Sodium in PDB 4p3k: Structure of Ancestral Pyrr Protein (Plumpyrr)

The structure of Structure of Ancestral Pyrr Protein (Plumpyrr), PDB code: 4p3k was solved by T.Perica, Y.Kondo, S.Tiwari, S.Mclaughlin, A.Steward, N.Reuter, J.Clarke, S.A.Teichmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.86 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.960, 57.240, 54.000, 90.00, 127.47, 90.00
R / Rfree (%)	16.4 / 21.2

The binding sites of Sodium atom in the Structure of Ancestral Pyrr Protein (Plumpyrr) (pdb code 4p3k). 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 Structure of Ancestral Pyrr Protein (Plumpyrr), PDB code: 4p3k:

Sodium binding site 1 out of 1 in the Structure of Ancestral Pyrr Protein (Plumpyrr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ancestral Pyrr Protein (Plumpyrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:42.1 occ:1.00 O A:HOH379 2.8 33.6 1.0 OD2 A:ASP106 3.3 25.9 1.0 OD1 A:ASP106 3.5 24.5 1.0 CG A:ASP106 3.7 24.7 1.0 O A:HOH376 3.7 22.7 1.0 O A:HOH387 3.7 32.9 1.0 CB A:ARG43 4.0 20.4 1.0 CE A:LYS41 4.1 43.9 1.0 CB A:LYS41 4.1 28.2 1.0 O A:HOH400 4.1 33.2 1.0 CD A:ARG43 4.2 28.0 1.0 NH1 A:ARG43 4.4 43.2 1.0 CG A:ARG43 4.4 25.4 1.0 CG A:LYS41 4.5 38.2 1.0 N A:ARG43 4.6 22.8 1.0 CA A:ARG43 4.9 20.4 1.0 CD A:LYS41 4.9 41.3 1.0 NZ A:LYS41 4.9 45.6 1.0 CB A:ASP106 4.9 19.6 1.0

T.Perica, Y.Kondo, S.Tiwari, S.Mclaughlin, K.Kemplen, X.Zhang, A.Steward, N.Reuter, J.Clarke, S.A.Teichmann. Evolution of Oligomeric State Through Allosteric Pathways That Mimic Ligand Binding Science 2014.
ISSN: ESSN 1095-9203