Manganese 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:

Iron

(Fe)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Dampnpp and Mn, PDB code: 6txf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 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 Manganese with other atoms in the Mn 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:Mn702 b:30.9 occ:1.00 O A:HOH822 2.0 30.4 1.0 OD1 A:ASP207 2.0 31.0 1.0 O2A A:DZ4705 2.1 29.2 1.0 NE2 A:HIS233 2.2 30.3 1.0 O A:HOH814 2.3 26.4 1.0 O A:HOH821 2.3 27.2 1.0 CD2 A:HIS233 3.1 31.4 1.0 CG A:ASP207 3.1 30.4 1.0 CE1 A:HIS233 3.2 31.4 1.0 PA A:DZ4705 3.3 31.8 1.0 OD2 A:ASP207 3.5 27.6 1.0 FE A:FE701 3.7 26.2 1.0 CD2 A:HIS206 3.8 29.4 1.0 N3A A:DZ4705 3.9 30.5 1.0 NE2 A:HIS210 3.9 33.1 1.0 O1A A:DZ4705 3.9 28.0 1.0 NE2 A:HIS206 4.2 29.5 1.0 O1B A:DZ4705 4.3 28.8 1.0 ND1 A:HIS233 4.3 29.6 1.0 CG A:HIS233 4.3 31.8 1.0 O A:HIS206 4.4 34.5 1.0 OE2 A:GLU234 4.4 37.1 1.0 CD2 A:HIS210 4.5 32.6 1.0 PB A:DZ4705 4.5 31.3 1.0 O A:HOH837 4.5 37.3 1.0 CB A:ASP207 4.5 30.0 1.0 O5' A:DZ4705 4.6 31.0 1.0 O2B A:DZ4705 4.6 31.2 1.0 CG A:GLU234 4.7 37.1 1.0 O A:HOH846 4.7 34.2 1.0 OD2 A:ASP311 4.7 29.2 1.0 CD A:GLU234 4.8 38.1 1.0 CA A:ASP207 4.8 30.7 1.0 CE1 A:HIS210 4.9 32.7 1.0 CG A:HIS206 5.0 29.8 1.0

Manganese binding site 2 out of 6 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 Manganese with other atoms in the Mn 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 A:Mn703 b:31.4 occ:1.00 O1G A:DZ4705 1.9 30.8 1.0 O A:HOH833 2.0 27.8 1.0 O A:HOH826 2.2 23.1 1.0 O1B A:DZ4705 2.2 28.8 1.0 O A:HOH827 2.3 37.8 1.0 O A:HOH809 2.3 27.3 1.0 PG A:DZ4705 3.4 30.1 1.0 PB A:DZ4705 3.4 31.3 1.0 O3B A:DZ4705 3.6 28.6 1.0 NZ A:LYS312 4.0 26.8 1.0 OD2 A:ASP309 4.1 27.8 1.0 O3G A:DZ4705 4.1 29.9 1.0 OD2 A:ASP311 4.2 29.2 1.0 O A:HOH822 4.4 30.4 1.0 N3A A:DZ4705 4.4 30.5 1.0 O A:HOH846 4.4 34.2 1.0 O2G A:DZ4705 4.4 29.6 1.0 OD1 A:ASP309 4.5 26.0 1.0 O A:HOH807 4.6 38.0 1.0 O2B A:DZ4705 4.6 31.2 1.0 OG A:SER302 4.6 33.9 1.0 CG A:ASP309 4.8 27.5 1.0 O A:HOH817 4.8 27.0 1.0

Manganese binding site 3 out of 6 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 Manganese with other atoms in the Mn binding site number 3 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:Mn704 b:33.5 occ:1.00 O2G B:DZ4701 2.0 33.2 1.0 O1B B:DZ4701 2.1 30.6 1.0 O14 A:CZF706 2.2 33.6 1.0 O9 A:CZF706 2.3 29.6 1.0 O A:HOH848 2.3 26.6 1.0 O12 A:CZF706 2.3 31.2 1.0 P2 A:CZF706 3.2 37.4 1.0 PG B:DZ4701 3.3 36.2 1.0 PB B:DZ4701 3.3 32.3 1.0 P3 A:CZF706 3.3 39.2 1.0 P1 A:CZF706 3.5 32.3 1.0 O10 A:CZF706 3.5 34.5 1.0 O3B B:DZ4701 3.5 32.5 1.0 O7 A:CZF706 3.6 33.4 1.0 O3 A:CZF706 3.9 26.1 1.0 O1G B:DZ4701 4.0 33.1 1.0 O2B B:DZ4701 4.1 29.2 1.0 O15 A:CZF706 4.3 34.5 1.0 O A:HOH828 4.3 35.1 1.0 O5 A:CZF706 4.4 31.5 1.0 O13 A:CZF706 4.4 38.5 1.0 C8 A:CZF706 4.5 28.6 1.0 O3G B:DZ4701 4.5 33.9 1.0 N3A B:DZ4701 4.6 29.1 1.0 O11 A:CZF706 4.6 36.8 1.0 C4 A:CZF706 4.7 26.4 1.0 O8 A:CZF706 4.7 30.9 1.0 O B:HOH834 4.7 45.2 1.0 CE A:LYS116 4.8 36.7 1.0

