Calcium in PDB 6i02: Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product

All present enzymatic activity of Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product:
5.1.3.17;

The structure of Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product, PDB code: 6i02 was solved by C.Debarnot, Y.R.Monneau, V.Roig-Zamboni, C.Le Narvor, A.Goulet, F.Fadel, R.R.Vives, D.Bonnaffe, H.Lortat-Jacob, Y.Bourne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.06 / 2.45
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.811, 99.811, 260.488, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.8

The binding sites of Calcium atom in the Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product (pdb code 6i02). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product, PDB code: 6i02:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1409 b:74.0 occ:1.00 OE1 A:GLU240 2.1 82.5 1.0 O A:THR238 2.3 68.8 1.0 O A:HOH1608 2.4 50.7 1.0 O A:ASN269 2.4 62.3 1.0 OD1 A:ASP392 2.6 62.3 1.0 OD2 A:ASP392 2.7 64.9 1.0 OG1 A:THR268 2.7 62.3 1.0 CG A:ASP392 3.0 61.4 1.0 CD A:GLU240 3.3 87.5 1.0 C A:THR238 3.5 68.1 1.0 CG2 A:THR268 3.5 62.5 1.0 C A:ASN269 3.6 67.2 1.0 CB A:THR268 3.6 65.4 1.0 N A:ASN269 3.9 68.7 1.0 CA A:THR238 4.1 66.2 1.0 CG A:GLU240 4.1 89.0 1.0 OE2 A:GLU240 4.2 86.0 1.0 OD1 A:ASN393 4.3 62.8 1.0 CA A:ASN269 4.3 69.0 1.0 C1 A:NAG1416 4.4 46.9 1.0 CB A:THR238 4.4 67.6 1.0 CB A:ASP392 4.5 58.0 1.0 N A:ALA239 4.6 71.5 1.0 CA A:THR268 4.6 68.2 1.0 C A:THR268 4.6 68.4 1.0 CB A:ALA239 4.6 72.8 1.0 N A:VAL270 4.6 69.1 1.0 N2 A:NAG1416 4.7 49.4 1.0 CG A:ASN393 4.8 61.0 1.0 ND2 A:ASN393 4.9 63.1 1.0 CB A:ASN269 5.0 70.8 1.0 C2 A:NAG1416 5.0 50.7 1.0

Calcium binding site 2 out of 2 in the Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human D-Glucuronyl C5 Epimerase in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca708 b:78.9 occ:1.00 OE2 B:GLU240 2.1 92.1 1.0 O B:THR238 2.3 80.3 1.0 O B:ASN269 2.6 86.2 1.0 OD1 B:ASP392 2.6 76.7 1.0 OD2 B:ASP392 2.8 72.5 1.0 OG1 B:THR268 2.8 81.7 1.0 CG B:ASP392 3.0 74.6 1.0 CD B:GLU240 3.3 96.0 1.0 C B:THR238 3.4 81.7 1.0 CG2 B:THR268 3.6 82.5 1.0 C B:ASN269 3.7 86.4 1.0 CB B:THR268 3.8 83.7 1.0 CA B:THR238 4.0 78.3 1.0 CG B:GLU240 4.0 97.7 1.0 OD1 B:ASN393 4.0 77.3 1.0 N B:ASN269 4.1 87.0 1.0 CB B:THR238 4.3 78.3 1.0 OE1 B:GLU240 4.3 95.5 1.0 C1 B:NAG714 4.3 65.3 1.0 CA B:ASN269 4.5 87.7 1.0 N B:ALA239 4.5 88.1 1.0 CB B:ASP392 4.6 72.7 1.0 CG B:ASN393 4.7 74.8 1.0 CB B:ALA239 4.7 92.4 1.0 CA B:THR268 4.7 86.8 1.0 C B:THR268 4.8 87.4 1.0 ND2 B:ASN393 4.8 80.5 1.0 N B:VAL270 4.8 87.0 1.0 N2 B:NAG714 5.0 69.5 1.0

C.Debarnot, Y.R.Monneau, V.Roig-Zamboni, V.Delauzun, C.Le Narvor, E.Richard, J.Henault, A.Goulet, F.Fadel, R.R.Vives, B.Priem, D.Bonnaffe, H.Lortat-Jacob, Y.Bourne. Substrate Binding Mode and Catalytic Mechanism of Human Heparan Sulfate D-Glucuronyl C5 Epimerase. Proc.Natl.Acad.Sci.Usa V. 116 6760 2019.
ISSN: ESSN 1091-6490
PubMed: 30872481
DOI: 10.1073/PNAS.1818333116