Magnesium in PDB 7yke: Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate

Enzymatic activity of Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate

All present enzymatic activity of Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate:
4.2.2.20;

Protein crystallography data

The structure of Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate, PDB code: 7yke was solved by M.Takashima, I.Watanabe, A.Miyanaga, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.07 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.069, 94.497, 229.356, 90, 90, 90
R / Rfree (%) 16.9 / 21.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate (pdb code 7yke). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate, PDB code: 7yke:

Magnesium binding site 1 out of 1 in 7yke

Go back to Magnesium Binding Sites List in 7yke
Magnesium binding site 1 out of 1 in the Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 4,6-Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:35.3
occ:1.00
 O A:MET70 2.2 32.2 1.0
O A:HIS43 2.3 35.4 1.0
O A:GLN73 2.3 40.9 1.0
OD1 A:ASP211 2.3 32.2 1.0
OD2 A:ASP211 2.4 32.4 1.0
CG A:ASP211 2.7 32.8 1.0
C A:HIS43 3.3 40.7 1.0
C A:MET70 3.4 34.5 1.0
O A:HOH1832 3.5 39.1 1.0
C A:GLN73 3.5 38.6 1.0
CA A:HIS43 3.6 38.6 1.0
CB A:HIS43 3.9 40.0 1.0
N A:MET70 4.0 32.2 1.0
O A:GLY71 4.0 46.7 1.0
CD2 A:PHE44 4.1 40.9 1.0
CB A:ASP211 4.2 31.7 1.0
CA A:MET70 4.2 32.8 1.0
N A:GLN73 4.2 39.6 1.0
C A:GLY71 4.3 46.2 1.0
N A:GLY71 4.4 38.5 1.0
CB A:SER68 4.4 35.5 1.0
N A:SER74 4.4 38.2 1.0
CA A:GLY71 4.4 41.7 1.0
CA A:GLN73 4.5 39.4 1.0
N A:PHE44 4.5 38.8 1.0
CA A:SER74 4.5 40.8 1.0
CB A:MET70 4.6 33.2 1.0
N A:ILE69 4.6 34.5 1.0
CE2 A:PHE44 4.9 38.7 1.0
CB A:PHE44 4.9 38.2 1.0
CG A:PHE44 5.0 39.4 1.0
N A:ARG212 5.0 34.3 1.0
CA A:ASP211 5.0 33.7 1.0

Reference:

I.Watanabe, A.Miyanaga, H.Hoshi, K.Suzuki, T.Eguchi. Biochemical and Crystallographic Assessments of the Effect of 4,6-O-Disulfated Disaccharide Moieties in Chondroitin Sulfate E on Chondroitinase Abc I Activity. Febs J. 2022.
ISSN: ISSN 1742-464X
PubMed: 36478634
DOI: 10.1111/FEBS.16685
Page generated: Thu Oct 3 15:31:14 2024

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