Manganese binding site 4 out of 6 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 Manganese with other atoms in the Mn binding site number 4 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:Mn703 b:41.6 occ:1.00 O B:HOH824 1.9 37.9 1.0 O2A B:DZ4706 2.2 39.8 1.0 OD1 B:ASP207 2.2 38.4 1.0 O B:HOH801 2.3 33.4 1.0 NE2 B:HIS233 2.3 46.6 1.0 O B:HOH812 2.6 35.4 1.0 PA B:DZ4706 3.1 31.8 1.0 CE1 B:HIS233 3.2 48.3 1.0 CG B:ASP207 3.2 37.3 1.0 CD2 B:HIS233 3.3 44.6 1.0 OD2 B:ASP207 3.6 32.6 1.0 N3A B:DZ4706 3.6 33.0 1.0 FE B:FE702 3.6 34.4 1.0 O1A B:DZ4706 3.7 34.5 1.0 CD2 B:HIS206 3.8 35.2 1.0 NE2 B:HIS210 4.0 34.1 1.0 PB B:DZ4706 4.1 33.0 1.0 O1B B:DZ4706 4.1 34.8 1.0 NE2 B:HIS206 4.2 36.2 1.0 O2B B:DZ4706 4.3 33.2 1.0 ND1 B:HIS233 4.4 43.7 1.0 O5' B:DZ4706 4.4 31.5 1.0 OE2 B:GLU234 4.4 53.4 1.0 CG B:HIS233 4.5 42.9 1.0 O B:HOH833 4.5 28.8 1.0 OD2 B:ASP311 4.6 31.4 1.0 O B:HIS206 4.6 37.7 1.0 CD2 B:HIS210 4.6 32.7 1.0 CB B:ASP207 4.7 36.8 1.0 CG B:GLU234 4.7 47.9 1.0 OD1 B:ASP311 4.8 31.1 1.0 CD B:GLU234 4.8 53.1 1.0 CG B:ASP311 4.9 32.6 1.0 CE1 B:HIS210 4.9 34.9 1.0 CA B:ASP207 5.0 37.1 1.0

Manganese binding site 5 out of 6 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 Manganese with other atoms in the Mn binding site number 5 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:Mn704 b:39.4 occ:1.00 O B:HOH822 2.0 40.3 1.0 O B:HOH802 2.1 40.5 1.0 O1B B:DZ4706 2.1 34.8 1.0 O1G B:DZ4706 2.1 33.8 1.0 O B:HOH829 2.2 32.3 1.0 O B:HOH810 2.2 28.6 1.0 PB B:DZ4706 3.4 33.0 1.0 PG B:DZ4706 3.4 35.6 1.0 O3B B:DZ4706 3.5 34.2 1.0 O B:HOH801 4.0 33.4 1.0 NZ B:LYS312 4.0 36.6 1.0 OD2 B:ASP309 4.2 39.4 1.0 O3G B:DZ4706 4.2 37.3 1.0 OD2 B:ASP311 4.3 31.4 1.0 N3A B:DZ4706 4.4 33.0 1.0 O B:HOH833 4.4 28.8 1.0 O2B B:DZ4706 4.5 33.2 1.0 O2G B:DZ4706 4.6 33.4 1.0 OD1 B:ASP309 4.6 32.5 1.0 OG B:SER302 4.7 40.2 1.0 CG B:ASP309 4.8 37.0 1.0 O B:HOH823 4.9 32.0 1.0 O B:HOH824 4.9 37.9 1.0

Manganese binding site 6 out of 6 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 Manganese with other atoms in the Mn binding site number 6 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:Mn705 b:45.9 occ:1.00 O2G A:DZ4707 1.9 38.8 1.0 O14 B:CZF707 2.0 44.7 1.0 O12 B:CZF707 2.1 39.1 1.0 O1B A:DZ4707 2.3 36.2 1.0 O9 B:CZF707 2.4 44.5 1.0 O A:HOH847 2.4 27.1 1.0 P2 B:CZF707 3.2 40.1 1.0 P3 B:CZF707 3.2 43.0 1.0 PG A:DZ4707 3.3 39.4 1.0 O10 B:CZF707 3.4 40.5 1.0 PB A:DZ4707 3.5 37.1 1.0 P1 B:CZF707 3.5 40.1 1.0 O3B A:DZ4707 3.6 37.9 1.0 O7 B:CZF707 3.7 42.9 1.0 O5 B:CZF707 3.8 40.0 1.0 O15 B:CZF707 4.1 43.6 1.0 O3 B:CZF707 4.1 34.0 1.0 O2B A:DZ4707 4.2 38.0 1.0 O1G A:DZ4707 4.2 41.6 1.0 O3G A:DZ4707 4.3 40.1 1.0 O13 B:CZF707 4.3 47.5 1.0 O11 B:CZF707 4.6 40.3 1.0 N3A A:DZ4707 4.7 33.7 1.0 O8 B:CZF707 4.8 40.9 1.0 C4 B:CZF707 4.8 34.8 1.0 CE B:LYS116 4.9 44.0 1.0 NZ B:LYS116 4.9 43.0 1.0 C8 B:CZF707 5.0 35.9 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