Calcium in PDB 6i01: Structure of Human D-Glucuronyl C5 Epimerase in Complex with Substrate

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

The structure of Structure of Human D-Glucuronyl C5 Epimerase in Complex with Substrate, PDB code: 6i01 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)	40.32 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.675, 99.675, 258.823, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 19.5

The binding sites of Calcium atom in the Structure of Human D-Glucuronyl C5 Epimerase in Complex with Substrate (pdb code 6i01). 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 Substrate, PDB code: 6i01:
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 Substrate


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 Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca728 b:60.1 occ:1.00 O A:HOH1013 2.1 46.9 1.0 O A:ASN269 2.3 59.9 1.0 O A:THR238 2.4 62.0 1.0 OE2 A:GLU240 2.4 79.8 1.0 OD2 A:ASP392 2.5 58.1 1.0 OG1 A:THR268 2.6 56.6 1.0 OD1 A:ASP392 2.6 53.6 1.0 CG A:ASP392 2.9 54.6 1.0 C A:ASN269 3.5 62.0 1.0 CD A:GLU240 3.5 80.9 1.0 C A:THR238 3.5 61.9 1.0 CB A:THR268 3.7 60.4 1.0 CG2 A:THR268 3.7 58.6 1.0 N A:ASN269 3.8 63.8 1.0 CG A:GLU240 4.0 79.5 1.0 CA A:THR238 4.1 58.6 1.0 CA A:ASN269 4.2 64.7 1.0 CB A:ASP392 4.4 52.4 1.0 O A:HOH803 4.4 58.6 1.0 CB A:THR238 4.4 59.8 1.0 OD1 A:ASN393 4.4 53.3 1.0 C A:THR268 4.5 63.3 1.0 OE1 A:GLU240 4.5 84.9 1.0 N A:VAL270 4.5 62.9 1.0 CA A:THR268 4.6 63.3 1.0 C1 A:NAG714 4.6 48.2 1.0 N A:ALA239 4.6 64.8 1.0 CB A:ALA239 4.7 67.7 1.0 CB A:ASN269 4.7 66.4 1.0 N2 A:NAG714 4.8 47.9 1.0 CA A:VAL270 4.8 61.8 1.0 C A:ALA239 4.9 71.0 1.0 CA A:ALA239 5.0 67.6 1.0

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


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 Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca727 b:71.1 occ:1.00 O B:ASN269 2.3 78.0 1.0 O B:THR238 2.4 74.0 1.0 OE2 B:GLU240 2.4 93.8 1.0 O B:HOH930 2.5 56.1 1.0 OD2 B:ASP392 2.5 67.2 1.0 OG1 B:THR268 2.6 74.9 1.0 OD1 B:ASP392 2.7 67.6 1.0 CG B:ASP392 2.9 65.8 1.0 C B:ASN269 3.5 77.2 1.0 C B:THR238 3.5 73.9 1.0 CD B:GLU240 3.6 96.3 1.0 CB B:THR268 3.7 76.3 1.0 CG2 B:THR268 3.7 74.8 1.0 N B:ASN269 3.8 79.5 1.0 CA B:THR238 4.1 69.7 1.0 CA B:ASN269 4.2 80.4 1.0 OE1 B:GLU240 4.2 98.4 1.0 CB B:ASP392 4.4 63.5 1.0 OD1 B:ASN393 4.4 65.1 1.0 CB B:THR238 4.4 69.8 1.0 C B:THR268 4.5 80.3 1.0 C1 B:NAG713 4.5 59.0 1.0 CA B:THR268 4.5 79.9 1.0 N B:VAL270 4.6 77.8 1.0 N B:ALA239 4.6 79.0 1.0 CG B:GLU240 4.7 95.8 1.0 CB B:ASN269 4.7 82.0 1.0 CB B:ALA239 4.8 84.9 1.0 N2 B:NAG713 4.8 61.8 1.0 CA B:VAL270 4.9 75.9 1.0 C B:ALA239 4.9 88.8 1.0 CG B:ASN393 5.0 64.8 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