Atomistry » Sodium » PDB 4u9u-4us7 » 4ue8
Atomistry »
  Sodium »
    PDB 4u9u-4us7 »
      4ue8 »

Sodium in PDB 4ue8: Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor

Protein crystallography data

The structure of Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor, PDB code: 4ue8 was solved by D.Peter, O.Weichenrieder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.645 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.450, 73.290, 38.260, 90.00, 112.49, 90.00
R / Rfree (%) 14.52 / 16.14

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor (pdb code 4ue8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor, PDB code: 4ue8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ue8

Go back to Sodium Binding Sites List in 4ue8
Sodium binding site 1 out of 2 in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1235

b:43.9
occ:1.00
OD2 A:ASP178 2.4 37.3 1.0
HD2 A:HIS176 2.5 25.6 1.0
OD1 A:ASP178 2.7 36.7 1.0
CG A:ASP178 2.9 33.1 1.0
HB3 A:HIS176 3.2 22.9 1.0
CD2 A:HIS176 3.3 21.3 1.0
HA A:HIS176 3.3 21.9 1.0
HG2 A:GLN179 3.3 23.6 1.0
CB A:HIS176 3.8 19.0 1.0
CG A:HIS176 3.8 18.6 1.0
HG3 A:GLN179 3.9 23.6 1.0
CA A:HIS176 4.0 18.2 1.0
CG A:GLN179 4.0 19.6 1.0
HB3 A:ALA206 4.1 19.4 1.0
H A:GLN179 4.2 23.7 1.0
HD22 A:ASN203 4.3 27.6 1.0
CB A:ASP178 4.4 24.4 1.0
NE2 A:HIS176 4.4 23.1 1.0
HB2 A:GLN179 4.5 20.7 1.0
O A:HIS176 4.5 19.1 1.0
C A:HIS176 4.6 18.9 1.0
HE21 A:GLN179 4.6 29.2 1.0
HB2 A:HIS176 4.7 22.9 1.0
N A:GLN179 4.7 19.8 1.0
H A:ASP178 4.7 23.2 1.0
HB2 A:ASP178 4.7 29.2 1.0
CB A:GLN179 4.8 17.2 1.0
HB2 A:ALA206 4.8 19.4 1.0
HB3 A:ASP178 4.8 29.2 1.0
ND2 A:ASN203 4.9 23.0 1.0
CB A:ALA206 4.9 16.2 1.0

Sodium binding site 2 out of 2 in 4ue8

Go back to Sodium Binding Sites List in 4ue8
Sodium binding site 2 out of 2 in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1236

b:34.2
occ:1.00
OD1 A:ASN160 2.2 28.4 1.0
O A:HOH2114 2.4 33.3 1.0
HA A:ASN160 2.4 17.6 1.0
O A:HOH2112 2.7 29.7 1.0
CG A:ASN160 2.8 26.7 1.0
HD21 A:LEU163 2.9 15.6 1.0
O A:HOH2160 3.2 28.1 1.0
CA A:ASN160 3.2 14.7 1.0
CB A:ASN160 3.3 19.5 1.0
HB3 A:ASN160 3.3 23.4 1.0
HB3 A:LEU163 3.7 12.5 1.0
H83 B:P4G1084 3.7 42.3 1.0
CD2 A:LEU163 3.8 13.0 1.0
ND2 A:ASN160 3.8 29.9 1.0
HD23 A:LEU163 3.9 15.6 1.0
N A:ASN160 4.0 12.8 1.0
H72 B:P4G1084 4.0 43.0 1.0
HD22 A:ASN160 4.1 35.9 1.0
O A:HOH2055 4.1 24.3 1.0
HB2 A:ASN160 4.2 23.4 1.0
H A:ASN160 4.4 15.4 1.0
HD22 A:LEU163 4.4 15.6 1.0
C A:ASN160 4.4 11.6 1.0
HH12 B:ARG63 4.4 17.1 1.0
CB A:LEU163 4.4 10.4 1.0
O B:HOH2015 4.4 43.2 1.0
HB2 A:LEU163 4.4 12.5 1.0
O A:ASN160 4.4 12.0 1.0
HZ1 B:LYS60 4.5 26.4 1.0
HD21 A:ASN160 4.5 35.9 1.0
C8 B:P4G1084 4.5 35.2 1.0
C7 B:P4G1084 4.6 35.9 1.0
C A:ASP159 4.6 11.8 1.0
O A:ASP159 4.6 12.3 1.0
H62 B:P4G1084 4.6 42.3 1.0
HZ2 B:LYS60 4.6 26.4 1.0
O A:HOH2116 4.6 46.3 1.0
O4 B:P4G1084 4.6 36.5 1.0
CG A:LEU163 4.6 10.6 1.0
H81 B:P4G1084 4.8 42.3 1.0
HG A:LEU163 4.8 12.7 1.0
HE2 B:LYS60 4.9 21.0 1.0
NZ B:LYS60 4.9 22.0 1.0

Reference:

D.Peter, C.Igreja, R.Weber, L.Wohlbold, C.Weiler, L.Ebertsch, O.Weichenrieder, E.Izaurralde. Molecular Architecture of 4E-Bp Translational Inhibitors Bound to EIF4E Mol.Cell 2015.
ISSN: ESSN 1097-4164
PubMed: 25702871
DOI: 10.1016/J.MOLCEL.2015.01.017
Page generated: Tue Dec 15 08:30:52 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