Magnesium in PDB 8uch: Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp

All present enzymatic activity of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp:
6.5.1.3;

The structure of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp, PDB code: 8uch 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)	46.72 / 2.14
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.02, 97.251, 140.101, 90, 90, 90
R / Rfree (%)	17 / 20.5

The structure of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Magnesium atom in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp (pdb code 8uch). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp, PDB code: 8uch:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp


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 K92A + Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:20.0 occ:1.00 O A:HOH557 2.0 14.3 1.0 O A:HOH536 2.0 13.9 1.0 O A:HOH558 2.0 19.0 1.0 O2A A:ATP401 2.1 30.7 1.0 O A:HOH581 2.2 17.4 1.0 O A:HOH544 2.2 11.1 1.0 PA A:ATP401 3.5 33.7 1.0 OE2 A:GLU144 3.9 14.4 1.0 O2B A:ATP401 3.9 41.4 1.0 O1A A:ATP401 3.9 27.6 1.0 O A:HOH600 4.1 27.4 1.0 OE2 A:GLU224 4.1 37.4 1.0 NZ A:LYS238 4.1 21.5 0.4 O A:GLY95 4.2 14.7 1.0 O4' A:ATP401 4.2 11.1 1.0 OD1 A:ASP94 4.3 16.2 1.0 O3A A:ATP401 4.4 58.3 1.0 C4' A:ATP401 4.4 20.9 1.0 OE1 A:GLU224 4.5 28.2 1.0 O5' A:ATP401 4.6 34.2 1.0 C1' A:ATP401 4.6 14.7 1.0 O A:HOH607 4.7 28.3 1.0 CD A:GLU224 4.7 36.4 1.0 N A:GLY95 4.7 13.3 1.0 O A:VAL93 4.7 13.4 1.0 PB A:ATP401 4.9 42.7 1.0 CA A:ASP94 4.9 20.6 1.0

Magnesium binding site 2 out of 3 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp


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 K92A + Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:16.8 occ:1.00 OE2 A:GLU155 1.9 17.7 1.0 O A:HOH599 2.0 21.3 1.0 OD1 A:ASP248 2.0 18.1 1.0 O A:HOH524 2.1 13.3 1.0 OD2 A:ASP94 2.1 17.9 1.0 O A:HOH556 2.1 10.8 1.0 CD A:GLU155 2.8 26.6 1.0 CG A:ASP248 3.1 16.2 1.0 CG A:ASP94 3.1 26.9 1.0 OE1 A:GLU155 3.2 31.1 1.0 OD1 A:ASP94 3.5 16.2 1.0 OD2 A:ASP248 3.5 21.6 1.0 O A:HOH540 3.6 27.1 1.0 O A:HOH697 3.9 44.9 1.0 O A:HOH641 4.0 19.2 1.0 CG A:GLU155 4.1 13.9 1.0 O A:ALA244 4.2 20.0 1.0 CB A:ASP248 4.4 10.1 1.0 CB A:ASP94 4.5 10.8 1.0 OE2 A:GLU224 4.5 37.4 1.0 CA A:ASP248 4.6 11.8 1.0 N A:ASP248 4.7 10.1 1.0 CB A:ALA244 4.9 11.4 1.0 CA A:ALA244 4.9 12.5 1.0

Magnesium binding site 3 out of 3 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp


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 K92A + Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:23.6 occ:1.00 O A:HOH511 1.7 42.5 1.0 O A:HOH504 1.7 36.7 1.0 O A:HOH505 2.1 46.5 1.0 O A:ASP306 2.4 41.5 1.0 O A:SER309 2.4 55.7 1.0 OD1 A:ASP312 2.7 60.1 1.0 OD2 A:ASP312 2.8 70.8 1.0 OD1 A:ASP306 3.1 49.6 1.0 CG A:ASP312 3.1 65.7 1.0 O A:HOH518 3.3 54.1 1.0 C A:ASP306 3.5 28.5 1.0 C A:SER309 3.6 64.2 1.0 O A:HOH696 4.0 52.9 1.0 O A:HOH517 4.1 25.2 1.0 CA A:ASP306 4.2 28.1 1.0 CG A:ASP306 4.3 45.8 1.0 OG A:SER309 4.4 70.3 1.0 N A:GLY310 4.5 57.5 1.0 N A:ILE307 4.5 31.1 1.0 CA A:GLY310 4.5 60.2 1.0 CA A:SER309 4.5 68.9 1.0 N A:SER309 4.6 47.7 1.0 CA A:ILE307 4.6 27.6 1.0 CB A:ASP312 4.6 55.1 1.0 CB A:SER309 4.8 57.8 1.0 CB A:ASP306 4.8 31.1 1.0 C A:ILE307 5.0 29.1 1.0 O A:ASP312 5.0 45.4 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.