Sodium in PDB 4xmy: Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide

The structure of Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xmy was solved by U.Gohlke, N.K.Broeker, U.Heinemann, R.Seckler, S.Barbirz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.64 / 1.45
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.234, 74.234, 174.578, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 17.5

The binding sites of Sodium atom in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide (pdb code 4xmy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xmy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:21.4 occ:1.00 O A:HOH1130 1.7 33.0 1.0 O A:HOH1164 2.2 31.2 1.0 O3 A:RAM1001 2.3 17.3 1.0 O A:GLY211 2.3 20.9 1.0 O2 A:RAM1001 2.4 18.6 1.0 O A:HOH1748 2.6 30.7 1.0 C3 A:RAM1001 3.2 17.0 1.0 C2 A:RAM1001 3.2 16.9 1.0 O A:HOH1143 3.3 39.1 1.0 C A:GLY211 3.5 20.0 1.0 C4 A:RAM1001 3.9 15.5 1.0 N A:HIS212 4.2 18.3 1.0 CA A:HIS212 4.2 17.3 1.0 O A:HOH1398 4.3 35.4 1.0 O A:HOH1651 4.4 34.3 1.0 CA A:GLY211 4.5 21.4 1.0 O A:HOH1678 4.5 12.6 1.0 ND1 A:HIS212 4.5 16.5 1.0 O4 A:RAM1001 4.6 15.0 1.0 O A:GLY250 4.6 24.3 1.0 C1 A:RAM1001 4.6 15.8 1.0 CG A:HIS212 4.8 16.7 1.0 CE1 A:HIS212 5.0 17.1 1.0

Sodium binding site 2 out of 2 in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1014 b:17.2 occ:1.00 O A:HOH1687 2.3 25.7 1.0 OE1 A:GLN594 2.4 22.2 1.0 O A:SER592 2.4 15.6 1.0 O A:HOH1708 2.4 30.1 1.0 O A:ALA565 2.4 10.2 1.0 O A:HOH1709 2.5 20.4 1.0 C A:ALA565 3.4 10.5 1.0 CD A:GLN594 3.4 20.2 1.0 C A:SER592 3.6 13.8 1.0 CA A:ALA565 3.6 10.9 1.0 NE2 A:GLN594 3.8 21.6 1.0 O A:HOH1177 4.0 32.3 1.0 CB A:ALA565 4.0 11.6 1.0 N A:GLN594 4.2 11.7 1.0 CA A:CYS593 4.4 12.8 1.0 N A:CYS593 4.4 12.3 1.0 O A:HOH1875 4.4 38.6 1.0 CA A:SER592 4.5 13.3 1.0 N A:SER566 4.6 9.8 1.0 O A:HOH1817 4.7 31.6 1.0 CG A:GLN594 4.7 16.6 1.0 O A:HOH1648 4.7 25.0 1.0 C A:CYS593 4.7 12.8 1.0 CB A:SER592 4.8 14.0 1.0 O A:PHE564 4.9 11.5 1.0 N A:ALA565 4.9 10.5 1.0

U.Gohlke, N.K.Broeker, S.Kunstmann, M.Santer, U.Heinemann, R.Lipowski, R.Seckler, S.Barbirz. Enthalpic Cost of Water Removal From A Hydrophobic Glucose Binding Cavity on HK620 Tailspike Protein. To Be Published.