Sodium in PDB 3pgu: PHE3GLU Mutant of Ecfadl

The structure of PHE3GLU Mutant of Ecfadl, PDB code: 3pgu was solved by B.W.Lepore, M.Indic, H.Pham, E.Hearn, D.Patel, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.51 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.200, 65.200, 280.280, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 18

The structure of PHE3GLU Mutant of Ecfadl also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Sodium atom in the PHE3GLU Mutant of Ecfadl (pdb code 3pgu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the PHE3GLU Mutant of Ecfadl, PDB code: 3pgu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the PHE3GLU Mutant of Ecfadl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PHE3GLU Mutant of Ecfadl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na442 b:48.1 occ:1.00 OD1 A:ASN72 3.1 19.8 1.0 O A:PRO54 3.3 14.5 1.0 O A:HOH694 3.4 43.4 1.0 OD1 A:ASP55 3.5 39.1 1.0 O A:HOH695 3.6 74.7 1.0 O A:HOH490 3.7 19.2 1.0 CG A:ASN72 3.8 23.1 1.0 CB A:ASP55 3.9 18.4 1.0 OD2 A:ASP53 4.0 18.7 1.0 CG A:ASP55 4.0 32.5 1.0 CA A:ASP55 4.1 13.7 1.0 ND2 A:ASN72 4.1 29.5 1.0 C A:PRO54 4.3 14.9 1.0 O A:HOH459 4.5 13.4 1.0 N A:ASP55 4.6 11.5 1.0 O A:HOH544 4.7 27.2 1.0 CB A:ASN72 4.8 14.7 1.0 CG A:ASP53 4.9 19.3 1.0 OD2 A:ASP55 5.0 47.3 1.0

Sodium binding site 2 out of 2 in the PHE3GLU Mutant of Ecfadl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of PHE3GLU Mutant of Ecfadl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na445 b:32.4 occ:1.00 OG A:SER67 2.9 18.9 1.0 O A:HOH554 2.9 28.1 1.0 O A:HOH516 2.9 25.9 1.0 CB A:SER67 3.6 16.2 1.0 O A:GLY60 3.7 15.1 1.0 CB A:LYS69 3.9 17.3 1.0 CA A:SER67 4.2 11.9 1.0 N A:LYS69 4.4 13.1 1.0 CD A:LYS69 4.5 31.6 1.0 O A:HOH598 4.6 43.0 1.0 N A:LEU68 4.6 13.0 1.0 OG1 A:THR61 4.7 17.0 1.0 CA A:LYS69 4.7 14.3 1.0 CG A:LYS69 4.7 22.8 1.0 C A:GLY60 4.8 12.7 1.0 C A:SER67 4.9 13.7 1.0

B.W.Lepore, M.Indic, H.Pham, E.M.Hearn, D.R.Patel, B.Van Den Berg. From the Cover: Ligand-Gated Diffusion Across the Bacterial Outer Membrane. Proc.Natl.Acad.Sci.Usa V. 108 10121 2011.
ISSN: ISSN 0027-8424
PubMed: 21593406
DOI: 10.1073/PNAS.1018532108