Sodium in PDB 4p4m: Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary P/T Complex

The structure of Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary P/T Complex, PDB code: 4p4m was solved by E.Mejia, M.Burak, A.Alonso, V.Larraga, T.A.Kunkel, K.Bebenek, M.Garcia-Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.95 / 1.92
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.680, 108.680, 151.641, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 18.2

The structure of Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary P/T Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary P/T Complex (pdb code 4p4m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary P/T Complex, PDB code: 4p4m:

Sodium binding site 1 out of 1 in the Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary P/T Complex


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 Leishmania Infantum Polymerase Beta: Ternary P/T Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:33.1 occ:1.00 O D:HOH104 2.4 38.0 1.0 O D:HOH110 2.4 48.4 1.0 OP1 D:DT4 2.6 32.7 1.0 O A:THR100 2.6 35.9 1.0 O A:PHE105 2.6 37.2 1.0 O A:VAL102 2.7 28.7 1.0 P D:DT4 3.5 35.2 1.0 OP2 D:DT4 3.5 37.8 1.0 C A:THR100 3.5 38.4 1.0 O A:HOH674 3.5 42.7 1.0 C A:VAL102 3.6 31.9 1.0 C A:PHE105 3.7 34.9 1.0 N A:PHE105 3.9 31.2 1.0 CA A:THR100 4.0 35.8 1.0 CA A:HIS103 4.2 24.9 0.5 O A:HOH699 4.2 45.4 1.0 N A:GLY104 4.2 28.2 1.0 CA A:HIS103 4.2 28.0 0.5 N A:HIS103 4.2 28.5 1.0 CA A:PHE105 4.2 29.9 1.0 N A:VAL102 4.3 33.3 1.0 C A:GLN101 4.3 39.2 1.0 CB A:THR100 4.4 40.3 1.0 O3' D:DG3 4.4 29.9 1.0 N A:GLN101 4.5 35.7 1.0 CA A:VAL102 4.5 30.6 1.0 C A:HIS103 4.6 27.6 1.0 O A:GLN101 4.6 36.5 1.0 CB A:PHE105 4.7 30.2 1.0 N A:GLY106 4.7 34.7 1.0 O5' D:DT4 4.7 33.6 1.0 CA A:GLN101 4.8 34.5 1.0 C A:GLY104 4.8 33.3 1.0 O A:HOH716 4.9 47.9 1.0

E.Mejia, M.Burak, A.Alonso, V.Larraga, T.A.Kunkel, K.Bebenek, M.Garcia-Diaz. Structures of the Leishmania Infantum Polymerase Beta. Dna Repair (Amst.) V. 18 1 2014.
ISSN: ISSN 1568-7856
PubMed: 24666693
DOI: 10.1016/J.DNAREP.2014.03.001