Magnesium in PDB 6sqz: Mouse Dctpase in Complex with Dcmpnpp

All present enzymatic activity of Mouse Dctpase in Complex with Dcmpnpp:
3.6.1.12;

The structure of Mouse Dctpase in Complex with Dcmpnpp, PDB code: 6sqz was solved by E.R.Scaletti, M.Claesson, H.Helleday, A.S.Jemth, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.52 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.997, 58.997, 142.650, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.7

The binding sites of Magnesium atom in the Mouse Dctpase in Complex with Dcmpnpp (pdb code 6sqz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mouse Dctpase in Complex with Dcmpnpp, PDB code: 6sqz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mouse Dctpase in Complex with Dcmpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse Dctpase in Complex with Dcmpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:22.2 occ:1.00 O A:HOH311 2.0 37.6 1.0 OE1 A:GLU63 2.1 22.5 1.0 OD2 A:ASP98 2.2 28.0 1.0 OE2 A:GLU66 2.2 33.0 1.0 OE1 A:GLU95 2.2 30.9 1.0 O2B A:0KX203 2.3 43.6 1.0 CD A:GLU63 3.1 22.3 1.0 CD A:GLU95 3.2 28.5 1.0 CD A:GLU66 3.2 31.4 1.0 CG A:ASP98 3.3 24.5 1.0 MG A:MG202 3.4 38.7 1.0 OE2 A:GLU95 3.4 30.7 1.0 PB A:0KX203 3.5 48.3 1.0 OE2 A:GLU63 3.5 25.5 1.0 OE1 A:GLU66 3.6 36.3 1.0 CB A:ASP98 3.8 22.1 1.0 O1B A:0KX203 3.8 46.6 1.0 O A:HOH314 4.0 46.5 1.0 O3B A:0KX203 4.2 52.8 1.0 OD1 A:ASP98 4.3 25.1 1.0 CG A:GLU66 4.4 28.3 1.0 CG A:GLU63 4.5 20.3 1.0 CB A:GLU66 4.5 24.7 1.0 CG A:GLU95 4.6 25.7 1.0 O3G A:0KX203 4.6 51.3 1.0 CA A:GLU95 4.7 21.2 1.0 O2A A:0KX203 4.8 45.3 1.0 N3A A:0KX203 4.8 45.9 1.0 CB A:GLU63 4.8 18.9 1.0 PG A:0KX203 4.9 56.5 1.0 O A:GLU94 4.9 21.2 1.0 O1G A:0KX203 4.9 57.4 1.0 CB A:GLU95 5.0 22.4 1.0

Magnesium binding site 2 out of 4 in the Mouse Dctpase in Complex with Dcmpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse Dctpase in Complex with Dcmpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.7 occ:1.00 O2A A:0KX203 2.1 45.3 1.0 O3G A:0KX203 2.2 51.3 1.0 O2B A:0KX203 2.2 43.6 1.0 O A:HOH330 2.2 55.6 1.0 OE1 A:GLU66 2.3 36.3 1.0 OE2 A:GLU63 2.3 25.5 1.0 CD A:GLU66 3.1 31.4 1.0 CD A:GLU63 3.2 22.3 1.0 OE2 A:GLU66 3.2 33.0 1.0 PB A:0KX203 3.3 48.3 1.0 OE1 A:GLU63 3.4 22.5 1.0 PG A:0KX203 3.4 56.5 1.0 MG A:MG201 3.4 22.2 1.0 PA A:0KX203 3.5 46.3 1.0 O3B A:0KX203 3.7 52.8 1.0 O A:HOH345 3.7 44.9 1.0 O D:HOH332 3.8 55.6 1.0 N3A A:0KX203 3.9 45.9 1.0 O A:HOH344 4.1 59.2 1.0 O1G A:0KX203 4.2 57.4 1.0 O A:HOH311 4.3 37.6 1.0 O5' A:0KX203 4.4 40.5 1.0 C5' A:0KX203 4.4 39.2 1.0 O D:HOH319 4.4 24.0 1.0 O2G A:0KX203 4.4 54.5 1.0 O1A A:0KX203 4.5 46.9 1.0 CG A:GLU63 4.6 20.3 1.0 CG A:GLU66 4.6 28.3 1.0 O1B A:0KX203 4.7 46.6 1.0 OE2 D:GLU69 4.7 37.9 1.0 OD2 A:ASP98 4.7 28.0 1.0 O A:HOH314 4.9 46.5 1.0 CD D:GLU69 4.9 34.7 1.0

