Calcium in PDB 6hzz: Structure of Human D-Glucuronyl C5 Epimerase

All present enzymatic activity of Structure of Human D-Glucuronyl C5 Epimerase:
5.1.3.17;

The structure of Structure of Human D-Glucuronyl C5 Epimerase, PDB code: 6hzz 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)	43.83 / 2.52
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.820, 99.820, 262.970, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22.6

The structure of Structure of Human D-Glucuronyl C5 Epimerase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Structure of Human D-Glucuronyl C5 Epimerase (pdb code 6hzz). 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, PDB code: 6hzz:
Jump to Calcium binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1013 b:70.1 occ:1.00 O A:ASN269 2.2 76.0 1.0 O A:HOH1115 2.3 65.7 1.0 OD2 A:ASP392 2.4 68.9 1.0 O A:THR238 2.4 72.5 1.0 OE1 A:GLU240 2.4 99.3 1.0 OG1 A:THR268 2.6 69.0 1.0 OD1 A:ASP392 2.8 68.5 1.0 CG A:ASP392 2.9 67.7 1.0 C A:ASN269 3.4 75.7 1.0 C A:THR238 3.5 74.3 1.0 CD A:GLU240 3.6 97.7 1.0 CG2 A:THR268 3.7 70.1 1.0 CB A:THR268 3.7 71.6 1.0 N A:ASN269 3.8 75.5 1.0 CA A:THR238 4.1 70.0 1.0 CA A:ASN269 4.1 75.7 1.0 C1 A:NAG1006 4.2 54.0 1.0 OE2 A:GLU240 4.3 94.9 1.0 CB A:ASP392 4.4 64.2 1.0 N A:VAL270 4.5 76.3 1.0 CB A:THR238 4.5 70.2 1.0 CG A:GLU240 4.6 98.4 1.0 C A:THR268 4.6 75.3 1.0 CB A:ALA239 4.6 83.2 1.0 OD1 A:ASN393 4.6 67.6 1.0 N A:ALA239 4.7 78.1 1.0 CA A:THR268 4.7 75.6 1.0 ND2 A:ASN393 4.7 71.7 1.0 N2 A:NAG1006 4.7 54.3 1.0 CB A:ASN269 4.7 76.6 1.0 CG A:ASN393 4.9 66.1 1.0 C2 A:NAG1006 4.9 56.3 1.0 CA A:VAL270 4.9 75.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1012 b:67.3 occ:0.50 O B:THR238 2.2 87.4 1.0 OE2 B:GLU240 2.3 0.3 1.0 O B:ASN269 2.4 93.9 1.0 OD2 B:ASP392 2.5 81.6 1.0 OD1 B:ASP392 2.8 85.5 1.0 OG1 B:THR268 2.8 84.5 1.0 CG B:ASP392 3.0 80.6 1.0 C B:THR238 3.3 91.4 1.0 CD B:GLU240 3.5 0.8 1.0 C B:ASN269 3.6 93.1 1.0 CA B:THR238 3.8 88.9 1.0 CB B:THR268 3.9 87.7 1.0 CG2 B:THR268 4.0 84.5 1.0 N B:ASN269 4.0 96.3 1.0 C1 B:NAG1006 4.2 67.5 1.0 CB B:THR238 4.2 88.0 1.0 CA B:ASN269 4.3 95.0 1.0 CG B:GLU240 4.3 0.1 1.0 N B:ALA239 4.4 98.4 1.0 OE1 B:GLU240 4.4 0.9 1.0 CB B:ASP392 4.5 77.3 1.0 CB B:ALA239 4.5 0.7 1.0 OD1 B:ASN393 4.5 73.3 1.0 N B:VAL270 4.6 92.3 1.0 ND2 B:ASN393 4.7 81.2 1.0 C B:THR268 4.8 94.6 1.0 CG B:ASN393 4.8 74.9 1.0 CB B:ASN269 4.9 96.5 1.0 CA B:THR268 4.9 91.7 1.0 N2 B:NAG1006 4.9 70.7 1.0 CA B:ALA239 4.9 0.7 1.0 O5 B:NAG1006 5.0 70.1 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