Sodium in PDB 4p4o: Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary Gap Complex

The structure of Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary Gap Complex, PDB code: 4p4o was solved by E.Mejia, M.Burak, A.Alonso, V.Larraga, T.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)	47.06 / 2.30
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 (%)	19.4 / 22.8

The structure of Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary Gap 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 Gap Complex (pdb code 4p4o). 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 Leishmania Infantum Polymerase Beta: Ternary Gap Complex, PDB code: 4p4o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary Gap 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 Gap Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:19.1 occ:1.00 O A:THR100 2.6 23.5 1.0 OP1 E:DA5 2.7 17.8 1.0 O A:PHE105 2.8 22.9 1.0 O A:VAL102 3.0 20.4 1.0 O A:HOH632 3.2 33.8 1.0 C A:THR100 3.5 25.9 1.0 P E:DA5 3.7 18.3 1.0 C A:PHE105 3.7 27.4 1.0 C A:VAL102 3.7 22.2 1.0 OP2 E:DA5 3.8 27.7 1.0 CA A:THR100 4.0 23.3 1.0 N A:PHE105 4.1 20.3 1.0 N A:VAL102 4.2 22.1 1.0 N A:HIS103 4.3 19.3 1.0 C A:GLN101 4.3 23.2 1.0 CA A:HIS103 4.4 16.9 1.0 N A:GLY104 4.4 18.3 1.0 CB A:THR100 4.5 28.9 1.0 CA A:PHE105 4.5 22.2 1.0 N A:GLN101 4.5 24.3 1.0 N A:GLY106 4.6 31.6 1.0 CA A:VAL102 4.6 20.2 1.0 O A:GLN101 4.7 23.8 1.0 CA A:GLN101 4.8 24.7 1.0 O3' E:DT4 4.8 30.3 1.0 O5' E:DA5 4.8 19.9 1.0 C A:HIS103 4.8 21.1 1.0 CA A:GLY106 4.8 25.0 1.0 CB A:PHE105 5.0 21.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leishmania Infantum Polymerase Beta: Ternary Gap Complex


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 Leishmania Infantum Polymerase Beta: Ternary Gap Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Na101 b:40.1 occ:1.00 O F:HOH205 2.0 29.6 1.0 OP1 F:DT10 2.2 22.4 1.0 O F:HOH209 2.2 17.8 1.0 O A:HOH508 2.3 20.9 1.0 O F:HOH213 2.7 28.4 1.0 P F:DT10 3.2 15.5 1.0 OP2 F:DT10 3.7 13.6 1.0 O5' F:DT10 3.8 18.1 1.0 O A:GLN237 4.1 12.2 1.0 O F:HOH201 4.2 29.5 1.0 C5' F:DT10 4.3 14.0 1.0 O A:HOH609 4.3 25.6 1.0 N A:GLN237 4.5 17.6 1.0 O A:HOH576 4.5 19.3 1.0 O F:HOH220 4.6 41.9 1.0 O3' F:DC9 4.6 17.9 1.0 C3' F:DT10 5.0 23.9 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