Atomistry » Sodium » PDB 4xea-4xn0 » 4xm3
Atomistry »
  Sodium »
    PDB 4xea-4xn0 »
      4xm3 »

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

Protein crystallography data

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

Sodium Binding Sites:

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 4xm3

Go back to Sodium Binding Sites List in 4xm3
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 4xm3

Go back to Sodium Binding Sites List in 4xm3
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 4xm3

Go back to Sodium Binding Sites List in 4xm3
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

Reference:

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.
Page generated: Tue Dec 15 09:47:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy