Atomistry » Sodium » PDB 5imd-5j28 » 5j14
Atomistry »
  Sodium »
    PDB 5imd-5j28 »
      5j14 »

Sodium in PDB 5j14: Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3

Protein crystallography data

The structure of Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3, PDB code: 5j14 was solved by L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.521, 49.053, 120.135, 90.00, 114.19, 90.00
R / Rfree (%) 16.7 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3 (pdb code 5j14). 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 Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3, PDB code: 5j14:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5j14

Go back to Sodium Binding Sites List in 5j14
Sodium binding site 1 out of 2 in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3


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 Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:30.0
occ:1.00
O A:HOH840 2.4 23.8 1.0
O A:HOH906 2.4 23.0 1.0
O A:ASP62 2.4 10.7 1.0
O A:PRO64 2.5 10.1 1.0
O A:HOH746 2.5 17.4 1.0
OD1 A:ASP60 2.6 8.2 1.0
OD2 A:ASP60 2.6 7.2 1.0
CG A:ASP60 3.0 7.8 1.0
C A:PRO64 3.6 10.6 1.0
C A:ASP62 3.6 11.4 1.0
O A:HOH850 4.0 30.4 1.0
CD A:PRO67 4.2 8.8 1.0
CA A:TYR65 4.3 9.2 1.0
N A:PRO64 4.3 12.4 1.0
N A:TYR65 4.4 9.6 1.0
CA A:ASP62 4.4 12.1 1.0
C A:ALA63 4.4 12.1 1.0
N A:ASP62 4.4 10.8 1.0
CB A:ASP62 4.4 13.9 1.0
CB A:ASP60 4.5 7.8 1.0
O A:HOH824 4.5 14.4 1.0
CA A:PRO64 4.6 11.9 1.0
CG A:PRO67 4.6 8.9 1.0
N A:LEU66 4.6 8.4 1.0
N A:ALA63 4.6 11.2 1.0
O A:HOH688 4.7 28.8 1.0
O A:ALA63 4.7 12.0 1.0
CA A:ALA63 4.8 11.7 1.0
CD A:PRO64 4.8 12.7 1.0
OE1 A:GLU70 4.9 26.0 1.0
C A:TYR65 4.9 8.7 1.0

Sodium binding site 2 out of 2 in 5j14

Go back to Sodium Binding Sites List in 5j14
Sodium binding site 2 out of 2 in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3


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 Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:30.0
occ:1.00
O B:ASP62 2.3 10.4 1.0
O B:HOH879 2.3 17.1 1.0
O B:PRO64 2.4 8.6 1.0
O B:HOH898 2.4 13.9 1.0
O B:HOH873 2.6 13.7 1.0
OD1 B:ASP60 2.6 9.1 1.0
OD2 B:ASP60 2.7 8.8 1.0
CG B:ASP60 3.0 8.9 1.0
C B:ASP62 3.5 10.7 1.0
C B:PRO64 3.5 9.0 1.0
N B:PRO64 4.2 9.9 1.0
CA B:TYR65 4.2 8.3 1.0
C B:ALA63 4.3 9.9 1.0
CA B:ASP62 4.3 11.6 1.0
N B:TYR65 4.3 8.5 1.0
N B:ASP62 4.3 10.3 1.0
CB B:ASP62 4.4 13.4 1.0
N B:ALA63 4.4 10.1 1.0
CA B:PRO64 4.4 9.6 1.0
CB B:ASP60 4.5 8.7 1.0
O B:ALA63 4.5 9.4 1.0
CA B:ALA63 4.6 10.0 1.0
CD B:PRO67 4.6 11.1 1.0
O B:HOH906 4.6 14.5 1.0
N B:LEU66 4.7 8.9 1.0
CG B:PRO67 4.8 11.2 1.0
CD B:PRO64 4.8 10.1 1.0
C B:TYR65 4.9 8.4 1.0
CG B:PRO64 5.0 10.2 1.0

Reference:

Y.B.Han, L.Q.Chen, Z.Li, Y.M.Tan, Y.Feng, G.Y.Yang. Structural Insights Into the Broad Substrate Specificity of A Novel Endoglycoceramidase I Belonging to A New Subfamily of GH5 Glycosidases J. Biol. Chem. V. 292 4789 2017.
ISSN: ESSN 1083-351X
PubMed: 28179425
DOI: 10.1074/JBC.M116.763821
Page generated: Tue Dec 15 11:07:05 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