Manganese 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
Iron	(Fe)	2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn702 b:57.8 occ:1.00 O1A A:0KX705 2.1 62.2 1.0 OD1 A:ASP207 2.2 52.0 1.0 NE2 A:HIS233 2.2 68.6 1.0 CE1 A:HIS233 3.2 71.3 1.0 PA A:0KX705 3.2 60.6 1.0 CD2 A:HIS233 3.3 67.9 1.0 CG A:ASP207 3.3 53.7 1.0 FE A:FE701 3.6 53.3 1.0 N3A A:0KX705 3.6 62.5 1.0 OD2 A:ASP207 3.7 52.2 1.0 CD2 A:HIS206 3.7 64.4 1.0 O1B A:0KX705 3.8 66.4 1.0 O2A A:0KX705 3.9 58.9 1.0 O A:HIS206 4.1 62.0 1.0 OD2 A:ASP311 4.2 71.9 1.0 PB A:0KX705 4.2 62.9 1.0 NE2 A:HIS206 4.2 65.5 1.0 OE2 A:GLU234 4.2 82.3 1.0 NE2 A:HIS210 4.2 74.5 1.0 ND1 A:HIS233 4.3 68.5 1.0 CG A:HIS233 4.4 65.5 1.0 CG A:GLU234 4.5 71.0 1.0 CD A:GLU234 4.5 76.4 1.0 O5' A:0KX705 4.6 57.6 1.0 CB A:ASP207 4.7 57.2 1.0 CD2 A:HIS210 4.8 73.4 1.0 O2B A:0KX705 4.8 64.2 1.0 CA A:ASP207 4.9 60.9 1.0 CG A:HIS206 4.9 59.7 1.0 C A:HIS206 4.9 63.1 1.0 CG A:ASP311 4.9 65.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn703 b:61.7 occ:1.00 OD1 B:ASP207 2.2 66.1 1.0 O1A B:0KX706 2.4 68.8 1.0 NE2 B:HIS233 2.4 74.0 1.0 PA B:0KX706 3.2 66.6 1.0 CG B:ASP207 3.3 63.9 1.0 CE1 B:HIS233 3.4 74.9 1.0 FE B:FE702 3.4 60.6 1.0 N3A B:0KX706 3.4 69.4 1.0 CD2 B:HIS233 3.4 75.1 1.0 OD2 B:ASP207 3.6 62.8 1.0 CD2 B:HIS206 3.6 68.4 1.0 O2A B:0KX706 3.8 64.0 1.0 O1B B:0KX706 3.9 71.7 1.0 NE2 B:HIS206 4.0 68.3 1.0 PB B:0KX706 4.0 70.3 1.0 OD2 B:ASP311 4.0 77.8 1.0 O B:HIS206 4.2 73.0 1.0 NE2 B:HIS210 4.2 73.5 1.0 O2B B:0KX706 4.4 69.4 1.0 OE2 B:GLU234 4.4 80.6 1.0 ND1 B:HIS233 4.5 73.6 1.0 CG B:HIS233 4.6 72.6 1.0 O5' B:0KX706 4.6 61.5 1.0 CB B:ASP207 4.6 63.7 1.0 CG B:GLU234 4.7 82.4 1.0 CD B:GLU234 4.8 84.6 1.0 CG B:ASP311 4.8 68.1 1.0 CG B:HIS206 4.8 67.9 1.0 CD2 B:HIS210 4.8 72.6 1.0 OD1 B:ASP311 4.8 64.5 1.0 CA B:ASP207 4.9 66.5 1.0 C B:HIS206 4.9 71.8 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