Calcium in PDB 5ue5: Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain

All present enzymatic activity of Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain:
3.4.24.23;

The structure of Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain also contains other interesting chemical elements:

Zinc

(Zn)

32 atoms

The binding sites of Calcium atom in the Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain (pdb code 5ue5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain, PDB code: 5ue5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:52.1 occ:1.00 O A:ASP133 2.4 52.0 1.0 OD1 A:ASP169 2.4 11.1 1.0 O A:GLY165 2.4 5.3 1.0 O A:LEU166 2.4 12.1 1.0 O A:GLY167 2.6 72.0 1.0 C A:LEU166 3.1 51.5 1.0 CG A:ASP169 3.2 74.3 1.0 C A:GLY167 3.4 1.1 1.0 HA A:LEU166 3.4 51.4 1.0 H A:ASP169 3.4 23.0 1.0 C A:ASP133 3.5 31.2 1.0 C A:GLY165 3.5 13.1 1.0 HA A:ILE134 3.6 63.0 1.0 N A:ASP169 3.6 51.4 1.0 OD2 A:ASP169 3.6 20.2 1.0 CA A:LEU166 3.7 52.3 1.0 H A:MET135 3.9 32.1 1.0 HA3 A:GLY168 3.9 74.5 1.0 HA A:ASP133 3.9 2.5 1.0 N A:GLY167 3.9 31.4 1.0 HG2 A:MET135 4.0 44.3 1.0 C A:GLY168 4.0 30.1 1.0 HA A:ASP169 4.1 13.3 1.0 N A:LEU166 4.1 70.5 1.0 CA A:GLY167 4.2 42.4 1.0 N A:GLY168 4.2 14.1 1.0 CA A:GLY168 4.2 24.4 1.0 CA A:ASP169 4.2 1.0 1.0 CA A:ASP133 4.3 3.1 1.0 CB A:ASP169 4.3 61.3 1.0 N A:ILE134 4.4 55.4 1.0 HA2 A:GLY167 4.4 43.5 1.0 HB3 A:ASP133 4.4 54.5 1.0 CA A:ILE134 4.5 3.4 1.0 HA2 A:GLY165 4.6 5.1 1.0 H A:GLY167 4.7 72.5 1.0 N A:MET135 4.7 21.1 1.0 CA A:GLY165 4.7 54.4 1.0 HG13 A:ILE134 4.7 20.4 1.0 HD23 A:LEU166 4.7 64.4 1.0 O A:GLY168 4.8 1.5 1.0 HH2 A:TRP84 4.9 34.4 1.0 O A:THR164 4.9 23.1 1.0 O A:ALA132 4.9 30.0 1.0 HB2 A:ASP169 4.9 13.3 1.0 CB A:ASP133 5.0 25.5 1.0

Calcium binding site 2 out of 2 in the Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:51.3 occ:1.00 OE2 A:GLU176 2.4 32.4 1.0 O A:THR155 2.4 44.3 1.0 O A:GLY151 2.4 23.3 1.0 OD2 A:ASP173 2.4 51.1 1.0 OD2 A:ASP150 2.6 32.1 1.0 HG2 A:GLU176 2.7 13.4 1.0 OD1 A:ASP150 2.7 62.1 1.0 O A:GLY153 2.7 30.2 1.0 CG A:ASP150 3.0 51.5 1.0 O A:ASN154 3.2 23.4 1.0 CD A:GLU176 3.2 32.1 1.0 CG A:GLU176 3.2 13.3 1.0 HA A:PRO152 3.3 54.2 1.0 HG3 A:GLU176 3.3 4.4 1.0 C A:GLY151 3.6 1.5 1.0 C A:PRO152 3.6 63.2 1.0 C A:THR155 3.6 13.3 1.0 HA A:LEU156 3.6 51.1 1.0 CG A:ASP173 3.7 65.5 1.0 C A:GLY153 3.8 4.3 1.0 CA A:PRO152 3.8 63.3 1.0 HB A:THR155 3.8 70.5 1.0 N A:GLY153 3.8 2.2 1.0 O A:PRO152 3.9 5.5 1.0 C A:ASN154 4.1 12.3 1.0 H A:GLY153 4.1 11.2 1.0 HB2 A:ASP175 4.1 54.1 1.0 HB3 A:ASP173 4.1 24.1 1.0 N A:PRO152 4.2 1.1 1.0 H A:GLY151 4.2 22.4 1.0 CB A:ASP173 4.4 72.1 1.0 OE1 A:GLU176 4.4 31.3 1.0 HB2 A:ASP173 4.4 0.2 1.0 CA A:GLY153 4.4 74.2 1.0 N A:GLY151 4.5 10.0 1.0 CA A:LEU156 4.5 43.5 1.0 N A:LEU156 4.5 62.0 1.0 CA A:THR155 4.5 5.2 1.0 CB A:ASP150 4.5 42.4 1.0 OD1 A:ASP173 4.6 51.2 1.0 CB A:THR155 4.6 62.4 1.0 CA A:GLY151 4.7 62.2 1.0 N A:THR155 4.7 63.3 1.0 CB A:GLU176 4.7 10.1 1.0 N A:ASN154 4.7 31.1 1.0 O A:LEU156 4.8 30.1 1.0 H A:GLU176 4.8 24.3 1.0 HB2 A:ASP150 4.9 61.4 1.0 O A:PHE149 4.9 44.0 1.0 HG21 A:THR155 4.9 42.3 1.0 HA A:GLU176 4.9 11.0 1.0 HB3 A:ASP150 5.0 73.1 1.0 CA A:ASN154 5.0 70.1 1.0

Y.G.Fulcher, S.H.Prior, S.Masuko, L.Li, D.Pu, F.Zhang, R.J.Linhardt, S.R.Van Doren. Glycan Activation of A Sheddase: Electrostatic Recognition Between Heparin and Prommp-7. Structure V. 25 1100 2017.
ISSN: ISSN 1878-4186
PubMed: 28648610
DOI: 10.1016/J.STR.2017.05.019