Calcium in PDB 5vyg: Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide

All present enzymatic activity of Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide:
3.4.21.22;

The structure of Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide, PDB code: 5vyg was solved by H.J.Yu, H.L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.16 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.417, 46.840, 37.259, 90.00, 92.58, 90.00
R / Rfree (%)	21.2 / 25.9

The binding sites of Calcium atom in the Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide (pdb code 5vyg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide, PDB code: 5vyg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide


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 HFA9 Egf Repeat with O-Glucose Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:27.0 occ:1.00 OD1 C:ASN58 2.3 23.1 1.0 O B:ASP65 2.3 26.8 1.0 O B:GLY48 2.4 26.5 1.0 OE1 B:GLN50 2.4 25.2 1.0 OD2 B:ASP64 2.5 24.7 1.0 OD1 B:ASP64 2.5 24.4 1.0 OD2 B:ASP47 2.6 33.4 1.0 CG B:ASP64 2.8 26.1 1.0 CG C:ASN58 3.4 23.0 1.0 CD B:GLN50 3.5 26.7 1.0 C B:ASP65 3.5 27.9 1.0 C B:GLY48 3.6 27.4 1.0 CG B:ASP47 3.7 36.9 1.0 NE2 B:GLN50 4.0 26.3 1.0 N B:ASN67 4.1 30.8 1.0 N B:GLN50 4.2 27.9 1.0 N B:ASP65 4.2 28.8 1.0 CB B:ASP47 4.2 33.9 1.0 CA C:ASN58 4.2 26.7 1.0 ND2 C:ASN58 4.3 21.9 1.0 CA B:ASP49 4.3 28.2 1.0 CB B:ASP64 4.3 25.7 1.0 N C:ASN58 4.3 26.2 1.0 O B:SER68 4.3 33.0 1.0 N B:ILE66 4.4 28.9 1.0 CA B:ILE66 4.4 29.7 1.0 N B:ASP49 4.4 27.4 1.0 CB C:ASN58 4.4 23.7 1.0 N B:GLY48 4.4 26.4 1.0 CA B:ASP65 4.5 27.9 1.0 C B:ASP47 4.5 29.2 1.0 CA B:GLY48 4.6 26.6 1.0 O B:ASP47 4.6 29.3 1.0 C B:ILE66 4.7 31.0 1.0 C B:ASP64 4.7 26.6 1.0 C B:ASP49 4.8 27.9 1.0 CG B:GLN50 4.8 27.0 1.0 OD1 B:ASP47 4.8 38.0 1.0 CB B:GLN50 4.9 27.8 1.0 N B:SER68 5.0 31.1 1.0 CA B:ASP64 5.0 26.5 1.0 CA B:ASN67 5.0 32.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:28.4 occ:1.00 OD1 B:ASN58 2.3 23.3 1.0 OE1 A:GLN50 2.3 26.3 1.0 O A:GLY48 2.4 32.6 1.0 O A:ASP65 2.4 24.9 1.0 OD1 A:ASP64 2.5 21.1 1.0 OD2 A:ASP64 2.5 21.7 1.0 OD1 A:ASP47 2.7 34.6 1.0 CG A:ASP64 2.8 23.0 1.0 CD A:GLN50 3.4 27.9 1.0 CG B:ASN58 3.5 23.4 1.0 C A:ASP65 3.5 26.9 1.0 C A:GLY48 3.6 33.1 1.0 CG A:ASP47 3.9 40.3 1.0 NE2 A:GLN50 3.9 26.8 1.0 N A:ASN67 4.0 27.8 1.0 N A:ASP65 4.2 25.0 1.0 N A:GLN50 4.2 30.0 1.0 CA B:ASN58 4.3 24.9 1.0 CA A:ASP49 4.3 33.0 1.0 CB A:ASP64 4.3 23.9 1.0 N B:ASN58 4.3 24.3 1.0 ND2 B:ASN58 4.3 22.7 1.0 O A:SER68 4.4 27.6 1.0 CA A:ILE66 4.4 29.1 1.0 N A:ILE66 4.4 27.0 1.0 CB A:ASP47 4.4 37.5 1.0 N A:ASP49 4.4 33.0 1.0 O A:ASP47 4.4 34.5 1.0 C A:ASP47 4.5 35.6 1.0 CA A:ASP65 4.5 25.6 1.0 CB B:ASN58 4.5 23.4 1.0 N A:GLY48 4.5 34.3 1.0 C A:ILE66 4.6 29.1 1.0 CA A:GLY48 4.6 32.8 1.0 CG A:GLN50 4.7 27.3 1.0 C A:ASP64 4.7 25.9 1.0 N A:SER68 4.8 27.4 1.0 C A:ASP49 4.8 32.9 1.0 O B:HOH203 4.8 36.6 1.0 CA A:ASN67 4.8 29.4 1.0 OD2 A:ASP47 4.9 41.1 1.0 CB A:GLN50 4.9 30.0 1.0 CA A:ASP64 5.0 25.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of HFA9 Egf Repeat with O-Glucose Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca102 b:31.2 occ:1.00 O C:ASP65 2.3 29.4 1.0 OE1 C:GLN50 2.4 33.4 1.0 O C:GLY48 2.4 39.5 1.0 OD1 C:ASP64 2.5 25.4 1.0 OD2 C:ASP64 2.6 27.4 1.0 OD2 C:ASP47 2.9 49.8 1.0 CG C:ASP64 2.9 26.5 1.0 CD C:GLN50 3.4 35.1 1.0 C C:ASP65 3.5 29.2 1.0 CG C:ASP47 3.6 50.1 1.0 C C:GLY48 3.6 39.0 1.0 NE2 C:GLN50 3.9 34.0 1.0 N C:ASN67 4.0 36.0 1.0 OD1 C:ASP47 4.1 51.9 1.0 N C:ASP65 4.2 26.4 1.0 CA C:ILE66 4.3 33.4 1.0 N C:GLN50 4.3 34.0 1.0 N C:ILE66 4.4 30.7 1.0 CB C:ASP47 4.4 42.8 1.0 CB C:ASP64 4.4 25.6 1.0 O C:SER68 4.4 33.4 1.0 CA C:ASP49 4.4 36.1 1.0 C C:ASP47 4.4 42.5 1.0 N C:ASP49 4.4 36.7 1.0 N C:GLY48 4.5 40.9 1.0 CA C:ASP65 4.5 29.7 1.0 O C:ASP47 4.5 38.5 1.0 C C:ILE66 4.6 34.6 1.0 CA C:GLY48 4.7 41.0 1.0 CG C:GLN50 4.7 35.0 1.0 CA C:ASN67 4.8 40.6 1.0 C C:ASP64 4.8 26.3 1.0 C C:ASP49 4.9 34.8 1.0 N C:SER68 4.9 39.3 1.0 CB C:GLN50 5.0 34.1 1.0

H.Takeuchi, H.Yu, H.Hao, M.Takeuchi, A.Ito, H.Li, R.S.Haltiwanger. O-Glycosylation Modulates the Stability of Epidermal Growth Factor-Like Repeats and Thereby Regulates Notch Trafficking J. Biol. Chem. V. 292 15964 2017.
ISSN: ESSN 1083-351X
PubMed: 28729422
DOI: 10.1074/JBC.M117.800102