Magnesium binding site 3 out of 4 in the Mouse Dctpase in Complex with Dcmpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mouse Dctpase in Complex with Dcmpnpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:29.5 occ:1.00 OE1 D:GLU63 2.1 27.5 1.0 OE1 D:GLU95 2.1 35.0 1.0 O D:HOH303 2.1 39.3 1.0 OD2 D:ASP98 2.2 34.4 1.0 OE2 D:GLU66 2.2 28.8 1.0 O1B D:0KX203 2.2 37.4 1.0 CD D:GLU95 3.1 34.1 1.0 CD D:GLU63 3.2 26.6 1.0 CD D:GLU66 3.2 27.3 1.0 CG D:ASP98 3.3 34.2 1.0 OE2 D:GLU95 3.4 35.9 1.0 PB D:0KX203 3.4 40.7 1.0 O2B D:0KX203 3.5 41.7 1.0 MG D:MG202 3.6 32.1 1.0 OE2 D:GLU63 3.6 27.8 1.0 OE1 D:GLU66 3.7 27.9 1.0 CB D:ASP98 3.7 31.9 1.0 O D:HOH306 4.0 43.3 1.0 CB D:GLU66 4.3 25.5 1.0 CG D:GLU66 4.4 25.9 1.0 OD1 D:ASP98 4.4 36.0 1.0 O3B D:0KX203 4.4 41.6 1.0 CG D:GLU63 4.5 25.6 1.0 CG D:GLU95 4.5 32.9 1.0 CA D:GLU95 4.6 33.0 1.0 O1G D:0KX203 4.7 37.0 1.0 N3A D:0KX203 4.7 41.0 1.0 CB D:GLU63 4.8 24.3 1.0 O D:GLU94 4.9 36.0 1.0 CB D:GLU95 4.9 32.0 1.0 O1A D:0KX203 5.0 37.6 1.0

Magnesium binding site 4 out of 4 in the Mouse Dctpase in Complex with Dcmpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mouse Dctpase in Complex with Dcmpnpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:32.1 occ:1.00 O1G D:0KX203 2.1 37.0 1.0 O1B D:0KX203 2.1 37.4 1.0 O1A D:0KX203 2.1 37.6 1.0 O A:HOH322 2.2 33.8 1.0 OE1 D:GLU66 2.2 27.9 1.0 OE2 D:GLU63 2.3 27.8 1.0 CD D:GLU66 3.1 27.3 1.0 PB D:0KX203 3.1 40.7 1.0 CD D:GLU63 3.2 26.6 1.0 OE2 D:GLU66 3.3 28.8 1.0 PG D:0KX203 3.4 41.1 1.0 OE1 D:GLU63 3.4 27.5 1.0 PA D:0KX203 3.4 40.1 1.0 MG D:MG201 3.6 29.5 1.0 O3B D:0KX203 3.7 41.6 1.0 N3A D:0KX203 3.7 41.0 1.0 O D:HOH317 3.8 32.2 1.0 O A:HOH303 4.1 54.2 1.0 O2G D:0KX203 4.1 40.9 1.0 OE2 A:GLU69 4.2 32.7 1.0 O2A D:0KX203 4.4 42.1 1.0 O A:HOH358 4.4 47.5 1.0 O5' D:0KX203 4.4 39.7 1.0 O2B D:0KX203 4.4 41.7 1.0 C5' D:0KX203 4.4 39.2 1.0 O A:HOH319 4.5 28.5 1.0 O3G D:0KX203 4.5 42.1 1.0 CG D:GLU66 4.5 25.9 1.0 CG D:GLU63 4.6 25.6 1.0 O D:HOH303 4.7 39.3 1.0 OD2 D:ASP98 4.8 34.4 1.0 CD A:GLU69 4.9 29.9 1.0 OE1 A:GLU69 4.9 31.9 1.0 O D:HOH306 4.9 43.3 1.0

E.Scaletti, M.Claesson, T.Helleday, A.S.Jemth, P.Stenmark. The First Structure of An Active Mammalian Dctpase and Its Complexes with Substrate Analogues and Products. J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638
PubMed: 31954130
DOI: 10.1016/J.JMB.2020.01.005