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

Protein crystallography data

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

Sodium Binding Sites:

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 6gvp

Go back to Sodium Binding Sites List in 6gvp
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 6gvp

Go back to Sodium Binding Sites List in 6gvp
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 6gvp

Go back to Sodium Binding Sites List in 6gvp
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

Reference:

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
Page generated: Tue Dec 15 12:18:28 2020

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