Atomistry » Sodium » PDB 6zl3-7c67 » 7c67
Atomistry »
  Sodium »
    PDB 6zl3-7c67 »
      7c67 »

Sodium in PDB 7c67: Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose

Protein crystallography data

The structure of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose, PDB code: 7c67 was solved by S.P.Kanaujia, M.Chandravanshi, R.Samanta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.670, 109.880, 110.890, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 23.1

Other elements in 7c67:

The structure of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose (pdb code 7c67). 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 Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose, PDB code: 7c67:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7c67

Go back to Sodium Binding Sites List in 7c67
Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose


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 Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:33.9
occ:1.00
O A:HOH611 2.6 34.9 1.0
O A:HOH692 2.7 26.6 1.0
O A:HOH714 3.2 41.4 1.0
CG2 B:THR50 3.5 26.6 1.0
CB B:THR50 3.6 25.4 1.0
NH1 A:ARG273 3.7 36.5 1.0
CD A:ARG273 3.8 29.9 1.0
OG1 B:THR50 3.8 22.0 1.0
CD B:LYS47 3.9 33.0 1.0
CB A:ALA245 3.9 23.7 1.0
OE2 A:GLU265 4.1 43.7 1.0
CA A:ALA245 4.1 21.9 1.0
CA B:LYS47 4.1 22.6 1.0
N A:ALA245 4.4 20.7 1.0
CZ A:ARG273 4.4 35.9 1.0
NE A:ARG273 4.4 35.5 1.0
O B:THR46 4.5 20.3 1.0
NZ B:LYS47 4.6 40.0 1.0
CG A:ARG273 4.6 27.7 1.0
CD A:GLU265 4.6 45.0 1.0
OE1 A:GLU265 4.6 42.2 1.0
CB B:LYS47 4.7 25.5 1.0
O A:ALA241 4.7 21.2 1.0
C A:GLN244 4.7 21.2 1.0
O B:LYS47 4.8 21.0 1.0
CG B:LYS47 4.8 29.2 1.0
N B:LYS47 4.8 20.4 1.0
C B:THR46 4.9 20.0 1.0
O A:GLN244 4.9 20.3 1.0
CE B:LYS47 4.9 36.8 1.0
CG2 B:THR46 4.9 22.1 1.0
CB A:GLN244 4.9 21.0 1.0
C B:LYS47 5.0 20.9 1.0

Sodium binding site 2 out of 2 in 7c67

Go back to Sodium Binding Sites List in 7c67
Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose


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 Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:33.2
occ:1.00
O B:HOH739 2.8 30.9 1.0
O A:HOH846 3.1 36.2 1.0
O A:HOH815 3.1 35.9 1.0
C B:GLN14 3.5 27.2 1.0
N B:GLU17 3.6 28.3 1.0
N B:ALA16 3.7 24.7 1.0
CA B:GLN14 3.8 30.3 1.0
N B:PRO15 3.8 25.7 1.0
CB B:GLN14 3.9 32.1 1.0
O B:GLN14 3.9 25.9 1.0
CB B:GLU17 4.0 35.6 1.0
CB B:ALA16 4.0 24.9 1.0
CD B:PRO15 4.1 26.2 1.0
CA B:ALA16 4.2 25.5 1.0
CG B:GLU17 4.2 40.7 1.0
C B:ALA16 4.4 26.4 1.0
CA B:GLU17 4.4 30.9 1.0
O A:HOH770 4.5 24.0 1.0
C B:PRO15 4.5 24.5 1.0
O A:HOH719 4.6 42.6 1.0
OE1 B:GLU17 4.7 48.2 1.0
O B:HOH773 4.7 41.8 1.0
CA B:PRO15 4.7 24.8 1.0
CG B:GLN14 4.8 35.1 1.0
CL A:CL502 4.9 39.5 1.0
CD B:GLU17 5.0 44.7 1.0

Reference:

M.Chandravanshi, R.Samanta, S.P.Kanaujia. Conformational Trapping of A Beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of Abc Importers. J.Mol.Biol. V. 432 5711 2020.
ISSN: ESSN 1089-8638
PubMed: 32866452
DOI: 10.1016/J.JMB.2020.08.021
Page generated: Tue Dec 15 17:35:40 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy