Sodium in PDB 2x85: Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide

The structure of Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide, PDB code: 2x85 was solved by N.K.Lorenzen, J.J.Mueller, 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)	37.13 / 1.50
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.250, 74.250, 174.440, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 19.8

The binding sites of Sodium atom in the Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide (pdb code 2x85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide, PDB code: 2x85:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Tailspike Protein 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 of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1710 b:16.5 occ:1.00 O A:HOH2541 2.3 24.3 1.0 OE1 A:GLN594 2.4 22.3 1.0 O A:SER592 2.4 14.4 1.0 O A:HOH2537 2.4 12.1 1.0 O A:ALA565 2.5 11.1 1.0 O A:HOH2543 2.6 26.5 1.0 CD A:GLN594 3.4 19.6 1.0 C A:ALA565 3.4 10.8 1.0 C A:SER592 3.6 14.3 1.0 CA A:ALA565 3.7 11.2 1.0 NE2 A:GLN594 3.8 25.6 1.0 O A:HOH2544 4.0 27.9 1.0 CB A:ALA565 4.1 12.7 1.0 N A:GLN594 4.3 10.8 1.0 O A:HOH2250 4.4 26.9 1.0 CA A:CYS593 4.4 12.5 1.0 N A:CYS593 4.5 12.0 1.0 CA A:SER592 4.5 14.0 1.0 N A:SER566 4.7 10.1 1.0 CG A:GLN594 4.7 15.9 1.0 O A:HOH2471 4.8 15.8 1.0 C A:CYS593 4.8 12.5 1.0 CB A:SER592 4.8 14.4 1.0 O A:PHE564 4.9 12.6 1.0 N A:ALA565 5.0 11.2 1.0

Sodium binding site 2 out of 4 in the Tailspike Protein 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 of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1711 b:26.3 occ:1.00 O A:HOH2409 2.5 19.9 1.0 O A:HOH2357 2.5 19.0 1.0 O2 A:GLC1720 2.7 13.6 1.0 OH A:TYR393 2.8 15.0 1.0 O5 A:NAG1719 3.1 15.2 1.0 O A:HOH2354 3.1 17.6 1.0 CZ A:TYR393 3.3 12.9 1.0 O A:HOH2358 3.3 12.6 1.0 C1 A:NAG1719 3.5 11.4 1.0 O6 A:NAG1719 3.5 17.9 1.0 C5 A:NAG1719 3.5 14.2 1.0 CE2 A:TYR393 3.6 12.2 1.0 O A:HOH2410 3.7 13.4 1.0 O1 A:NAG1719 3.8 18.4 1.0 C2 A:GLC1720 3.8 12.0 1.0 C1 A:GLC1720 3.9 14.2 1.0 O A:HOH2184 3.9 40.1 1.0 C6 A:NAG1719 4.1 14.8 1.0 CE1 A:TYR393 4.1 12.6 1.0 OD1 A:ASN471 4.5 16.1 1.0 CD2 A:TYR393 4.7 12.2 1.0 C3 A:GLC1720 4.7 13.1 1.0 C2 A:NAG1719 4.9 13.8 1.0 C4 A:NAG1719 4.9 14.2 1.0 OD2 A:ASP339 4.9 23.5 1.0

Sodium binding site 3 out of 4 in the Tailspike Protein 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 of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1712 b:23.1 occ:1.00 O A:GLY211 2.4 20.3 1.0 O2 A:RAM1715 2.4 21.2 1.0 O3 A:RAM1715 2.4 21.2 1.0 C2 A:RAM1715 3.3 22.3 1.0 C3 A:RAM1715 3.3 20.1 1.0 C A:GLY211 3.5 20.2 1.0 O A:HOH2139 3.5 21.2 1.0 C4 A:RAM1715 3.9 20.9 1.0 CA A:HIS212 4.3 18.6 1.0 N A:HIS212 4.3 19.6 1.0 O A:GLY250 4.3 37.3 1.0 ND1 A:HIS212 4.4 18.4 1.0 CA A:GLY211 4.4 21.3 1.0 O A:HOH2679 4.4 26.5 1.0 O A:HOH2680 4.5 26.9 1.0 O4 A:RAM1715 4.6 19.3 1.0 C1 A:RAM1715 4.6 21.3 1.0 CG A:HIS212 4.8 17.3 1.0 CE1 A:HIS212 4.8 18.7 1.0 O A:HOH2142 4.9 8.4 1.0 O5 A:RAM1715 4.9 19.2 1.0

Sodium binding site 4 out of 4 in the Tailspike Protein 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 4 of Tailspike Protein of E. Coli Bacteriophage HK620 in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1713 b:26.4 occ:1.00 OD1 A:ASP339 2.4 24.4 1.0 O1 A:NAG1719 2.4 18.4 1.0 OG A:SER341 2.6 17.5 1.0 O A:HOH2344 2.8 15.4 1.0 O A:HIS340 2.8 14.4 1.0 C A:HIS340 3.2 13.0 1.0 CG A:ASP339 3.4 21.2 1.0 N A:HIS340 3.6 13.0 1.0 O A:ILE367 3.7 15.1 1.0 N A:SER341 3.7 12.5 1.0 C1 A:NAG1719 3.7 11.4 1.0 OE2 A:GLU372 3.8 15.7 1.0 CB A:SER341 3.8 12.3 1.0 N2 A:NAG1719 3.8 13.1 1.0 OD2 A:ASP339 3.9 23.5 1.0 CB A:CYS369 4.0 13.1 1.0 C7 A:NAG1719 4.0 12.0 1.0 CA A:HIS340 4.0 12.2 1.0 O A:HOH2357 4.0 19.0 1.0 CA A:SER341 4.1 12.7 1.0 C8 A:NAG1719 4.2 16.1 1.0 C2 A:NAG1719 4.3 13.8 1.0 N A:CYS369 4.3 13.1 1.0 C A:ASP339 4.4 13.8 1.0 CB A:ASP339 4.5 16.8 1.0 CE1 A:TYR393 4.5 12.6 1.0 O7 A:NAG1719 4.6 17.1 1.0 CA A:ASP339 4.7 15.3 1.0 O5 A:NAG1719 4.8 15.2 1.0 CA A:CYS369 4.8 12.2 1.0 O A:HOH2315 4.9 24.3 1.0 C A:ILE367 4.9 13.9 1.0 CD A:GLU372 5.0 13.7 1.0

N.K.Broeker, U.Gohlke, J.J.Muller, C.Uetrecht, U.Heinemann, R.Seckler, S.Barbirz. Single Amino Acid Exchange in Bacteriophage HK620 Tailspike Protein Results in Thousand-Fold Increase of Its Oligosaccharide Affinity. Glycobiology V. 23 59 2013.
ISSN: ISSN 0959-6658
PubMed: 22923442
DOI: 10.1093/GLYCOB/CWS126