Zinc 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:

Calcium

(Ca)

32 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Prommp-7 with Heparin Octasaccharide Bound to the Catalytic Domain, PDB code: 5ue5:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn303 b:52.1 occ:1.00 NE2 A:HIS143 2.3 62.3 1.0 OD2 A:ASP145 2.3 0.0 1.0 NE2 A:HIS158 2.3 3.3 1.0 ND1 A:HIS171 2.5 43.2 1.0 HE1 A:HIS171 2.5 4.3 1.0 CG A:ASP145 2.8 21.5 1.0 CE1 A:HIS171 2.8 13.2 1.0 HZ A:PHE160 2.9 0.2 1.0 CD2 A:HIS143 3.0 25.4 1.0 CE1 A:HIS158 3.0 2.4 1.0 HD2 A:HIS143 3.1 63.1 1.0 OD1 A:ASP145 3.2 21.2 1.0 HE1 A:HIS158 3.2 12.0 1.0 CD2 A:HIS158 3.2 74.5 1.0 CE1 A:HIS143 3.3 23.3 1.0 HB3 A:ASP145 3.5 35.2 1.0 HD2 A:HIS158 3.6 54.2 1.0 HE1 A:HIS143 3.7 44.3 1.0 CB A:ASP145 3.7 33.0 1.0 CZ A:PHE160 3.9 44.5 1.0 CG A:HIS171 3.9 4.2 1.0 NE2 A:HIS171 4.1 3.5 1.0 ND1 A:HIS158 4.1 2.5 1.0 CG A:HIS158 4.2 1.3 1.0 CG A:HIS143 4.2 43.3 1.0 HA2 A:GLY141 4.2 4.4 1.0 HB2 A:ASP145 4.3 41.3 1.0 ND1 A:HIS143 4.3 12.3 1.0 HB2 A:HIS171 4.5 53.4 1.0 HE2 A:PHE160 4.6 61.2 1.0 HB3 A:HIS171 4.6 61.3 1.0 HE1 A:PHE160 4.6 31.1 1.0 CD2 A:HIS171 4.6 22.2 1.0 HB1 A:ALA139 4.6 24.4 1.0 CB A:HIS171 4.7 62.3 1.0 CE2 A:PHE160 4.7 74.3 1.0 CE1 A:PHE160 4.7 43.1 1.0 HE2 A:HIS171 4.8 4.2 1.0 H A:GLY144 4.9 34.0 1.0 CA A:ASP145 5.0 14.2 1.0 HD1 A:HIS158 5.0 30.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn304 b:42.1 occ:1.00 NE2 A:HIS198 2.2 31.1 1.0 NE2 A:HIS204 2.3 12.2 1.0 NE2 A:HIS194 2.3 20.4 1.0 SG A:CYS67 2.5 42.5 1.0 HE1 A:HIS204 2.6 31.4 1.0 CE1 A:HIS204 2.7 64.5 1.0 HB3 A:CYS67 2.8 10.5 1.0 CE1 A:HIS198 2.9 74.2 1.0 CB A:CYS67 3.0 71.3 1.0 HE1 A:HIS198 3.0 4.2 1.0 HB2 A:CYS67 3.1 41.2 1.0 CE1 A:HIS194 3.1 24.4 1.0 CD2 A:HIS194 3.2 51.2 1.0 HG A:CYS67 3.2 24.4 1.0 CD2 A:HIS198 3.3 14.5 1.0 HE1 A:HIS194 3.4 11.1 1.0 HG23 A:VAL69 3.5 34.5 1.0 HD2 A:HIS194 3.5 72.5 1.0 CD2 A:HIS204 3.5 12.0 1.0 HD2 A:HIS198 3.7 72.5 1.0 HB A:VAL69 3.7 13.3 1.0 ND1 A:HIS204 3.8 21.2 1.0 HG21 A:VAL69 4.0 42.4 1.0 ND1 A:HIS198 4.0 15.1 1.0 HD2 A:HIS204 4.1 5.4 1.0 ND1 A:HIS194 4.1 61.4 1.0 CG2 A:VAL69 4.1 24.1 1.0 CG A:HIS194 4.2 24.3 1.0 CG A:HIS204 4.2 24.4 1.0 CG A:HIS198 4.2 60.3 1.0 HE1 A:MET212 4.3 41.2 1.0 H A:VAL69 4.4 51.4 1.0 CB A:VAL69 4.5 12.4 1.0 HD1 A:HIS204 4.5 33.1 1.0 NH2 A:ARG66 4.5 11.5 1.0 CZ A:ARG66 4.5 24.3 1.0 CA A:CYS67 4.6 1.2 1.0 HH21 A:ARG66 4.7 41.3 1.0 NE A:ARG66 4.7 51.0 1.0 HH22 A:ARG66 4.8 20.2 1.0 HD2 A:ARG66 4.8 1.0 1.0 HE A:ARG66 4.8 20.4 1.0 HB3 A:MET212 4.9 34.3 1.0 HG2 A:ARG66 4.9 63.5 1.0 HD1 A:HIS198 4.9 23.0 1.0 NH1 A:ARG66 4.9 74.1 1.0 HA A:CYS67 4.9 50.3 1.0 OD2 A:ASP71 5.0 70.1 1.0 H A:GLY68 5.0 25.4 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