Sodium in PDB 4yej: Tailspike Protein Double Mutant D339A/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide

The structure of Tailspike Protein Double Mutant D339A/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4yej 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)	43.68 / 1.40
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.339, 74.339, 174.703, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 17.2

The binding sites of Sodium atom in the Tailspike Protein Double Mutant D339A/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide (pdb code 4yej). 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/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4yej:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein Double Mutant D339A/E372Q 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/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:15.8 occ:1.00 O A:HOH1677 2.3 23.5 1.0 O A:SER592 2.3 14.6 1.0 OE1 A:GLN594 2.4 21.6 1.0 O A:HOH1724 2.4 25.9 1.0 O A:ALA565 2.4 9.2 1.0 O A:HOH1738 2.5 19.8 1.0 C A:ALA565 3.4 9.1 1.0 CD A:GLN594 3.4 21.1 1.0 C A:SER592 3.6 13.0 1.0 CA A:ALA565 3.6 9.6 1.0 NE2 A:GLN594 3.8 23.3 1.0 O A:HOH1128 3.8 39.1 1.0 CB A:ALA565 4.0 10.1 1.0 N A:GLN594 4.2 11.1 1.0 CA A:CYS593 4.4 11.6 1.0 N A:CYS593 4.4 11.0 1.0 CA A:SER592 4.5 12.5 1.0 N A:SER566 4.6 8.4 1.0 CG A:GLN594 4.7 16.0 1.0 O A:HOH1893 4.7 37.7 1.0 O A:HOH1874 4.7 30.7 1.0 C A:CYS593 4.7 11.7 1.0 O A:HOH1493 4.8 25.1 1.0 O A:PHE564 4.8 10.4 1.0 CB A:SER592 4.9 12.9 1.0 N A:ALA565 5.0 9.3 1.0 CB A:GLN594 5.0 12.6 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein Double Mutant D339A/E372Q 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/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:22.3 occ:1.00 O A:HOH1247 2.0 38.2 1.0 O A:HOH1144 2.3 31.4 1.0 O A:GLY211 2.3 19.7 1.0 O A:HOH1762 2.4 32.3 1.0 O3 A:RAM1000 2.4 17.2 1.0 O2 A:RAM1000 2.5 18.6 1.0 C3 A:RAM1000 3.4 15.4 1.0 C2 A:RAM1000 3.4 16.2 1.0 C A:GLY211 3.5 19.1 1.0 C4 A:RAM1000 3.9 15.0 1.0 N A:HIS212 4.3 18.1 1.0 CA A:HIS212 4.3 16.8 1.0 O A:HOH1346 4.4 35.0 1.0 O A:HOH1666 4.4 36.1 1.0 CA A:GLY211 4.4 20.8 1.0 O A:GLY250 4.5 23.9 1.0 O A:HOH1690 4.6 12.8 1.0 ND1 A:HIS212 4.6 15.9 1.0 O4 A:RAM1000 4.6 15.4 1.0 C1 A:RAM1000 4.6 15.5 1.0 CG A:HIS212 4.9 16.5 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein Double Mutant D339A/E372Q 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 3 of Tailspike Protein Double Mutant D339A/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:20.9 occ:1.00 OD1 A:ASN517 2.2 18.2 1.0 O A:HOH1288 2.3 20.2 1.0 O A:HOH1857 2.9 33.9 1.0 O A:HOH1382 3.1 29.8 1.0 CG A:ASN517 3.3 12.6 1.0 ND2 A:ASN517 3.7 13.4 1.0 O A:HOH1444 4.0 14.7 1.0 CB A:ASN517 4.6 9.2 1.0 O A:HOH1605 4.9 14.2 1.0 O A:HOH1310 5.0 12.1 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.