Sodium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A + Atp, PDB code: 8uch:
Jump to Sodium binding site number: 1; 2; 3;

Sodium 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 Sodium with other atoms in the Na 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:Na410 b:35.3 occ:1.00 O A:HOH614 1.9 35.1 1.0 O A:HOH664 2.4 36.1 1.0 O A:HOH551 2.4 33.2 1.0 O A:PRO148 2.5 15.9 1.0 O A:HOH516 2.8 29.1 1.0 O A:HOH672 2.9 36.1 1.0 O A:HOH685 3.0 49.7 1.0 C A:PRO148 3.6 19.2 1.0 O A:HOH542 3.7 27.2 1.0 O A:VAL154 4.4 28.2 1.0 CB A:PHE318 4.4 22.2 1.0 CA A:PRO148 4.5 14.1 1.0 CA A:VAL154 4.5 26.3 1.0 N A:GLU149 4.5 14.8 1.0 O A:LEU153 4.5 20.7 1.0 CA A:GLU149 4.6 15.8 1.0 CA A:PHE318 4.6 23.8 1.0 C A:VAL154 4.7 26.2 1.0 N A:THR319 4.7 19.5 1.0 N A:SER150 4.8 15.0 1.0 O A:HOH689 4.8 47.8 1.0 O A:LEU317 5.0 29.6 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na411 b:26.7 occ:1.00 O A:HOH523 1.9 48.6 1.0 O1B A:ATP401 2.0 49.8 1.0 O A:HOH510 2.0 51.4 1.0 O2G A:ATP401 2.7 66.2 1.0 PB A:ATP401 3.0 42.7 1.0 O3B A:ATP401 3.3 67.7 1.0 O A:HOH593 3.4 29.1 1.0 PG A:ATP401 3.4 98.0 1.0 O3A A:ATP401 3.5 58.3 1.0 O A:HOH535 3.6 26.7 1.0 NZ A:LYS238 3.7 25.0 0.6 O1G A:ATP401 3.7 62.9 1.0 CD2 A:HIS67 3.8 54.4 1.0 N A:ILE68 3.9 20.9 1.0 NH1 A:ARG112 4.0 23.4 1.0 C5' A:ATP401 4.0 22.5 1.0 CA A:HIS67 4.1 37.1 1.0 NH2 A:ARG112 4.3 30.0 1.0 O2B A:ATP401 4.4 41.4 1.0 O A:ILE68 4.4 20.4 1.0 CB A:HIS67 4.5 35.7 1.0 CG A:HIS67 4.5 53.5 1.0 C A:HIS67 4.5 26.6 1.0 O5' A:ATP401 4.6 34.2 1.0 CZ A:ARG112 4.6 41.7 1.0 PA A:ATP401 4.8 33.7 1.0 O3G A:ATP401 4.8 69.1 1.0 O3' A:ATP401 4.9 22.9 1.0 CE A:LYS238 4.9 22.6 0.6 CA A:ILE68 4.9 15.0 1.0 NE2 A:HIS67 5.0 63.1 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na412 b:27.6 occ:1.00 O A:HOH667 1.9 47.7 1.0 O A:VAL349 2.5 33.2 1.0 O A:HOH711 2.7 53.6 1.0 O A:HOH709 3.4 58.3 1.0 CG1 A:VAL349 3.5 47.6 1.0 C A:VAL349 3.7 29.4 1.0 N A:VAL349 4.3 28.5 1.0 CA A:VAL349 4.4 25.0 1.0 CB A:VAL349 4.6 26.6 1.0 OD1 A:ASP351 4.7 61.6 1.0 N A:LEU350 4.7 26.6 1.0 OE1 A:GLU348 4.8 66.3 1.0 CA A:LEU350 4.9 34.5 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.