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Sodium in PDB 2oyl: Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex

Enzymatic activity of Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex

All present enzymatic activity of Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex:
3.2.1.123;

Protein crystallography data

The structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex, PDB code: 2oyl 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) 53.15 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.752, 93.246, 94.432, 90.00, 98.35, 90.00
R / Rfree (%) 17.4 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex (pdb code 2oyl). 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.: Cellobiose-Like Imidazole Complex, PDB code: 2oyl:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2oyl

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Sodium binding site 1 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole 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.: Cellobiose-Like Imidazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:16.7
occ:1.00
O A:HOH812 2.3 21.2 1.0
O A:VAL225 2.3 14.4 1.0
O A:HOH771 2.4 15.9 1.0
O A:ASN222 2.4 17.5 1.0
O A:HOH707 2.4 17.6 1.0
O A:HOH763 2.5 18.6 1.0
C A:VAL225 3.5 14.4 1.0
C A:ASN222 3.5 18.5 1.0
O A:HOH1074 3.7 33.1 1.0
N A:VAL225 4.0 15.4 1.0
CA A:VAL225 4.1 15.0 1.0
OG1 A:THR267 4.1 15.7 1.0
CB A:VAL225 4.2 15.1 1.0
O A:ALA220 4.3 18.8 1.0
CA A:ASP223 4.3 18.8 1.0
N A:ASP223 4.3 18.3 1.0
O A:PHE219 4.4 16.8 1.0
O A:HOH747 4.4 27.1 1.0
C A:ASP223 4.4 18.3 1.0
O A:HOH659 4.4 20.3 1.0
N A:ASN222 4.5 19.1 1.0
CA A:ASN222 4.5 18.6 1.0
N A:VAL226 4.6 13.8 1.0
O A:ASP223 4.6 18.8 1.0
O A:HOH881 4.6 34.2 1.0
O A:HOH760 4.7 38.7 1.0
N A:ALA224 4.8 17.6 1.0
CA A:VAL226 4.9 13.7 0.5
CG1 A:VAL225 4.9 14.8 1.0
CA A:VAL226 4.9 13.5 0.5
C A:ALA220 5.0 18.8 1.0
C A:ALA224 5.0 16.5 1.0

Sodium binding site 2 out of 4 in 2oyl

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Sodium binding site 2 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole 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.: Cellobiose-Like Imidazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:32.5
occ:1.00
O A:HOH1035 2.1 23.5 1.0
O A:HOH1034 2.3 35.7 1.0
O A:HOH927 2.3 34.2 1.0
O A:THR165 2.3 17.6 1.0
O A:ALA162 2.5 17.4 1.0
C A:THR165 3.4 17.9 1.0
C A:ALA162 3.6 17.8 1.0
N A:THR165 4.0 17.4 1.0
CA A:THR165 4.1 17.1 1.0
O A:HOH781 4.1 22.7 1.0
CB A:THR165 4.1 16.9 1.0
CA A:TRP163 4.4 17.7 1.0
C A:TRP163 4.4 17.6 1.0
N A:TRP163 4.4 17.8 1.0
O A:TRP163 4.4 17.5 1.0
N A:TYR166 4.5 18.5 1.0
CA A:ALA162 4.6 17.7 1.0
CA A:TYR166 4.8 19.2 1.0
CD1 A:TYR166 4.9 22.1 1.0
CG2 A:THR165 4.9 16.1 1.0
N A:ALA164 4.9 17.2 1.0
CB A:ALA162 5.0 18.0 1.0

Sodium binding site 3 out of 4 in 2oyl

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Sodium binding site 3 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole 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.: Cellobiose-Like Imidazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:19.6
occ:1.00
O B:VAL225 2.3 17.6 1.0
O B:HOH726 2.4 22.1 1.0
O B:HOH795 2.4 22.9 1.0
O B:ASN222 2.4 20.7 1.0
O B:HOH781 2.4 22.0 1.0
O B:HOH802 2.5 28.3 1.0
C B:ASN222 3.5 20.7 1.0
C B:VAL225 3.5 16.9 1.0
N B:VAL225 4.0 17.5 1.0
CA B:ASP223 4.0 20.6 1.0
CA B:VAL225 4.1 17.2 1.0
CB B:VAL225 4.2 17.0 1.0
N B:ASP223 4.2 20.5 1.0
O B:ALA220 4.2 21.1 1.0
C B:ASP223 4.2 20.3 1.0
O B:HOH834 4.2 26.7 1.0
OG1 B:THR267 4.2 18.3 1.0
O B:HOH968 4.3 36.0 1.0
O B:ASP223 4.4 21.2 1.0
O B:PHE219 4.4 19.8 1.0
N B:ASN222 4.4 21.1 1.0
O B:HOH738 4.5 26.9 1.0
CA B:ASN222 4.5 20.8 1.0
N B:VAL226 4.6 16.3 1.0
N B:ALA224 4.7 19.4 1.0
CG1 B:VAL225 4.8 16.9 1.0
CA B:VAL226 4.9 16.2 1.0
C B:ALA224 4.9 18.1 1.0
C B:ALA220 4.9 20.9 1.0

Sodium binding site 4 out of 4 in 2oyl

Go back to Sodium Binding Sites List in 2oyl
Sodium binding site 4 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole 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.: Cellobiose-Like Imidazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:41.5
occ:1.00
O B:HOH736 2.3 29.7 1.0
O B:HOH924 2.3 30.0 1.0
O B:THR165 2.4 18.2 1.0
O B:ALA162 2.5 18.7 1.0
C B:THR165 3.5 18.5 1.0
C B:ALA162 3.6 18.3 1.0
O B:HOH702 4.0 19.1 1.0
N B:THR165 4.1 18.1 1.0
O B:HOH893 4.1 36.0 1.0
CA B:THR165 4.1 17.8 1.0
CB B:THR165 4.2 17.8 1.0
CA B:TRP163 4.3 17.7 1.0
N B:TRP163 4.4 18.1 1.0
C B:TRP163 4.4 17.7 1.0
O B:TRP163 4.5 17.0 1.0
CA B:ALA162 4.5 18.3 1.0
N B:TYR166 4.6 18.5 1.0
CB B:ALA162 4.9 18.5 1.0
CG2 B:THR165 5.0 16.9 1.0
N B:ALA164 5.0 17.7 1.0
CA B:TYR166 5.0 19.0 1.0

Reference:

M.E.Caines, S.M.Hancock, C.A.Tarling, T.M.Wrodnigg, R.V.Stick, A.E.Stutz, A.Vasella, S.G.Withers, N.C.Strynadka. The Structural Basis of Glycosidase Inhibition By Five-Membered Iminocyclitols: the Clan A Glycoside Hydrolase Endoglycoceramidase As A Model System. Angew.Chem.Int.Ed.Engl. V. 46 4474 2007.
ISSN: ISSN 1433-7851
PubMed: 17487923
DOI: 10.1002/ANIE.200700268
Page generated: Tue Dec 15 05:53:15 2020

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