Atomistry » Sodium » PDB 3vif-3way » 3w5n
Atomistry »
  Sodium »
    PDB 3vif-3way »
      3w5n »

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: Mon Oct 7 13:54:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy