Sodium in PDB 4xlf: Tailspike Protein Double Mutant D339N/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide

The structure of Tailspike Protein Double Mutant D339N/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xlf 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)	43.17 / 1.75
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.279, 74.279, 174.726, 90.00, 90.00, 120.00
R / Rfree (%)	13.9 / 17.5

The binding sites of Sodium atom in the Tailspike Protein Double Mutant D339N/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide (pdb code 4xlf). 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/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xlf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein Double Mutant D339N/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 D339N/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:36.9 occ:1.00 OD1 A:ASN517 2.3 21.7 1.0 O A:HOH1299 2.4 22.8 1.0 O A:HOH1678 2.9 31.1 1.0 O A:HOH1184 3.0 37.6 1.0 CG A:ASN517 3.4 14.9 1.0 ND2 A:ASN517 3.9 16.1 1.0 O A:HOH1514 4.1 17.7 1.0 CB A:ASN517 4.7 12.1 1.0 O A:HOH1481 5.0 14.2 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein Double Mutant D339N/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 D339N/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:17.3 occ:1.00 O A:HOH1623 2.3 27.0 1.0 O A:HOH1589 2.3 30.7 1.0 OE1 A:GLN594 2.3 23.4 1.0 O A:SER592 2.5 17.6 1.0 O A:ALA565 2.5 9.8 1.0 O A:HOH1606 2.6 21.5 1.0 CD A:GLN594 3.3 21.2 1.0 C A:ALA565 3.4 10.3 1.0 C A:SER592 3.7 15.8 1.0 CA A:ALA565 3.7 10.6 1.0 NE2 A:GLN594 3.7 23.4 1.0 CB A:ALA565 4.1 11.1 1.0 N A:GLN594 4.2 12.9 1.0 CA A:CYS593 4.5 13.4 1.0 N A:CYS593 4.5 14.0 1.0 CA A:SER592 4.6 16.4 1.0 N A:SER566 4.7 9.6 1.0 CG A:GLN594 4.7 18.4 1.0 C A:CYS593 4.8 13.6 1.0 O A:HOH1731 4.9 34.9 1.0 CB A:SER592 4.9 16.6 1.0 O A:HOH1388 5.0 26.9 1.0 O A:PHE564 5.0 12.2 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein Double Mutant D339N/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 3 of Tailspike Protein Double Mutant D339N/E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:20.9 occ:1.00 O A:HOH1168 2.0 30.3 1.0 O A:HOH1154 2.2 23.3 1.0 O A:HOH1635 2.3 36.9 1.0 O A:GLY211 2.4 21.0 1.0 O3 A:RAM1001 2.4 18.1 1.0 O2 A:RAM1001 2.4 18.1 1.0 O A:HOH1116 3.2 32.5 1.0 C2 A:RAM1001 3.4 16.9 1.0 C3 A:RAM1001 3.4 17.2 1.0 C A:GLY211 3.5 20.1 1.0 C4 A:RAM1001 3.9 16.2 1.0 CA A:HIS212 4.3 17.7 1.0 N A:HIS212 4.3 18.5 1.0 ND1 A:HIS212 4.5 17.3 1.0 CA A:GLY211 4.5 22.3 1.0 O A:GLY250 4.6 24.4 1.0 O4 A:RAM1001 4.6 15.8 1.0 O A:HOH1580 4.6 11.8 1.0 C1 A:RAM1001 4.7 17.4 1.0 O A:HOH1428 4.7 35.8 1.0 CG A:HIS212 4.8 17.4 1.0 CE1 A:HIS212 5.0 17.5 1.0 O5 A:RAM1001 5.0 15.4 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.