Atomistry » Sodium » PDB 6mc0-6myi » 6mji
Atomistry »
  Sodium »
    PDB 6mc0-6myi »
      6mji »

Sodium in PDB 6mji: Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex

Protein crystallography data

The structure of Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex, PDB code: 6mji was solved by D.M.Zajonc, A.Bitra, J.Janssens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.61 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.216, 191.161, 151.095, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex (pdb code 6mji). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex, PDB code: 6mji:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6mji

Go back to Sodium Binding Sites List in 6mji
Sodium binding site 1 out of 2 in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:99.0
occ:1.00
O C:ASP160 2.5 55.4 1.0
OD1 D:ASP170 3.1 47.1 1.0
C C:ASP160 3.2 54.7 1.0
O C:LYS161 3.4 50.2 1.0
CG D:ASP170 3.7 44.9 1.0
CB C:CYS162 3.7 56.0 1.0
NH2 D:ARG190 3.7 52.4 1.0
N C:ASP160 3.7 50.4 1.0
CD D:PRO171 3.7 52.0 1.0
C C:LYS161 3.8 51.8 1.0
CA D:ASP170 3.8 44.6 1.0
CA C:ASP160 3.8 55.0 1.0
CB D:ASP170 3.9 44.3 1.0
O C:HOH479 4.0 51.0 1.0
CB C:ASP160 4.0 59.5 1.0
OG1 C:THR159 4.0 46.5 1.0
CB C:THR159 4.0 46.3 1.0
N C:LYS161 4.1 53.6 1.0
N C:CYS162 4.3 50.8 1.0
CA C:LYS161 4.3 53.3 1.0
C C:THR159 4.4 48.1 1.0
CA C:CYS162 4.5 51.5 1.0
CZ D:ARG190 4.5 51.5 1.0
NH1 D:ARG190 4.6 52.7 1.0
OD2 D:ASP170 4.6 46.1 1.0
N D:ASP170 4.6 42.1 1.0
SG C:CYS162 4.7 63.7 1.0
N D:PRO171 4.7 50.6 1.0
CA C:THR159 4.8 46.5 1.0
C D:ASP170 4.8 46.3 1.0
CG D:PRO171 4.9 52.6 1.0

Sodium binding site 2 out of 2 in 6mji

Go back to Sodium Binding Sites List in 6mji
Sodium binding site 2 out of 2 in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na605

b:64.9
occ:1.00
OE1 D:GLU131 2.3 46.6 1.0
O D:THR139 3.1 35.5 1.0
N D:SER128 3.2 47.5 1.0
CD D:GLU131 3.4 46.6 1.0
CA D:PRO127 3.7 43.5 1.0
CD1 C:LEU126 3.7 44.4 1.0
CB D:THR139 3.8 36.4 1.0
CG C:LEU126 3.8 44.7 1.0
N D:THR139 3.8 36.8 1.0
CD2 C:LEU126 3.8 45.3 1.0
CB D:GLU131 3.9 46.4 1.0
CB D:SER128 3.9 51.1 1.0
CD2 C:LEU138 4.0 43.5 1.0
C D:THR139 4.0 36.2 1.0
C D:PRO127 4.0 44.6 1.0
CA D:THR139 4.0 37.4 1.0
CG D:GLU131 4.2 46.8 1.0
CA D:SER128 4.2 49.2 1.0
CB D:PRO127 4.2 43.3 1.0
OE2 D:GLU131 4.3 45.6 1.0
OG1 D:THR139 4.5 37.3 1.0
O D:SER128 4.6 46.5 1.0
CB C:TYR124 4.6 43.9 1.0
CG2 D:THR139 4.8 37.5 1.0
N D:PRO127 4.9 42.2 1.0
CD2 C:TYR124 4.9 44.6 1.0
C D:SER128 4.9 48.3 1.0
CG C:TYR124 5.0 44.0 1.0
C D:ALA138 5.0 37.0 1.0

Reference:

J.Janssens, A.Bitra, J.Wang, T.Decruy, K.Venken, J.Van Der Eycken, D.Elewaut, D.M.Zajonc, S.Van Calenbergh. 4"-O-Alkylated Alpha-Galactosylceramide Analogues As Inkt-Cell Antigens: Synthetic, Biological, and Structural Studies. Chemmedchem V. 14 147 2019.
ISSN: ESSN 1860-7187
PubMed: 30556652
DOI: 10.1002/CMDC.201800649
Page generated: Tue Dec 15 12:36:03 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy