NH2 A:ARG164 3.8 14.6 1.0 N3A A:DZ4705 3.8 14.0 1.0 CB A:ASP207 4.2 13.3 1.0 CG A:HIS206 4.3 13.4 1.0 ND1 A:HIS206 4.3 13.1 1.0 CB A:ASP311 4.3 13.6 1.0 ND1 A:HIS167 4.3 11.5 1.0 CG A:HIS167 4.3 11.9 1.0 O5' A:DZ4705 4.6 14.3 1.0 O A:HOH845 4.7 11.1 1.0 CG2 A:VAL171 4.8 13.5 1.0 O A:HOH865 4.9 11.1 1.0 O A:HOH884 5.0 18.1 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, 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 H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe701 b:13.9 occ:1.00 O1A B:DZ4705 2.0 14.6 1.0 O B:HOH822 2.0 11.7 1.0 OD1 B:ASP311 2.1 13.3 1.0 NE2 B:HIS206 2.2 14.3 1.0 NE2 B:HIS167 2.2 11.1 1.0 OD2 B:ASP207 2.2 13.2 1.0 CG B:ASP207 3.0 14.2 1.0 CG B:ASP311 3.1 14.2 1.0 CD2 B:HIS206 3.1 14.7 1.0 CD2 B:HIS167 3.2 11.3 1.0 CE1 B:HIS206 3.2 14.9 1.0 CE1 B:HIS167 3.2 11.3 1.0 PA B:DZ4705 3.2 14.8 1.0 OD1 B:ASP207 3.4 14.2 1.0 OD2 B:ASP311 3.5 15.4 1.0 MG B:MG702 3.7 9.6 1.0 O2A B:DZ4705 3.7 16.8 1.0 NH1 B:ARG164 3.9 13.5 1.0 N3A B:DZ4705 3.9 14.8 1.0 CB B:ASP207 4.2 14.1 1.0 CG B:HIS206 4.3 14.9 1.0 ND1 B:HIS206 4.3 15.4 1.0 CB B:ASP311 4.3 13.9 1.0 ND1 B:HIS167 4.3 10.9 1.0 CG B:HIS167 4.3 11.5 1.0 O5' B:DZ4705 4.6 13.7 1.0 CG2 B:VAL171 4.8 13.8 1.0 O B:HOH850 4.8 11.9 1.0 O B:HOH901 4.9 22.2 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


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 Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe702 b:13.4 occ:1.00 OD1 C:ASP311 2.1 13.5 1.0 O C:HOH825 2.1 18.6 1.0 OD2 C:ASP207 2.1 12.5 1.0 NE2 C:HIS167 2.1 11.4 1.0 NE2 C:HIS206 2.2 11.5 1.0 O1A C:DZ4706 2.2 13.6 1.0 CG C:ASP207 3.0 13.4 1.0 CG C:ASP311 3.1 14.1 1.0 CD2 C:HIS167 3.1 11.5 1.0 CD2 C:HIS206 3.1 11.8 1.0 CE1 C:HIS167 3.2 11.3 1.0 CE1 C:HIS206 3.2 11.8 1.0 PA C:DZ4706 3.3 14.2 1.0 OD1 C:ASP207 3.4 13.1 1.0 OD2 C:ASP311 3.5 15.4 1.0 MG C:MG703 3.7 9.2 1.0 O2A C:DZ4706 3.7 14.0 1.0 NH2 C:ARG164 3.8 15.0 1.0 N3A C:DZ4706 3.9 13.8 1.0 CB C:ASP207 4.2 13.5 1.0 CG C:HIS167 4.3 12.1 1.0 CB C:ASP311 4.3 14.3 1.0 CG C:HIS206 4.3 12.4 1.0 ND1 C:HIS206 4.3 11.8 1.0 ND1 C:HIS167 4.3 11.1 1.0 O5' C:DZ4706 4.6 14.1 1.0 CG2 C:VAL171 4.7 12.1 1.0 O C:HOH841 4.9 13.1 1.0 O C:HOH832 4.9 13.7 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


