Magnesium in PDB 7eir: Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 6S

Enzymatic activity of Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 6S

All present enzymatic activity of Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 6S:
4.2.2.20;

Protein crystallography data

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

Resolution Low / High (Å) 49.13 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.324, 94.776, 229.497, 90, 90, 90
R / Rfree (%) 16.6 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 6S (pdb code 7eir). 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 6S, PDB code: 7eir:

Magnesium binding site 1 out of 1 in 7eir

Go back to Magnesium Binding Sites List in 7eir
Magnesium binding site 1 out of 1 in the Crystal Structure of Chondroitin Abc Lyase I in Complex with Chondroitin Disaccharide 6S


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 6S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:48.4
occ:1.00
 O A:MET70 2.0 46.8 1.0
O A:HIS43 2.4 48.4 1.0
OD1 A:ASP211 2.4 45.1 1.0
O A:GLN73 2.4 54.2 1.0
OD2 A:ASP211 2.5 44.9 1.0
CG A:ASP211 2.8 46.2 1.0
O A:HOH1555 3.2 41.0 1.0
C A:MET70 3.3 46.3 1.0
C A:HIS43 3.3 52.3 1.0
C A:GLN73 3.6 52.8 1.0
CA A:HIS43 3.6 50.5 1.0
O A:GLY71 3.9 51.9 1.0
CB A:HIS43 3.9 51.2 1.0
N A:MET70 4.0 44.8 1.0
CA A:MET70 4.1 45.5 1.0
C A:GLY71 4.2 54.2 1.0
CD2 A:PHE44 4.2 52.8 1.0
N A:GLY71 4.2 49.0 1.0
CB A:ASP211 4.3 46.3 1.0
N A:GLN73 4.3 53.0 1.0
CB A:SER68 4.3 49.5 1.0
CA A:GLY71 4.4 51.7 1.0
CB A:MET70 4.5 46.3 1.0
CA A:GLN73 4.5 54.9 1.0
N A:SER74 4.6 54.0 1.0
N A:PHE44 4.6 52.8 1.0
N A:ILE69 4.7 46.7 1.0
CA A:SER74 4.7 55.6 1.0
CB A:PHE44 4.9 53.6 1.0
N A:ARG212 4.9 44.0 1.0
N A:ASN72 5.0 54.9 1.0
OG A:SER68 5.0 49.1 1.0

Reference:

M.Takashima, I.Watanabe, A.Miyanaga, T.Eguchi. Substrate Specificity of Chondroitinase Abc I Based on Analyses of Biochemical Reactions and Crystal Structures in Complex with Disaccharides. Glycobiology 2021.
ISSN: ESSN 1460-2423
PubMed: 34392362
DOI: 10.1093/GLYCOB/CWAB086
Page generated: Fri Sep 24 15:14:48 2021

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