Sodium in PDB 6g0x: Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide

The structure of Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 6g0x was solved by U.Gohlke, N.K.Broeker, R.Seckler, S.Barbirz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.21 / 1.41
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.320, 74.320, 174.871, 90.00, 90.00, 120.00
R / Rfree (%)	14.7 / 17.7

The binding sites of Sodium atom in the Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide (pdb code 6g0x). 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 of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 6g0x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein 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 of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:12.3 occ:0.50 OD1 A:ASN517 2.2 20.1 1.0 O A:HOH1241 2.3 22.7 1.0 O A:HOH1789 2.8 35.1 1.0 O A:HOH1203 3.2 34.7 1.0 CG A:ASN517 3.3 13.8 1.0 ND2 A:ASN517 3.7 14.4 1.0 O A:HOH1491 4.0 16.1 1.0 CB A:ASN517 4.5 10.7 1.0 O A:HOH1576 5.0 15.5 1.0 O A:HOH1254 5.0 12.7 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein 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 of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1014 b:16.6 occ:1.00 O A:HOH1659 2.3 25.9 1.0 O A:HOH1683 2.3 25.5 1.0 OE1 A:GLN594 2.3 21.8 1.0 O A:SER592 2.4 15.2 1.0 O A:ALA565 2.5 9.3 1.0 O A:HOH1692 2.5 21.4 1.0 CD A:GLN594 3.4 20.3 1.0 C A:ALA565 3.4 9.3 1.0 CA A:ALA565 3.6 10.2 1.0 C A:SER592 3.6 13.3 1.0 NE2 A:GLN594 3.8 24.6 1.0 O A:HOH1155 3.9 34.8 1.0 CB A:ALA565 4.0 10.9 1.0 N A:GLN594 4.2 11.5 1.0 CA A:CYS593 4.4 12.6 1.0 O A:HOH1845 4.4 38.1 1.0 N A:CYS593 4.5 12.0 1.0 CA A:SER592 4.6 13.1 1.0 N A:SER566 4.6 9.0 1.0 CG A:GLN594 4.6 16.1 1.0 O A:HOH1614 4.7 24.6 1.0 C A:CYS593 4.7 12.6 1.0 O A:HOH1790 4.8 30.9 1.0 CB A:SER592 4.9 13.6 1.0 O A:PHE564 4.9 10.7 1.0 N A:ALA565 5.0 10.0 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein 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 of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1015 b:23.2 occ:1.00 O A:GLY211 2.3 19.8 1.0 O3 A:RAM1001 2.4 18.4 1.0 O A:HOH1735 2.4 31.9 1.0 O A:HOH1168 2.4 30.4 1.0 O A:HOH1581 2.4 36.9 1.0 O2 A:RAM1001 2.5 17.2 1.0 O A:HOH1139 3.1 28.0 1.0 C3 A:RAM1001 3.3 16.8 1.0 C2 A:RAM1001 3.3 16.5 1.0 C A:GLY211 3.5 18.8 1.0 C4 A:RAM1001 3.9 15.1 1.0 CA A:HIS212 4.3 16.2 1.0 N A:HIS212 4.3 17.4 1.0 O A:HOH1642 4.5 37.3 1.0 CA A:GLY211 4.5 20.6 1.0 ND1 A:HIS212 4.5 16.5 1.0 O A:HOH1313 4.5 35.5 1.0 O A:HOH1671 4.5 13.2 1.0 O4 A:RAM1001 4.6 14.4 1.0 O A:GLY250 4.7 21.2 1.0 C1 A:RAM1001 4.7 16.2 1.0 CG A:HIS212 4.9 15.7 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