Magnesium in PDB 8uce: Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp

The structure of Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp, PDB code: 8uce was solved by M.D.Rousseau, J.L.Hicks, T.Oulavallickal, A.Williamson, V.L.Arcus, M.W.Patrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.93 / 2.12
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.216, 98.799, 142.977, 90, 90, 90
R / Rfree (%)	18.9 / 23.7

The binding sites of Magnesium atom in the Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp (pdb code 8uce). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp, PDB code: 8uce:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:16.8 occ:1.00 O A:HOH592 1.9 17.9 1.0 O2P A:AMP401 2.0 15.4 1.0 O A:HOH538 2.1 15.4 1.0 O A:HOH506 2.1 15.7 1.0 O A:HOH525 2.1 15.5 1.0 O A:HOH562 2.3 17.1 1.0 P A:AMP401 3.4 16.2 1.0 NZ A:LYS92 3.7 16.8 1.0 OE2 A:GLU144 4.0 15.8 1.0 O4' A:AMP401 4.0 15.5 1.0 O A:HOH563 4.0 45.7 1.0 O A:HOH565 4.1 17.6 1.0 O A:GLY95 4.1 15.8 1.0 OE2 A:GLU224 4.1 16.2 1.0 OD1 A:ASP94 4.2 16.4 1.0 O1P A:AMP401 4.3 20.0 1.0 C4' A:AMP401 4.3 15.4 1.0 OE1 A:GLU224 4.4 18.0 1.0 O5' A:AMP401 4.5 17.2 1.0 C1' A:AMP401 4.6 16.9 1.0 CD A:GLU224 4.7 21.1 1.0 O A:VAL93 4.8 16.7 1.0 N A:GLY95 4.8 16.8 1.0 O A:HOH514 4.8 27.6 1.0 O A:HOH596 4.9 18.7 1.0 CA A:ASP94 5.0 18.2 1.0

Magnesium binding site 2 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:24.7 occ:1.00 OE2 A:GLU155 2.0 17.1 1.0 O A:HOH605 2.1 22.5 1.0 O A:HOH585 2.2 20.2 1.0 OD2 A:ASP94 2.2 18.2 1.0 OD1 A:ASP248 2.2 24.1 1.0 O A:HOH583 2.3 19.8 1.0 CD A:GLU155 2.9 21.0 1.0 CG A:ASP248 3.2 19.5 1.0 CG A:ASP94 3.2 25.9 1.0 OE1 A:GLU155 3.3 22.9 1.0 OD2 A:ASP248 3.5 20.4 1.0 OD1 A:ASP94 3.5 16.4 1.0 O A:HOH621 3.8 17.2 1.0 O A:HOH632 3.9 28.2 1.0 O A:HOH711 4.1 48.8 1.0 CG A:GLU155 4.2 16.2 1.0 O A:ALA244 4.3 16.4 1.0 OE2 A:GLU224 4.5 16.2 1.0 CB A:ASP248 4.5 15.4 1.0 CB A:ASP94 4.5 17.8 1.0 CA A:ASP248 4.7 15.6 1.0 CG A:GLU224 4.8 19.7 1.0 N A:ASP248 4.8 15.7 1.0 CD A:GLU224 4.8 21.1 1.0 CA A:ALA244 5.0 16.9 1.0

Magnesium binding site 3 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:14.3 occ:1.00 O B:HOH584 1.9 14.4 1.0 O B:HOH530 2.0 14.5 1.0 O1P B:AMP401 2.1 19.6 1.0 O B:HOH503 2.1 14.0 1.0 O B:HOH534 2.1 14.1 1.0 O B:HOH546 2.2 14.8 1.0 P B:AMP401 3.4 16.7 1.0 NZ B:LYS92 3.7 16.9 1.0 OE2 B:GLU144 4.0 14.5 1.0 O4' B:AMP401 4.1 14.6 1.0 OE2 B:GLU224 4.1 20.5 1.0 OD1 B:ASP94 4.1 19.1 1.0 O B:HOH539 4.1 21.7 1.0 O B:GLY95 4.1 14.4 1.0 OE1 B:GLU224 4.2 21.4 1.0 O B:HOH617 4.3 32.0 1.0 O2P B:AMP401 4.3 19.8 1.0 C4' B:AMP401 4.3 14.8 1.0 O5' B:AMP401 4.6 15.8 1.0 C1' B:AMP401 4.6 14.7 1.0 CD B:GLU224 4.6 24.3 1.0 O B:HOH526 4.7 33.3 1.0 N B:GLY95 4.7 14.1 1.0 NH1 B:ARG112 4.8 45.6 1.0 O B:VAL93 4.8 15.9 1.0 CA B:ASP94 5.0 16.4 1.0

Magnesium binding site 4 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermophilic Rna Ligase From Palaeococcus Pacificus + Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:21.4 occ:1.00 O B:HOH538 2.0 14.5 1.0 O B:HOH559 2.1 17.5 1.0 OD2 B:ASP94 2.1 21.2 1.0 OE2 B:GLU155 2.1 23.1 1.0 O B:HOH658 2.2 20.4 1.0 OD1 B:ASP248 2.3 24.9 1.0 CG B:ASP94 3.0 21.1 1.0 CD B:GLU155 3.1 24.1 1.0 CG B:ASP248 3.2 19.1 1.0 OD1 B:ASP94 3.3 19.1 1.0 OD2 B:ASP248 3.4 18.3 1.0 OE1 B:GLU155 3.5 19.8 1.0 O B:HOH554 3.7 29.2 1.0 O B:HOH619 4.1 21.2 1.0 OE2 B:GLU224 4.2 20.5 1.0 CG B:GLU155 4.3 19.4 1.0 CB B:ASP94 4.4 19.1 1.0 O B:HOH503 4.5 14.0 1.0 CB B:ASP248 4.6 13.5 1.0 CD B:GLU224 4.6 24.3 1.0 O B:ALA244 4.6 19.8 1.0 CG B:GLU224 4.7 18.9 1.0 CA B:ASP248 4.9 17.8 1.0

M.D.Rousseau, J.L.Hicks, T.Oulavallickal, A.Williamson, V.L.Arcus, M.W.Patrick. Characterisation and Engineering of A Thermophilic Rna Ligase From Palaeococcus Pacificus To Be Published.