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

The structure of Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide, PDB code: 4yel 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)	43.67 / 1.72
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.360, 74.360, 174.679, 90.00, 90.00, 120.00
R / Rfree (%)	13.5 / 17.1

The binding sites of Sodium atom in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide (pdb code 4yel). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide, PDB code: 4yel:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide


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 Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:36.2 occ:1.00 OD1 A:ASN517 2.3 23.1 1.0 O A:HOH1321 2.4 21.6 1.0 O A:HOH1748 3.0 34.8 1.0 O A:HOH1327 3.1 38.1 1.0 CG A:ASN517 3.4 16.0 1.0 ND2 A:ASN517 3.9 17.1 1.0 O A:HOH1538 4.0 19.3 1.0 CB A:ASN517 4.7 12.4 1.0 O A:HOH1567 5.0 16.1 1.0 O A:HOH1363 5.0 13.7 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide


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 Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1014 b:18.5 occ:1.00 O A:HOH1641 2.3 29.6 1.0 O A:SER592 2.4 18.5 1.0 O A:HOH1654 2.4 30.5 1.0 OE1 A:GLN594 2.4 27.6 1.0 O A:HOH1664 2.5 24.6 1.0 O A:ALA565 2.5 10.6 1.0 CD A:GLN594 3.4 23.8 1.0 C A:ALA565 3.4 11.8 1.0 CA A:ALA565 3.6 12.6 1.0 C A:SER592 3.6 16.6 1.0 NE2 A:GLN594 3.7 24.6 1.0 O A:HOH1145 3.9 51.1 1.0 CB A:ALA565 4.0 13.5 1.0 O A:HOH1253 4.1 33.3 1.0 N A:GLN594 4.2 14.2 1.0 CA A:CYS593 4.4 15.0 1.0 N A:CYS593 4.5 15.5 1.0 CA A:SER592 4.6 16.5 1.0 N A:SER566 4.6 10.4 1.0 CG A:GLN594 4.7 20.2 1.0 O A:HOH1789 4.7 30.9 1.0 C A:CYS593 4.8 14.6 1.0 CB A:SER592 4.8 16.6 1.0 O A:HOH1606 4.9 25.1 1.0 O A:PHE564 4.9 14.6 1.0 N A:ALA565 5.0 11.8 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Tailspike Protein Double Mutant D339A/E372A of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1015 b:26.4 occ:1.00 O A:HOH1282 1.9 40.5 1.0 O A:HOH1225 2.1 35.4 1.0 O A:GLY211 2.4 24.9 1.0 O3 A:RAM1000 2.4 20.7 1.0 O2 A:RAM1000 2.5 21.9 1.0 O A:HOH1710 2.5 34.3 1.0 C2 A:RAM1000 3.3 19.8 1.0 C3 A:RAM1000 3.4 19.8 1.0 C A:GLY211 3.5 22.8 1.0 C4 A:RAM1000 4.0 17.3 1.0 CA A:HIS212 4.3 19.5 1.0 N A:HIS212 4.3 20.5 1.0 CA A:GLY211 4.5 24.3 1.0 O A:HOH1569 4.5 16.1 1.0 ND1 A:HIS212 4.6 18.8 1.0 O A:HOH1526 4.6 39.1 1.0 O A:GLY250 4.6 24.6 1.0 C1 A:RAM1000 4.7 19.5 1.0 O4 A:RAM1000 4.7 15.9 1.0 CG A:HIS212 4.9 18.7 1.0 O5 A:RAM1000 5.0 16.6 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.