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 Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe702 b:15.5 occ:1.00 OD1 D:ASP311 2.0 16.3 1.0 OD2 D:ASP207 2.2 13.8 1.0 NE2 D:HIS206 2.2 16.3 1.0 O1A D:DZ4706 2.2 13.7 1.0 O D:HOH847 2.2 13.6 1.0 NE2 D:HIS167 2.2 13.5 1.0 CG D:ASP207 3.0 15.3 1.0 CG D:ASP311 3.0 16.6 1.0 CD2 D:HIS206 3.1 16.3 1.0 CD2 D:HIS167 3.2 14.2 1.0 CE1 D:HIS167 3.2 14.0 1.0 CE1 D:HIS206 3.2 16.4 1.0 PA D:DZ4706 3.3 15.0 1.0 OD1 D:ASP207 3.4 15.3 1.0 OD2 D:ASP311 3.5 17.5 1.0 MG D:MG703 3.7 8.9 1.0 O2A D:DZ4706 3.8 14.1 1.0 NH1 D:ARG164 3.9 15.5 1.0 N3A D:DZ4706 3.9 15.5 1.0 CB D:ASP207 4.2 15.4 1.0 CG D:HIS206 4.3 16.4 1.0 CB D:ASP311 4.3 15.6 1.0 ND1 D:HIS206 4.3 16.7 1.0 ND1 D:HIS167 4.3 13.9 1.0 CG D:HIS167 4.3 13.7 1.0 O5' D:DZ4706 4.6 14.4 1.0 CG2 D:VAL171 4.7 14.9 1.0 O D:HOH840 4.9 14.1 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe701 b:17.7 occ:1.00 OD1 E:ASP311 2.0 20.1 1.0 O1A E:DZ4705 2.1 20.1 1.0 NE2 E:HIS206 2.2 16.2 1.0 OD2 E:ASP207 2.2 18.1 1.0 NE2 E:HIS167 2.2 15.6 1.0 O E:HOH837 2.3 23.4 1.0 CG E:ASP311 3.0 20.8 1.0 CG E:ASP207 3.0 18.6 1.0 CD2 E:HIS206 3.1 17.2 1.0 CE1 E:HIS206 3.2 16.3 1.0 PA E:DZ4705 3.2 19.4 1.0 CE1 E:HIS167 3.2 15.4 1.0 CD2 E:HIS167 3.2 15.0 1.0 OD1 E:ASP207 3.4 18.3 1.0 OD2 E:ASP311 3.4 20.9 1.0 MG E:MG702 3.6 15.5 1.0 O2A E:DZ4705 3.7 19.7 1.0 NH2 E:ARG164 3.8 18.0 1.0 N3A E:DZ4705 3.9 21.1 1.0 CB E:ASP311 4.2 20.3 1.0 CG E:HIS206 4.3 17.5 1.0 CB E:ASP207 4.3 17.9 1.0 ND1 E:HIS206 4.3 16.8 1.0 ND1 E:HIS167 4.3 14.9 1.0 CG E:HIS167 4.4 14.9 1.0 O5' E:DZ4705 4.6 18.6 1.0 O E:HOH862 4.7 25.8 1.0 CG2 E:VAL171 4.8 16.1 1.0 O E:HOH826 4.8 14.6 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe701 b:14.3 occ:1.00 OD1 F:ASP311 2.0 14.9 1.0 O1A F:DZ4705 2.1 13.2 1.0 NE2 F:HIS206 2.1 14.2 1.0 O F:HOH869 2.1 12.2 1.0 OD2 F:ASP207 2.2 17.3 1.0 NE2 F:HIS167 2.2 10.8 1.0 CG F:ASP207 3.0 16.2 1.0 CG F:ASP311 3.0 15.1 1.0 CD2 F:HIS206 3.1 14.9 1.0 CE1 F:HIS206 3.1 14.7 1.0 CD2 F:HIS167 3.2 