Sodium in PDB 3e9l: Crystal Structure of Human PRP8, Residues 1755-2016

The structure of Crystal Structure of Human PRP8, Residues 1755-2016, PDB code: 3e9l was solved by V.Pena, A.Rozov, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.95
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.426, 83.426, 96.263, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.8

The structure of Crystal Structure of Human PRP8, Residues 1755-2016 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human PRP8, Residues 1755-2016 (pdb code 3e9l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human PRP8, Residues 1755-2016, PDB code: 3e9l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human PRP8, Residues 1755-2016


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human PRP8, Residues 1755-2016 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:34.2 occ:1.00 O A:HOH2036 2.2 9.7 0.3 O A:LEU1889 2.3 40.8 1.0 O A:HOH2295 2.3 46.1 1.0 O A:HOH2249 2.5 53.3 1.0 O A:SER1887 2.6 38.4 1.0 OE1 A:GLN1890 2.6 46.8 1.0 C A:LEU1889 3.5 39.7 1.0 CD A:GLN1890 3.5 45.4 1.0 C A:SER1887 3.6 38.6 1.0 O A:HOH2034 4.0 30.6 1.0 C A:GLU1888 4.0 39.6 1.0 N A:LEU1889 4.2 39.3 1.0 NE2 A:GLN1890 4.2 44.3 1.0 CA A:GLN1890 4.2 38.6 1.0 O A:THR1864 4.2 35.1 1.0 CB A:GLN1890 4.3 39.1 1.0 O A:GLU1888 4.3 39.3 1.0 N A:GLN1890 4.3 39.1 1.0 CA A:GLU1888 4.4 39.8 1.0 N A:GLU1888 4.4 38.5 1.0 CB A:SER1887 4.4 38.7 1.0 CA A:LEU1889 4.5 39.8 1.0 CG A:GLN1890 4.5 41.3 1.0 CA A:SER1887 4.5 38.3 1.0 OG A:SER1887 4.6 40.2 1.0 O A:HOH2020 4.6 20.6 1.0 O A:HOH2251 4.6 62.8 1.0 N A:SER1887 4.9 37.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human PRP8, Residues 1755-2016


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human PRP8, Residues 1755-2016 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2017 b:43.6 occ:1.00 O A:HOH2071 2.3 39.5 1.0 O A:HOH2060 2.3 34.6 1.0 O A:HOH2277 2.4 48.2 1.0 O A:HOH2183 2.4 49.2 1.0 O A:HOH2167 2.5 46.4 1.0 O A:HOH2067 2.6 30.2 1.0 O A:HOH2111 3.7 39.6 1.0 O A:HOH2146 3.7 43.3 1.0 OD1 A:ASP1973 3.9 41.0 1.0 O A:LEU1971 3.9 35.1 1.0 O A:HOH2299 4.1 42.5 1.0 O A:HOH2075 4.2 33.5 1.0 O A:HOH2063 4.2 38.1 1.0 OG1 A:THR1926 5.0 37.3 1.0

V.Pena, A.Rozov, P.Fabrizio, R.Luhrmann, M.C.Wahl. Structure and Function of An Rnase H Domain at the Heart of the Spliceosome. Embo J. V. 27 2929 2008.
ISSN: ISSN 0261-4189
PubMed: 18843295
DOI: 10.1038/EMBOJ.2008.209