Sodium in PDB 4xm3: Tailspike Protein Mutant E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide

The structure of Tailspike Protein Mutant E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xm3 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)	43.26 / 1.27
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.354, 74.354, 175.187, 90.00, 90.00, 120.00
R / Rfree (%)	13.4 / 17

The binding sites of Sodium atom in the Tailspike Protein Mutant E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide (pdb code 4xm3). 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 E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide, PDB code: 4xm3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tailspike Protein Mutant 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 Mutant E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1015 b:20.7 occ:1.00 O A:GLY211 2.3 20.2 1.0 O A:HOH1148 2.3 27.7 1.0 O3 A:RAM1001 2.3 17.1 1.0 O2 A:RAM1001 2.4 15.9 1.0 O A:HOH1635 2.5 29.0 1.0 O A:HOH1568 2.5 33.0 1.0 O A:HOH1169 3.1 26.8 1.0 C3 A:RAM1001 3.3 15.3 1.0 C2 A:RAM1001 3.3 14.9 1.0 C A:GLY211 3.5 17.6 1.0 C4 A:RAM1001 3.8 13.6 1.0 CA A:HIS212 4.2 13.3 1.0 O A:HOH1678 4.2 22.9 1.0 N A:HIS212 4.3 15.1 1.0 O A:HOH1213 4.4 33.2 1.0 O A:HOH1592 4.5 13.5 1.0 ND1 A:HIS212 4.5 14.4 1.0 CA A:GLY211 4.5 18.2 1.0 O4 A:RAM1001 4.6 13.9 1.0 O A:GLY250 4.6 23.4 1.0 C1 A:RAM1001 4.7 14.8 1.0 CG A:HIS212 4.9 15.1 1.0 CE1 A:HIS212 5.0 14.1 1.0 O5 A:RAM1001 5.0 13.4 1.0

Sodium binding site 2 out of 3 in the Tailspike Protein Mutant 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 Mutant E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1016 b:22.3 occ:1.00 ND2 A:ASN517 2.2 18.6 1.0 O A:HOH1440 2.3 22.4 1.0 O2 A:FMT1011 2.8 31.9 1.0 C A:FMT1011 2.8 25.7 1.0 O1 A:FMT1011 3.3 27.9 1.0 CG A:ASN517 3.4 12.2 1.0 OD1 A:ASN517 3.8 15.3 1.0 O A:HOH1123 3.9 16.2 1.0 CB A:ASN517 4.5 8.8 1.0 O A:HOH1118 4.7 31.7 1.0 O A:HOH1562 4.9 15.6 1.0

Sodium binding site 3 out of 3 in the Tailspike Protein Mutant 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 Mutant E372A of E. Coli Bacteriophage HK620 in Complex with Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1017 b:15.9 occ:1.00 O A:HOH1606 2.3 27.3 1.0 O A:SER592 2.4 14.9 1.0 O A:HOH1613 2.4 26.8 1.0 OE1 A:GLN594 2.4 19.1 1.0 O A:ALA565 2.5 8.4 1.0 O A:HOH1611 2.5 21.0 1.0 CD A:GLN594 3.4 16.5 1.0 C A:ALA565 3.4 8.7 1.0 C A:SER592 3.6 12.1 1.0 CA A:ALA565 3.7 9.7 1.0 NE2 A:GLN594 3.7 27.1 1.0 CB A:ALA565 4.1 11.4 1.0 N A:GLN594 4.2 9.5 1.0 CA A:CYS593 4.4 10.5 1.0 N A:CYS593 4.4 10.5 1.0 CA A:SER592 4.6 12.2 1.0 O A:HOH1680 4.6 34.4 1.0 N A:SER566 4.6 7.8 1.0 CG A:GLN594 4.7 15.8 1.0 C A:CYS593 4.8 10.0 1.0 O A:HOH1489 4.8 24.4 1.0 O A:PHE564 4.9 10.8 1.0 CB A:SER592 4.9 14.1 1.0 N A:ALA565 5.0 8.6 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.