11.4 1.0 CE1 F:HIS167 3.2 11.0 1.0 PA F:DZ4705 3.2 13.6 1.0 OD1 F:ASP207 3.4 16.4 1.0 OD2 F:ASP311 3.5 15.3 1.0 MG F:MG702 3.7 9.8 1.0 O2A F:DZ4705 3.8 13.1 1.0 N3A F:DZ4705 3.8 12.9 1.0 NH1 F:ARG164 3.9 14.8 1.0 CB F:ASP207 4.2 15.6 1.0 CG F:HIS206 4.2 15.0 1.0 ND1 F:HIS206 4.3 14.4 1.0 CB F:ASP311 4.3 15.7 1.0 ND1 F:HIS167 4.3 10.9 1.0 CG F:HIS167 4.3 11.4 1.0 O5' F:DZ4705 4.5 12.9 1.0 CG2 F:VAL171 4.7 18.5 1.0 O F:HOH843 4.8 12.7 1.0 O F:HOH914 4.9 23.6 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe702 b:13.1 occ:1.00 OD1 G:ASP311 2.0 16.8 1.0 O1A G:DZ4706 2.1 13.4 1.0 NE2 G:HIS206 2.1 16.0 1.0 O G:HOH847 2.2 12.9 1.0 NE2 G:HIS167 2.2 11.8 1.0 OD2 G:ASP207 2.2 15.2 1.0 CG G:ASP311 3.0 15.9 1.0 CG G:ASP207 3.0 15.1 1.0 CD2 G:HIS206 3.1 16.1 1.0 CE1 G:HIS167 3.2 11.9 1.0 CE1 G:HIS206 3.2 16.5 1.0 CD2 G:HIS167 3.2 12.2 1.0 PA G:DZ4706 3.3 14.5 1.0 OD1 G:ASP207 3.4 15.9 1.0 OD2 G:ASP311 3.5 16.5 1.0 MG G:MG703 3.7 11.5 1.0 O2A G:DZ4706 3.8 13.1 1.0 N3A G:DZ4706 3.8 13.3 1.0 NH2 G:ARG164 3.9 13.9 1.0 CB G:ASP311 4.2 15.4 1.0 CB G:ASP207 4.3 15.3 1.0 CG G:HIS206 4.3 16.8 1.0 ND1 G:HIS206 4.3 16.9 1.0 ND1 G:HIS167 4.3 12.2 1.0 CG G:HIS167 4.3 12.4 1.0 O5' G:DZ4706 4.5 12.8 1.0 CG2 G:VAL171 4.7 16.5 1.0 O G:HOH866 4.8 17.7 1.0 O G:HOH900 4.9 19.1 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe702 b:20.5 occ:1.00 OD1 H:ASP311 2.0 22.3 1.0 OD2 H:ASP207 2.2 23.7 1.0 NE2 H:HIS206 2.2 23.9 1.0 O1A H:DZ4706 2.2 23.0 1.0 NE2 H:HIS167 2.2 19.9 1.0 O H:HOH845 2.3 21.9 1.0 CG H:ASP207 3.0 22.4 1.0 CG H:ASP311 3.0 22.1 1.0 CD2 H:HIS206 3.1 23.8 1.0 PA H:DZ4706 3.1 22.4 1.0 CD2 H:HIS167 3.2 19.1 1.0 CE1 H:HIS167 3.2 18.9 1.0 CE1 H:HIS206 3.2 24.6 1.0 OD1 H:ASP207 3.4 21.0 1.0 OD2 H:ASP311 3.5 22.0 1.0 MG H:MG703 3.7 15.4 1.0 O2A H:DZ4706 3.7 22.2 1.0 N3A H:DZ4706 3.8 24.5 1.0 NH1 H:ARG164 3.9 23.1 1.0 CB H:ASP207 4.2 21.5 1.0 CG H:HIS206 4.3 23.1 1.0 CB H:ASP311 4.3 22.2 1.0 ND1 H:HIS206 4.3 24.7 1.0 ND1 H:HIS167 4.3 18.3 1.0 CG H:HIS167 4.4 18.3 1.0 O5' H:DZ4706 4.5 21.6 1.0 CG2 H:VAL171 4.8 19.0 1.0 O H:HOH833 4.9 20.9 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