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Calcium 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:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Streptomyces Avermitilis Alpha-L-Rhamnosidase Complexed with L-Rhamnose, PDB code: 3w5n:

Calcium binding site 1 out of 1 in 3w5n

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1201

b:13.6
occ:1.00
 OD1 A:ASP179 2.3 11.5 1.0
OD1 A:ASN228 2.4 14.5 1.0
O4 A:RAM1203 2.4 16.0 1.0
O3 A:RAM1203 2.4 15.8 1.0
O A:PRO233 2.4 12.9 1.0
O A:HOH2250 2.4 13.3 1.0
OD1 A:ASN180 2.5 15.2 1.0
C4 A:RAM1203 3.2 16.6 1.0
CG A:ASP179 3.2 11.6 1.0
C3 A:RAM1203 3.3 16.0 1.0
CG A:ASN180 3.4 15.0 1.0
OD2 A:ASP179 3.5 11.8 1.0
CG A:ASN228 3.5 14.0 1.0
C A:PRO233 3.6 13.6 1.0
ND2 A:ASN180 3.7 15.1 1.0
ND2 A:ASN228 4.2 14.1 1.0
O A:HOH2721 4.3 21.6 1.0
N A:PRO233 4.3 14.4 1.0
N A:ALA229 4.4 15.4 1.0
O A:SER230 4.4 18.0 1.0
CA A:PRO233 4.5 13.3 1.0
C A:GLY232 4.5 15.0 1.0
C A:ASP179 4.5 12.1 1.0
O A:ASP179 4.6 12.4 1.0
N A:ALA234 4.6 12.5 1.0
CB A:ASP179 4.6 11.6 1.0
O A:GLY232 4.6 16.0 1.0
O A:HOH2684 4.6 20.0 1.0
CA A:ALA234 4.6 12.3 1.0
CB A:ASN228 4.7 14.0 1.0
N A:ASN180 4.7 12.1 1.0
CB A:ASN180 4.7 14.1 1.0
C2 A:RAM1203 4.7 17.9 1.0
C5 A:RAM1203 4.7 17.6 1.0
CD A:PRO233 4.7 14.1 1.0
CA A:ASN228 4.7 14.4 1.0
CA A:ASP179 4.9 12.1 1.0
CB A:PRO233 4.9 13.8 1.0
O2 A:RAM1203 5.0 16.3 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 Jul 8 17:45:08 2025

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