Sodium in PDB 6gvp: Tailspike Protein Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide

The structure of Tailspike Protein Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide, PDB code: 6gvp was solved by Y.Roske, U.Gohlke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.78 / 1.71
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.125, 74.125, 175.122, 90.00, 90.00, 120.00
R / Rfree (%)	13.6 / 17.4

The binding sites of Sodium atom in the Tailspike Protein Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide (pdb code 6gvp). 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 Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide, PDB code: 6gvp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein Mutant E372Q (Delta N471/S472) 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 Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:20.1 occ:1.00 O A:HOH1649 2.3 27.8 1.0 OE1 A:GLN594 2.3 27.9 1.0 O A:HOH1625 2.4 43.7 1.0 O A:SER592 2.4 17.0 1.0 O A:HOH1650 2.5 27.5 1.0 O A:ALA565 2.5 12.0 1.0 CD A:GLN594 3.4 23.9 1.0 C A:ALA565 3.4 12.4 1.0 CA A:ALA565 3.6 12.9 1.0 C A:SER592 3.7 16.3 1.0 NE2 A:GLN594 3.8 25.7 1.0 CB A:ALA565 4.0 13.3 1.0 O A:HOH1426 4.0 36.5 1.0 N A:GLN594 4.2 14.8 1.0 CA A:CYS593 4.4 15.3 1.0 N A:CYS593 4.5 15.3 1.0 CA A:SER592 4.6 16.4 1.0 N A:SER566 4.6 11.9 1.0 CG A:GLN594 4.7 20.5 1.0 O A:HOH1807 4.7 36.6 1.0 O A:HOH1268 4.8 26.6 1.0 C A:CYS593 4.8 15.5 1.0 O A:PHE564 4.9 14.1 1.0 CB A:SER592 4.9 17.0 1.0 CB A:GLN594 5.0 17.4 1.0 N A:ALA565 5.0 12.9 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein Mutant E372Q (Delta N471/S472) 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 Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:26.6 occ:1.00 OD1 A:ASN517 2.2 20.0 1.0 O A:HOH1406 2.4 21.8 1.0 O A:HOH1668 2.7 34.1 1.0 CG A:ASN517 3.3 15.3 1.0 ND2 A:ASN517 3.8 15.2 1.0 O A:HOH1394 4.0 21.6 1.0 CB A:ASN517 4.6 13.4 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein Mutant E372Q (Delta N471/S472) 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 Mutant E372Q (Delta N471/S472) of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:26.3 occ:1.00 O A:HOH1437 2.0 34.5 1.0 O A:HOH1425 2.1 33.5 1.0 O A:GLY211 2.4 23.7 1.0 O A:HOH1667 2.4 41.0 1.0 O3 A:RAM1001 2.5 21.0 1.0 O2 A:RAM1001 2.6 22.2 1.0 C2 A:RAM1001 3.3 20.3 1.0 C3 A:RAM1001 3.4 20.3 1.0 C A:GLY211 3.4 22.8 1.0 O A:HOH1197 3.7 33.6 1.0 C4 A:RAM1001 3.9 19.0 1.0 N A:HIS212 4.2 21.8 1.0 CA A:HIS212 4.2 20.9 1.0 O A:HOH1131 4.4 27.0 1.0 CA A:GLY211 4.4 23.8 1.0 ND1 A:HIS212 4.4 21.2 1.0 O4 A:RAM1001 4.5 18.5 1.0 O A:HOH1311 4.6 41.8 1.0 O A:GLY250 4.6 28.5 1.0 C1 A:RAM1001 4.7 19.3 1.0 CG A:HIS212 4.8 20.8 1.0 CE1 A:HIS212 4.9 21.5 1.0 O5 A:RAM1001 5.0 18.1 1.0

S.Kunstmann, U.Gohlke, N.K.Broeker, Y.Roske, U.Heinemann, M.Santer, S.Barbirz. Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in An Extended Protein Binding Site. J. Am. Chem. Soc. V. 140 10447 2018.
ISSN: ESSN 1520-5126
PubMed: 30044908
DOI: 10.1021/JACS.8B03719