Magnesium in PDB 8uci: Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + Amp

All present enzymatic activity of Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + Amp:
6.5.1.3;

The structure of Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + Amp, PDB code: 8uci 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)	47.08 / 2.14
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.849, 99.722, 143.073, 90, 90, 90
R / Rfree (%)	20.6 / 24

The binding sites of Magnesium atom in the Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + Amp (pdb code 8uci). 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 K238G + Amp, PDB code: 8uci:
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 K238G + 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 K238G + Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:6.9 occ:1.00 O2P A:AMP401 2.1 12.6 1.0 O A:HOH525 2.1 5.5 1.0 O A:HOH726 2.2 9.9 1.0 O A:HOH503 2.2 6.9 1.0 O A:HOH550 2.3 5.8 1.0 O A:HOH545 2.3 6.6 1.0 P A:AMP401 3.5 27.2 1.0 O4' A:AMP401 3.9 5.3 1.0 OE2 A:GLU224 3.9 12.2 1.0 OE2 A:GLU144 4.0 6.1 1.0 NZ A:LYS92 4.1 19.1 1.0 O A:HOH728 4.2 35.6 1.0 OD1 A:ASP94 4.2 5.8 1.0 O A:GLY95 4.2 6.1 1.0 C4' A:AMP401 4.2 7.4 1.0 OE1 A:GLU224 4.2 7.0 1.0 O A:HOH622 4.3 16.7 1.0 O1P A:AMP401 4.4 15.9 1.0 O5' A:AMP401 4.5 23.1 1.0 C1' A:AMP401 4.5 5.3 1.0 CD A:GLU224 4.5 10.5 1.0 O A:HOH676 4.6 6.1 1.0 O A:VAL93 4.7 5.8 1.0 O A:HOH675 4.7 26.1 1.0 N A:GLY95 4.8 5.8 1.0 C5' A:AMP401 4.9 15.8 1.0 O A:HOH619 4.9 22.1 1.0 CA A:ASP94 4.9 8.8 1.0 O A:HOH601 5.0 5.8 1.0

Magnesium binding site 2 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + 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 K238G + Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:6.4 occ:1.00 OE2 A:GLU155 2.1 6.2 1.0 OD2 A:ASP94 2.1 6.2 1.0 O A:HOH633 2.1 9.9 1.0 OD1 A:ASP248 2.2 14.8 1.0 O A:HOH613 2.2 9.3 1.0 O A:HOH601 2.3 5.8 1.0 CD A:GLU155 3.0 14.0 1.0 CG A:ASP248 3.1 12.9 1.0 CG A:ASP94 3.2 8.6 1.0 OD2 A:ASP248 3.4 12.2 1.0 OE1 A:GLU155 3.4 8.8 1.0 OD1 A:ASP94 3.6 5.8 1.0 O A:HOH635 3.8 7.2 1.0 O A:ALA244 3.9 9.2 1.0 O A:HOH659 4.2 15.8 1.0 OE2 A:GLU224 4.2 12.2 1.0 CG A:GLU155 4.3 6.4 1.0 CB A:ASP248 4.4 6.0 1.0 CB A:ASP94 4.5 6.1 1.0 CA A:ALA244 4.6 10.0 1.0 CB A:ALA244 4.6 8.7 1.0 C A:ALA244 4.7 9.3 1.0 CA A:ASP248 4.7 6.3 1.0 N A:ASP248 4.7 8.7 1.0 O A:HOH675 4.7 26.1 1.0 O A:HOH770 4.7 35.8 1.0 CD A:GLU224 4.7 10.5 1.0 O A:HOH503 4.7 6.9 1.0 CG A:GLU224 4.9 8.8 1.0

Magnesium binding site 3 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + 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 K238G + Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg409 b:9.9 occ:1.00 O2P B:AMP401 2.0 20.1 1.0 O B:HOH526 2.0 8.8 1.0 O B:HOH622 2.1 8.3 1.0 O B:HOH507 2.1 8.2 1.0 O B:HOH568 2.1 8.7 1.0 O B:HOH540 2.1 8.2 1.0 P B:AMP401 3.5 43.5 1.0 O4' B:AMP401 3.9 9.1 1.0 OE2 B:GLU144 3.9 8.6 1.0 OE2 B:GLU224 4.0 12.4 1.0 NZ B:LYS92 4.1 14.0 1.0 O B:GLY95 4.1 8.3 1.0 OD1 B:ASP94 4.1 8.3 1.0 O1P B:AMP401 4.2 8.9 1.0 O B:HOH548 4.2 14.3 1.0 C4' B:AMP401 4.2 9.4 1.0 OE1 B:GLU224 4.4 9.2 1.0 C1' B:AMP401 4.5 9.2 1.0 O B:HOH658 4.5 10.7 1.0 O5' B:AMP401 4.5 19.7 1.0 CD B:GLU224 4.6 12.9 1.0 N B:GLY95 4.7 7.9 1.0 O B:VAL93 4.7 8.1 1.0 O B:HOH640 4.7 9.9 1.0 CA B:ASP94 4.9 7.6 1.0 C5' B:AMP401 4.9 11.4 1.0 O B:HOH608 5.0 23.2 1.0 CG B:ASP94 5.0 13.1 1.0

Magnesium binding site 4 out of 4 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K238G + 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 K238G + Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg410 b:9.6 occ:1.00 O B:HOH563 2.1 8.4 1.0 OD2 B:ASP94 2.1 15.1 1.0 O B:HOH549 2.1 7.0 1.0 O B:HOH640 2.2 9.9 1.0 OD1 B:ASP248 2.2 10.3 1.0 OE2 B:GLU155 2.3 11.1 1.0 CG B:ASP94 3.0 13.1 1.0 CD B:GLU155 3.1 13.0 1.0 CG B:ASP248 3.1 10.5 1.0 OD1 B:ASP94 3.2 8.3 1.0 OD2 B:ASP248 3.3 7.6 1.0 OE1 B:GLU155 3.5 9.4 1.0 O B:HOH582 3.9 14.2 1.0 OE2 B:GLU224 4.1 12.4 1.0 CG B:GLU155 4.2 9.8 1.0 O B:HOH667 4.2 9.6 1.0 O B:HOH583 4.2 26.3 1.0 O B:HOH507 4.4 8.2 1.0 CB B:ASP94 4.4 8.9 1.0 O B:HOH751 4.4 34.8 1.0 O B:ALA244 4.5 12.4 1.0 CB B:ASP248 4.5 7.3 1.0 CD B:GLU224 4.7 12.9 1.0 CA B:ASP248 4.9 7.9 1.0 CG B:GLU224 4.9 10.3 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.