Magnesium in PDB 6yb9: Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium

All present enzymatic activity of Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium:
4.1.1.21; 6.3.2.6;

The structure of Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium, PDB code: 6yb9 was solved by J.Skerlova, J.Unterlass, M.Gottmann, E.Homan, T.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)	47.33 / 2.41
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.263, 154.019, 223.624, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.9

The binding sites of Magnesium atom in the Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium (pdb code 6yb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium, PDB code: 6yb9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:48.7 occ:1.00 O2B A:ANP501 2.2 47.7 1.0 O2A A:ANP501 2.9 41.7 1.0 O A:HOH658 3.0 57.5 1.0 O1G A:ANP501 3.3 61.1 1.0 PB A:ANP501 3.6 42.2 1.0 O A:HOH617 3.6 49.6 1.0 O A:HOH602 3.7 55.7 1.0 O3A A:ANP501 3.8 42.5 1.0 OD2 A:ASP207 3.8 59.3 1.0 PA A:ANP501 3.9 43.9 1.0 OD1 A:ASP207 4.1 47.8 1.0 NZ A:LYS19 4.3 44.9 1.0 PG A:ANP501 4.3 60.3 1.0 CG A:ASP207 4.3 46.7 1.0 N3B A:ANP501 4.3 47.2 1.0 O5' A:ANP501 4.6 41.8 1.0 O3G A:ANP501 4.7 48.1 1.0 O1B A:ANP501 4.8 40.5 1.0 O03 A:OK8502 4.8 0.8 1.0 OG1 A:THR18 4.8 40.9 1.0 O01 A:OK8502 4.8 0.9 1.0 OE2 A:GLU193 4.9 40.2 1.0 O A:HOH621 4.9 44.2 1.0

Magnesium binding site 2 out of 4 in the Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:50.2 occ:1.00 OE2 A:GLU97 2.1 54.1 1.0 N13 A:OK8502 2.4 51.0 1.0 OD2 A:ASP137 3.0 59.0 1.0 O11 A:OK8502 3.0 49.3 1.0 CD A:GLU97 3.3 43.2 1.0 C12 A:OK8502 3.3 53.0 1.0 C14 A:OK8502 3.5 46.2 1.0 O A:HOH690 3.5 44.9 1.0 C10 A:OK8502 3.5 48.5 1.0 O A:HOH689 3.7 39.6 1.0 OE1 A:GLU97 3.7 53.7 1.0 CG A:ASP137 3.9 58.4 1.0 CB A:ASP137 4.0 48.6 1.0 O A:HOH675 4.3 38.4 1.0 CG A:GLU97 4.6 41.5 1.0 C16 A:OK8502 4.6 44.8 1.0 O A:HOH694 4.6 54.5 1.0 N15 A:OK8502 4.7 42.1 1.0 O A:HOH686 4.7 44.7 1.0 N09 A:OK8502 4.8 68.3 1.0 CB A:GLU97 4.8 36.1 1.0

Magnesium binding site 3 out of 4 in the Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:53.2 occ:1.00 O2B B:ANP702 2.3 46.8 1.0 O B:HOH826 2.3 57.8 1.0 O2A B:ANP702 2.6 51.8 1.0 O1G B:ANP702 3.3 70.6 1.0 PB B:ANP702 3.6 43.4 1.0 OD2 B:ASP207 3.7 47.8 1.0 PA B:ANP702 3.8 42.6 1.0 OD1 B:ASP207 3.8 48.7 1.0 O3A B:ANP702 3.8 49.0 1.0 NZ B:LYS19 4.1 59.1 1.0 CG B:ASP207 4.1 50.6 1.0 O B:HOH805 4.3 49.7 1.0 PG B:ANP702 4.3 67.4 1.0 N3B B:ANP702 4.3 59.7 1.0 O5' B:ANP702 4.3 40.0 1.0 O3G B:ANP702 4.8 51.6 1.0 O1B B:ANP702 4.8 44.0 1.0 OE2 B:GLU193 4.9 46.9 1.0 OG1 B:THR18 5.0 47.1 1.0

Magnesium binding site 4 out of 4 in the Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Octameric Paics in Complex with Saicar, Amp-Pnp, and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg706 b:37.1 occ:1.00 OE2 B:GLU97 2.1 53.9 1.0 N13 B:OK8703 2.3 46.4 1.0 O11 B:OK8703 2.8 52.0 1.0 OD2 B:ASP137 2.9 59.0 1.0 O B:HOH925 3.0 41.4 1.0 C12 B:OK8703 3.2 50.1 1.0 CD B:GLU97 3.2 44.3 1.0 C10 B:OK8703 3.4 50.1 1.0 C14 B:OK8703 3.5 47.8 1.0 OE1 B:GLU97 3.6 50.5 1.0 CG B:ASP137 3.9 66.0 1.0 O B:HOH853 4.0 42.0 1.0 CB B:ASP137 4.1 56.7 1.0 C16 B:OK8703 4.5 45.5 1.0 CG B:GLU97 4.5 40.1 1.0 N15 B:OK8703 4.6 46.1 1.0 N09 B:OK8703 4.7 69.7 1.0 CB B:GLU97 4.8 36.1 1.0 O B:HOH864 4.9 46.3 1.0 O B:HOH913 4.9 42.0 1.0 O B:HOH917 4.9 47.8 1.0

J.Skerlova, J.Unterlass, M.Gottmann, P.Marttila, E.Homan, T.Helleday, A.S.Jemth, P.Stenmark. Crystal Structures of Human Paics Reveal Substrate and Product Binding of An Emerging Cancer Target. J.Biol.Chem. V. 295 11656 2020.
ISSN: ESSN 1083-351X
PubMed: 32571877
DOI: 10.1074/JBC.RA120.013695