Magnesium in PDB 7du3: Thil in Complex with Amp-Pnp

All present enzymatic activity of Thil in Complex with Amp-Pnp:
2.7.4.16;

The structure of Thil in Complex with Amp-Pnp, PDB code: 7du3 was solved by J.Q.Lin, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.59 / 2.54
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	112.82, 115.8, 132.47, 90, 90, 90
R / Rfree (%)	17.1 / 21

The binding sites of Magnesium atom in the Thil in Complex with Amp-Pnp (pdb code 7du3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Thil in Complex with Amp-Pnp, PDB code: 7du3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Thil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:44.1 occ:1.00 OD1 A:ASP52 1.9 42.7 1.0 O A:HOH521 2.4 43.7 1.0 CG A:ASP52 3.1 46.9 1.0 CB A:ASP52 3.7 42.4 1.0 OD2 A:ASP52 4.1 51.3 1.0 O1G A:ANP401 4.4 58.9 1.0 CA A:ASP52 4.4 48.1 1.0 N3B A:ANP401 4.7 59.5 1.0 O A:HOH509 4.8 45.8 1.0 MG A:MG406 4.9 49.5 1.0

Magnesium binding site 2 out of 6 in the Thil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:62.1 occ:1.00 O2G A:ANP401 2.0 56.7 1.0 OD1 A:ASP144 2.1 52.5 1.0 O A:HOH533 2.1 54.0 1.0 O2A A:ANP401 2.3 50.1 1.0 O1B A:ANP401 2.3 69.1 1.0 O A:HOH510 2.4 56.1 1.0 CG A:ASP144 3.2 46.3 1.0 PG A:ANP401 3.3 68.0 1.0 O A:HOH503 3.3 48.5 1.0 PB A:ANP401 3.3 66.8 1.0 PA A:ANP401 3.4 52.6 1.0 O3A A:ANP401 3.5 51.2 1.0 OD2 A:ASP144 3.7 42.7 1.0 O3G A:ANP401 3.7 59.5 1.0 N3B A:ANP401 3.9 59.5 1.0 O A:HOH541 4.1 46.0 1.0 O1A A:ANP401 4.2 59.3 1.0 O A:HOH539 4.4 56.0 1.0 CB A:ASP144 4.4 38.9 1.0 O1G A:ANP401 4.4 58.9 1.0 N A:THR145 4.4 41.4 1.0 CA A:ASP144 4.5 41.6 1.0 O A:THR145 4.6 44.8 1.0 O5' A:ANP401 4.6 54.1 1.0 O2B A:ANP401 4.7 66.2 1.0

Magnesium binding site 3 out of 6 in the Thil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:49.5 occ:1.00 O1G A:ANP401 1.8 58.9 1.0 O A:HOH509 2.2 45.8 1.0 PG A:ANP401 3.2 68.0 1.0 O A:HOH521 3.5 43.7 1.0 O2G A:ANP401 3.6 56.7 1.0 O A:HOH502 3.7 41.5 1.0 O3G A:ANP401 4.0 59.5 1.0 O A:HOH503 4.0 48.5 1.0 O A:HOH549 4.1 50.8 1.0 N3B A:ANP401 4.3 59.5 1.0 MG A:MG404 4.9 44.1 1.0

Magnesium binding site 4 out of 6 in the Thil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:39.0 occ:1.00 OD1 B:ASP233 2.0 43.6 1.0 OD1 B:ASP97 2.1 42.9 1.0 O B:HOH531 2.2 45.7 1.0 O B:HOH518 2.3 40.9 1.0 O B:HOH520 2.3 39.2 1.0 CG B:ASP233 3.0 44.0 1.0 CG B:ASP97 3.3 44.1 1.0 OD2 B:ASP233 3.4 43.4 1.0 OD2 B:ASP97 3.8 42.6 1.0 O2G B:ANP401 3.9 48.3 1.0 NH2 B:ARG168 3.9 43.0 1.0 O B:ASP233 4.1 43.8 1.0 N B:ASP233 4.4 41.5 1.0 CB B:ASP233 4.4 39.7 1.0 CB B:ASP97 4.5 41.7 1.0 O B:HOH506 4.5 52.0 1.0 N3B B:ANP401 4.6 47.9 1.0 CA B:ASP97 4.6 43.4 1.0 O B:HOH512 4.7 39.5 1.0 CA B:ASP233 4.7 42.1 1.0 OG B:SER235 4.7 52.6 1.0 MG B:MG403 4.7 45.5 1.0 C B:ASP233 4.7 45.4 1.0 CB B:ALA100 4.8 41.6 1.0 CB B:SER235 4.9 48.4 1.0 PG B:ANP401 5.0 44.8 1.0

Magnesium binding site 5 out of 6 in the Thil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:45.5 occ:1.00 O2G B:ANP401 1.9 48.3 1.0 OD2 B:ASP97 2.0 42.6 1.0 O B:HOH502 2.0 45.2 1.0 O B:HOH512 2.1 39.5 1.0 OD2 B:ASP69 2.2 43.5 1.0 OD1 B:ASP69 2.3 42.0 1.0 CG B:ASP69 2.6 42.9 1.0 PG B:ANP401 3.2 44.8 1.0 CG B:ASP97 3.2 44.1 1.0 O B:HOH501 3.3 34.3 1.0 O1G B:ANP401 3.5 50.3 1.0 O B:HOH520 3.7 39.2 1.0 OD1 B:ASP97 3.8 42.9 1.0 O3G B:ANP401 3.8 48.0 1.0 O B:HOH518 3.9 40.9 1.0 O B:THR68 4.0 43.2 1.0 CB B:ASP69 4.1 39.7 1.0 O B:HOH503 4.1 44.5 1.0 OG B:SER67 4.1 44.7 1.0 O B:HOH507 4.3 42.5 1.0 O B:HOH509 4.4 42.0 1.0 CB B:ASP97 4.4 41.7 1.0 N3B B:ANP401 4.5 47.9 1.0 MG B:MG402 4.7 39.0 1.0 C B:THR68 4.8 41.5 1.0 CA B:ASP69 4.8 39.5 1.0 O B:VAL93 4.8 44.4 1.0

Magnesium binding site 6 out of 6 in the Thil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:50.9 occ:1.00 O1B B:ANP401 2.1 51.9 1.0 O2A B:ANP401 2.3 45.8 1.0 O1G B:ANP401 2.3 50.3 1.0 O B:HOH561 2.4 45.6 1.0 PB B:ANP401 3.3 50.2 1.0 O B:HOH509 3.4 42.0 1.0 PA B:ANP401 3.4 47.5 1.0 PG B:ANP401 3.5 44.8 1.0 O3A B:ANP401 3.7 47.0 1.0 N3B B:ANP401 3.9 47.9 1.0 O3G B:ANP401 3.9 48.0 1.0 O B:HOH568 4.0 61.3 1.0 O1A B:ANP401 4.1 42.5 1.0 O B:HOH537 4.1 58.0 1.0 O B:HOH535 4.3 48.8 1.0 O B:HOH508 4.3 51.3 1.0 O B:HOH543 4.5 53.5 1.0 O2B B:ANP401 4.5 55.5 1.0 O5' B:ANP401 4.7 46.7 1.0 O B:HOH555 4.8 47.7 1.0 O2G B:ANP401 4.8 48.3 1.0

J.Q.Lin, J.Lescar. Thil in Complex with Amp-Pnp To Be Published.