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Sodium in PDB 3w5n: Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose

Enzymatic activity of Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose

All present enzymatic activity of Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose:
3.2.1.40;

Protein crystallography data

The structure of Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose, PDB code: 3w5n was solved by Z.Fujimoto, A.Jackson, M.Michikawa, T.Maehara, M.Momma, B.F.Henrissat, H.J.Gilbert, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.56 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.063, 128.559, 75.260, 90.00, 99.85, 90.00
R / Rfree (%) 16.3 / 19.4

Other elements in 3w5n:

The structure of Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose (pdb code 3w5n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose, PDB code: 3w5n:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3w5n

Go back to Sodium Binding Sites List in 3w5n
Sodium binding site 1 out of 3 in the Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose


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 Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1210

b:29.4
occ:1.00
 O2 A:RAM1205 2.4 30.6 1.0
O3 A:RAM1205 2.4 32.2 1.0
C2 A:RAM1205 2.5 32.2 1.0
O A:HOH2725 2.5 20.1 1.0
O A:PHE273 2.6 15.4 1.0
O A:HOH2705 2.6 21.7 1.0
C3 A:RAM1205 2.9 33.5 1.0
C A:PHE273 3.6 16.3 1.0
C4 A:RAM1205 3.8 34.5 1.0
CA A:ASP274 4.0 15.2 1.0
C1 A:RAM1205 4.1 33.9 1.0
O A:ASP272 4.1 24.9 1.0
C A:ASP272 4.2 21.9 1.0
O A:HOH2707 4.2 24.3 1.0
O A:PRO271 4.2 21.5 1.0
OD1 A:ASP275 4.2 15.0 1.0
N A:ASP274 4.2 15.4 1.0
NH2 A:ARG160 4.3 10.6 1.0
N A:ASP275 4.3 14.5 1.0
N A:PHE273 4.4 19.1 1.0
O A:HOH2575 4.5 22.0 1.0
CA A:PHE273 4.7 17.4 1.0
O4 A:RAM1205 4.7 33.6 1.0
CA A:ASP272 4.7 23.6 1.0
O5 A:RAM1205 4.7 34.5 1.0
C A:ASP274 4.7 14.6 1.0
OD1 A:ASP274 4.8 17.4 1.0
C5 A:RAM1205 4.9 34.1 1.0
O A:HOH2706 5.0 28.0 1.0
O1 A:RAM1205 5.0 35.2 1.0
CB A:ASP274 5.0 16.1 1.0

Sodium binding site 2 out of 3 in 3w5n

Go back to Sodium Binding Sites List in 3w5n
Sodium binding site 2 out of 3 in the Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose


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 Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1211

b:26.1
occ:1.00
 O A:HOH2762 2.2 28.4 1.0
O A:HOH2763 2.3 33.3 1.0
O A:HOH2814 2.3 33.0 1.0
OD2 A:ASP69 2.4 18.0 0.5
O A:VAL71 2.4 13.4 1.0
OD1 A:ASP69 2.6 17.2 0.5
CG A:ASP69 2.9 17.3 0.5
O A:HOH2701 3.6 24.8 1.0
C A:VAL71 3.6 13.0 1.0
O A:HOH2173 4.1 25.2 1.0
O A:LEU72 4.2 12.2 1.0
O A:HOH2663 4.2 30.2 1.0
CB A:ASP69 4.4 17.2 0.5
C A:LEU72 4.4 12.6 1.0
CA A:VAL71 4.4 14.0 1.0
O A:HOH2388 4.5 28.1 1.0
N A:VAL71 4.5 13.1 1.0
CG A:ASP69 4.5 19.4 0.5
CB A:VAL71 4.6 14.6 1.0
N A:LEU72 4.6 12.2 1.0
OD1 A:ASP69 4.7 19.9 0.5
CB A:LEU72 4.7 12.7 1.0
CB A:ASP69 4.7 18.3 0.5
OD2 A:ASP69 4.7 20.4 0.5
CA A:LEU72 4.8 12.4 1.0
CG1 A:VAL71 4.8 15.8 1.0
N A:VAL73 4.9 11.9 1.0

Sodium binding site 3 out of 3 in 3w5n

Go back to Sodium Binding Sites List in 3w5n
Sodium binding site 3 out of 3 in the Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1212

b:24.1
occ:1.00
 O A:HOH2696 2.3 22.2 1.0
O A:HOH2695 2.3 16.5 1.0
O A:HOH2698 2.4 30.7 1.0
O A:LEU18 2.4 13.0 1.0
O A:HOH2697 2.4 24.7 1.0
O A:HOH2700 2.4 19.7 1.0
C A:LEU18 3.6 13.6 1.0
O A:HOH2694 3.8 21.3 1.0
N A:LEU18 4.2 13.0 1.0
O A:HOH2699 4.2 20.9 1.0
O A:HOH2458 4.2 20.6 1.0
O A:HOH2488 4.2 17.5 1.0
O A:HOH2598 4.3 14.1 1.0
CA A:LEU18 4.4 13.0 1.0
O A:HOH2482 4.4 23.3 1.0
O A:GLY19 4.4 15.7 1.0
O A:HOH2423 4.4 37.0 1.0
O A:HOH2139 4.5 24.3 1.0
N A:GLY19 4.6 13.7 1.0
C A:GLY19 4.6 14.4 1.0
CA A:GLY19 4.7 14.1 1.0
CB A:LEU18 4.7 13.6 1.0
O A:HOH2247 4.9 18.7 1.0
O A:THR358 4.9 10.0 1.0

Reference:

Z.Fujimoto, A.Jackson, M.Michikawa, T.Maehara, M.Momma, B.F.Henrissat, H.J.Gilbert, S.Kaneko. The Structure of A Streptomyces Avermitilis Alpha-L-Rhamnosidase Reveals A Novel Carbohydrate-Binding Module CBM67 Within the Six-Domain Arrangement. J.Biol.Chem. V. 288 12376 2013.
ISSN: ISSN 0021-9258
PubMed: 23486481
DOI: 10.1074/JBC.M113.460097
Page generated: Tue Dec 15 06:29:29 2020

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