Sodium in PDB 4xor: Tailspike Protein Double Mutant D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide

The structure of Tailspike Protein Double Mutant D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xor 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)	43.14 / 1.50
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.257, 74.257, 174.512, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / 16.9

The binding sites of Sodium atom in the Tailspike Protein Double Mutant D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide (pdb code 4xor). 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 D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xor:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein Double Mutant D339N/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 D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:22.9 occ:1.00 OD1 A:ASN517 2.2 19.1 1.0 O A:HOH1216 2.3 21.8 1.0 O A:HOH1704 2.6 31.8 1.0 CG A:ASN517 3.3 13.6 1.0 ND2 A:ASN517 3.8 14.5 1.0 O A:HOH1520 3.9 17.5 1.0 CB A:ASN517 4.6 10.9 1.0 O A:HOH1558 4.9 15.0 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein Double Mutant D339N/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 D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:17.5 occ:1.00 O A:HOH1615 2.3 27.7 1.0 O A:HOH1660 2.3 27.7 1.0 O A:SER592 2.3 17.6 1.0 OE1 A:GLN594 2.4 22.1 1.0 O A:ALA565 2.5 10.4 1.0 O A:HOH1673 2.5 21.1 1.0 CD A:GLN594 3.4 21.6 1.0 C A:ALA565 3.4 10.3 1.0 C A:SER592 3.6 15.4 1.0 CA A:ALA565 3.7 11.1 1.0 NE2 A:GLN594 3.8 22.9 1.0 O A:HOH1139 4.0 32.6 1.0 CB A:ALA565 4.1 11.9 1.0 N A:GLN594 4.2 12.7 1.0 CA A:CYS593 4.4 13.3 1.0 N A:CYS593 4.4 13.7 1.0 CA A:SER592 4.5 14.7 1.0 O A:HOH1494 4.7 28.1 1.0 N A:SER566 4.7 10.0 1.0 CG A:GLN594 4.7 18.3 1.0 O A:HOH1745 4.8 33.8 1.0 C A:CYS593 4.8 13.9 1.0 CB A:SER592 4.8 15.3 1.0 O A:PHE564 4.9 12.0 1.0 N A:ALA565 5.0 10.6 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein Double Mutant D339N/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 D339N/E372Q of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1014 b:23.5 occ:1.00 O A:HOH1531 2.0 33.8 1.0 O A:HOH1397 2.2 37.3 1.0 O A:HOH1689 2.2 33.5 1.0 O3 A:RAM1001 2.4 18.4 1.0 O A:GLY211 2.4 23.0 1.0 O2 A:RAM1001 2.5 18.6 1.0 C2 A:RAM1001 3.3 17.1 1.0 C3 A:RAM1001 3.3 17.1 1.0 C A:GLY211 3.6 20.3 1.0 C4 A:RAM1001 3.9 16.4 1.0 O1 A:FMT1011 4.1 19.6 1.0 CA A:HIS212 4.3 17.6 1.0 N A:HIS212 4.4 18.4 1.0 O4 A:RAM1001 4.6 16.0 1.0 CA A:GLY211 4.6 21.5 1.0 ND1 A:HIS212 4.6 16.7 1.0 C1 A:RAM1001 4.7 17.3 1.0 O A:GLY250 4.7 23.8 1.0 O A:HOH1780 4.9 38.1 1.0 CG A:HIS212 5.0 17.1 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.