Calcium in PDB 5ue2: Prommp-7 with Heparin Octasaccharide Bridging Between Domains

All present enzymatic activity of Prommp-7 with Heparin Octasaccharide Bridging Between Domains:
3.4.24.23;

The structure of Prommp-7 with Heparin Octasaccharide Bridging Between Domains also contains other interesting chemical elements:

Zinc

(Zn)

32 atoms

The binding sites of Calcium atom in the Prommp-7 with Heparin Octasaccharide Bridging Between Domains (pdb code 5ue2). 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 Bridging Between Domains, PDB code: 5ue2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Prommp-7 with Heparin Octasaccharide Bridging Between Domains


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 Bridging Between Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:45.3 occ:1.00 O A:ASP133 2.4 30.0 1.0 OD1 A:ASP169 2.4 54.3 1.0 O A:GLY165 2.4 5.2 1.0 O A:LEU166 2.5 1.1 1.0 O A:GLY167 2.6 12.4 1.0 H A:ASP169 2.9 4.2 1.0 N A:ASP169 3.1 51.2 1.0 HA A:ILE134 3.1 21.3 1.0 CG A:ASP169 3.1 75.2 1.0 C A:GLY167 3.2 64.4 1.0 C A:LEU166 3.2 53.2 1.0 HA3 A:GLY168 3.4 41.1 1.0 C A:ASP133 3.4 24.3 1.0 C A:GLY168 3.5 42.1 1.0 C A:GLY165 3.6 42.0 1.0 HA A:ASP169 3.6 61.3 1.0 CA A:GLY168 3.7 14.2 1.0 OD2 A:ASP169 3.7 3.5 1.0 N A:GLY168 3.7 0.1 1.0 CA A:ASP169 3.8 3.1 1.0 HA A:LEU166 3.8 32.2 1.0 H A:MET135 3.9 61.4 1.0 N A:GLY167 3.9 64.2 1.0 HH2 A:TRP84 4.0 61.0 1.0 CA A:LEU166 4.0 45.1 1.0 CA A:GLY167 4.0 61.2 1.0 CB A:ASP169 4.1 70.3 1.0 CA A:ILE134 4.1 61.4 1.0 N A:ILE134 4.2 12.0 1.0 HB3 A:ASP133 4.2 30.1 1.0 HA A:ASP133 4.2 44.2 1.0 O A:GLY168 4.2 11.3 1.0 HA2 A:GLY167 4.3 32.1 1.0 N A:LEU166 4.3 31.2 1.0 HG2 A:MET135 4.3 60.5 1.0 CA A:ASP133 4.3 10.2 1.0 HA2 A:GLY165 4.5 63.2 1.0 H A:GLY168 4.6 63.2 1.0 HG12 A:ILE134 4.6 11.5 1.0 N A:MET135 4.6 51.2 1.0 CA A:GLY165 4.7 53.4 1.0 HB2 A:ASP169 4.7 32.4 1.0 O A:THR164 4.7 31.1 1.0 H A:GLY167 4.7 32.1 1.0 HA2 A:GLY168 4.8 23.3 1.0 CB A:ASP133 4.8 32.2 1.0 C A:ILE134 4.8 70.2 1.0 HB3 A:ASP169 4.8 4.3 1.0 HZ2 A:TRP84 4.8 70.2 1.0 CH2 A:TRP84 5.0 11.4 1.0

Calcium binding site 2 out of 2 in the Prommp-7 with Heparin Octasaccharide Bridging Between Domains


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 Bridging Between Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:25.1 occ:1.00 OE2 A:GLU176 2.4 25.1 1.0 O A:THR155 2.4 63.4 1.0 OD2 A:ASP173 2.4 41.4 1.0 O A:GLY151 2.4 34.3 1.0 OD1 A:ASP150 2.7 43.3 1.0 O A:GLY153 2.7 52.4 1.0 HG2 A:GLU176 3.0 15.2 1.0 HA A:PRO152 3.1 14.1 1.0 O A:ASN154 3.1 24.4 1.0 HB A:THR155 3.4 50.1 1.0 CD A:GLU176 3.4 33.5 1.0 CG A:GLU176 3.6 34.2 1.0 C A:GLY151 3.6 34.4 1.0 C A:PRO152 3.6 60.2 1.0 C A:THR155 3.6 12.4 1.0 CG A:ASP173 3.7 3.4 1.0 HG3 A:GLU176 3.7 21.5 1.0 CA A:PRO152 3.7 74.4 1.0 C A:GLY153 3.8 70.4 1.0 O A:PRO152 3.9 21.1 1.0 CG A:ASP150 3.9 3.1 1.0 N A:GLY153 3.9 25.3 1.0 O A:PHE149 4.0 14.3 1.0 HA A:LEU156 4.0 15.3 1.0 C A:ASN154 4.0 3.1 1.0 H A:GLY153 4.1 33.3 1.0 N A:PRO152 4.2 42.0 1.0 HB3 A:ASP175 4.2 24.5 1.0 O A:ASP150 4.3 13.3 1.0 CB A:THR155 4.3 62.2 1.0 CA A:THR155 4.4 75.2 1.0 HB3 A:ASP173 4.4 13.1 1.0 OD2 A:ASP150 4.5 13.4 1.0 CA A:GLY153 4.5 64.4 1.0 CB A:ASP173 4.5 72.2 1.0 OD1 A:ASP173 4.6 23.2 1.0 HB2 A:ASP173 4.6 41.1 1.0 OE1 A:GLU176 4.6 32.3 1.0 C A:ASP150 4.6 15.1 1.0 N A:THR155 4.6 25.2 1.0 N A:LEU156 4.7 20.1 1.0 N A:ASN154 4.7 3.5 1.0 CA A:LEU156 4.8 74.5 1.0 CA A:GLY151 4.8 70.0 1.0 N A:GLY151 4.8 51.3 1.0 HG21 A:THR155 4.9 3.5 1.0 CA A:ASN154 5.0 2.4 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