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Sodium in PDB 2osx: Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex

Enzymatic activity of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex

All present enzymatic activity of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex:
3.2.1.123;

Protein crystallography data

The structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex, PDB code: 2osx was solved by M.E.C.Caines, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.23 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.801, 61.984, 102.846, 90.00, 112.25, 90.00
R / Rfree (%) 12.1 / 13.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex (pdb code 2osx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex, PDB code: 2osx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2osx

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Sodium binding site 1 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:8.4
occ:1.00
O A:HOH696 2.3 10.1 1.0
O A:VAL225 2.3 8.2 1.0
O A:ASN222 2.4 8.6 1.0
O A:HOH745 2.4 6.2 0.5
O A:HOH758 2.4 12.7 1.0
O A:HOH717 2.5 13.0 1.0
O A:HOH745 3.2 13.5 0.5
C A:VAL225 3.4 6.9 1.0
C A:ASN222 3.5 8.8 1.0
O A:HOH1150 3.8 29.9 1.0
N A:VAL225 3.9 7.3 1.0
CA A:VAL225 4.0 7.0 1.0
CA A:ASP223 4.1 10.8 1.0
CB A:VAL225 4.2 7.3 1.0
N A:ASP223 4.2 9.8 1.0
O A:HOH856 4.2 19.3 1.0
OG1 A:THR267 4.3 8.3 1.0
O A:HOH680 4.3 17.1 1.0
O A:ALA220 4.3 10.7 1.0
C A:ASP223 4.3 10.8 1.0
N A:ASN222 4.4 9.4 1.0
O A:PHE219 4.4 7.5 1.0
CA A:ASN222 4.5 9.1 1.0
O A:HOH779 4.5 16.1 1.0
N A:VAL226 4.6 6.5 1.0
O A:HOH777 4.6 12.3 0.5
N A:ALA224 4.7 8.5 1.0
O A:HOH1086 4.7 27.4 1.0
O A:ASP223 4.8 13.9 1.0
O A:HOH777 4.8 9.3 0.5
CG1 A:VAL225 4.8 8.6 1.0
CA A:VAL226 4.9 7.0 1.0
C A:ALA224 4.9 8.0 1.0
CB A:ASN222 5.0 8.8 1.0

Sodium binding site 2 out of 4 in 2osx

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Sodium binding site 2 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:17.2
occ:1.00
O A:HOH923 2.1 18.2 1.0
O A:HOH797 2.3 10.6 0.5
O A:ALA162 2.4 7.9 1.0
O A:HOH979 2.4 29.1 1.0
O A:THR165 2.5 7.5 1.0
O A:HOH797 2.5 18.7 0.5
O A:HOH1179 3.4 27.5 1.0
C A:ALA162 3.5 7.2 1.0
C A:THR165 3.6 6.7 1.0
O A:HOH750 3.8 22.0 1.0
CB A:THR165 4.0 6.8 1.0
O A:HOH1034 4.0 17.2 1.0
N A:THR165 4.1 6.5 1.0
CA A:THR165 4.1 6.5 1.0
CA A:ALA162 4.3 8.0 1.0
N A:TRP163 4.4 7.4 1.0
CA A:TRP163 4.5 7.2 1.0
O A:HOH1178 4.5 25.8 1.0
O A:HOH1154 4.6 22.3 1.0
CB A:ALA162 4.6 9.3 1.0
C A:TRP163 4.6 6.9 1.0
N A:TYR166 4.7 6.2 1.0
O A:HOH1049 4.7 28.1 1.0
CG2 A:THR165 4.7 7.3 1.0
O A:TRP163 4.8 7.8 1.0

Sodium binding site 3 out of 4 in 2osx

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Sodium binding site 3 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:16.1
occ:1.00
O A:ASP291 2.3 9.8 1.0
O A:HOH976 2.3 23.4 1.0
O A:HOH847 2.4 23.7 1.0
O A:HOH676 2.4 12.1 1.0
O A:HOH988 2.5 28.8 1.0
OE1 A:GLN297 2.6 11.8 1.0
C A:ASP291 3.4 8.6 1.0
CD A:GLN297 3.5 10.5 1.0
CG A:GLN297 3.6 11.6 1.0
N A:ASP291 3.9 8.6 1.0
O A:HOH998 4.1 32.9 1.0
CA A:ASP291 4.1 8.2 1.0
CB A:ASP291 4.2 8.2 1.0
O A:ARG293 4.3 11.4 1.0
O A:HOH925 4.4 22.3 1.0
N A:PRO292 4.5 8.9 1.0
O A:HOH1008 4.6 24.2 1.0
CA A:PRO292 4.7 9.7 1.0
O A:GLY295 4.7 15.0 1.0
NE2 A:GLN297 4.7 10.7 1.0
CB A:GLN297 4.8 9.2 1.0
C A:PRO292 5.0 9.9 1.0
C A:ASP290 5.0 9.2 1.0
CA A:GLN297 5.0 8.1 1.0

Sodium binding site 4 out of 4 in 2osx

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Sodium binding site 4 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside GM3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:7.5
occ:0.50
O A:HOH1166 1.5 14.6 0.5
O A:PRO69 2.2 11.2 1.0
O A:HOH1053 2.4 8.0 0.5
O A:HOH1166 2.5 16.0 0.5
O A:HOH671 2.5 10.4 1.0
C A:PRO69 3.4 9.7 1.0
O A:HOH1053 3.6 9.7 0.5
O A:HOH637 3.7 8.6 1.0
NH2 A:ARG99 4.0 7.1 1.0
O A:HOH769 4.1 7.6 1.0
CA A:ASP70 4.2 8.4 1.0
N A:ASP70 4.2 8.8 1.0
O A:HOH763 4.4 15.6 1.0
CA A:PRO69 4.4 10.4 1.0
NH2 A:ARG115 4.6 9.9 1.0
C A:ASP70 4.6 7.8 1.0
OG A:SER100 4.8 6.5 1.0
N A:GLY71 4.9 7.1 1.0

Reference:

M.E.Caines, M.D.Vaughan, C.A.Tarling, S.M.Hancock, R.A.Warren, S.G.Withers, N.C.Strynadka. Structural and Mechanistic Analyses of Endo-Glycoceramidase II, A Membrane-Associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-Bound Forms. J.Biol.Chem. V. 282 14300 2007.
ISSN: ISSN 0021-9258
PubMed: 17329247
DOI: 10.1074/JBC.M611455200
Page generated: Tue Dec 15 05:52:48 2020

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