Zinc 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:

Calcium

(Ca)

32 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Prommp-7 with Heparin Octasaccharide Bridging Between Domains, PDB code: 5ue2:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn303 b:72.2 occ:1.00 NE2 A:HIS143 2.2 10.3 1.0 OD2 A:ASP145 2.3 72.0 1.0 NE2 A:HIS158 2.3 42.3 1.0 ND1 A:HIS171 2.5 11.2 1.0 HE1 A:HIS171 2.5 4.4 1.0 HZ A:PHE160 2.7 53.5 1.0 CE1 A:HIS171 2.8 22.1 1.0 CG A:ASP145 2.8 3.1 1.0 CD2 A:HIS143 3.0 35.2 1.0 CE1 A:HIS158 3.1 23.3 1.0 HD2 A:HIS143 3.1 35.3 1.0 CD2 A:HIS158 3.2 1.1 1.0 HB3 A:ASP145 3.2 52.4 1.0 CE1 A:HIS143 3.3 1.4 1.0 CB A:ASP145 3.4 32.3 1.0 HE1 A:HIS158 3.4 54.1 1.0 HD2 A:HIS158 3.4 4.4 1.0 HB2 A:ASP145 3.4 13.2 1.0 OD1 A:ASP145 3.5 44.3 1.0 HE1 A:HIS143 3.6 51.5 1.0 CZ A:PHE160 3.6 62.5 1.0 CG A:HIS171 3.9 0.4 1.0 NE2 A:HIS171 4.0 61.0 1.0 HE1 A:PHE160 4.1 71.3 1.0 ND1 A:HIS158 4.2 63.2 1.0 CG A:HIS158 4.2 13.0 1.0 CG A:HIS143 4.2 14.0 1.0 ND1 A:HIS143 4.3 72.4 1.0 CE1 A:PHE160 4.3 62.2 1.0 HB2 A:HIS171 4.5 32.5 1.0 HE2 A:PHE160 4.6 24.2 1.0 CE2 A:PHE160 4.6 71.4 1.0 CD2 A:HIS171 4.6 4.5 1.0 HB3 A:HIS171 4.6 34.5 1.0 CB A:HIS171 4.7 40.4 1.0 HE2 A:HIS171 4.8 24.4 1.0 HB2 A:ALA139 4.8 41.2 1.0 CA A:ASP145 4.9 75.3 1.0 HA2 A:GLY141 4.9 2.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn304 b:44.4 occ:1.00 NE2 A:HIS198 2.2 31.3 1.0 NE2 A:HIS204 2.3 54.5 1.0 NE2 A:HIS194 2.3 64.2 1.0 SG A:CYS67 2.5 70.1 1.0 HE1 A:HIS204 2.7 4.3 1.0 CE1 A:HIS204 2.7 22.2 1.0 HB3 A:CYS67 2.8 32.3 1.0 CE1 A:HIS198 2.9 35.1 1.0 HB2 A:CYS67 3.0 32.2 1.0 CB A:CYS67 3.0 53.4 1.0 CE1 A:HIS194 3.0 61.1 1.0 HE1 A:HIS198 3.0 31.2 1.0 HG A:CYS67 3.2 72.3 1.0 HE1 A:HIS194 3.2 74.3 1.0 CD2 A:HIS194 3.3 71.4 1.0 CD2 A:HIS198 3.3 31.1 1.0 CD2 A:HIS204 3.5 61.4 1.0 HD2 A:HIS194 3.6 44.1 1.0 HG22 A:VAL69 3.6 14.2 1.0 HD2 A:HIS198 3.7 25.4 1.0 HB A:VAL69 3.7 14.3 1.0 ND1 A:HIS204 3.8 35.5 1.0 HD2 A:HIS204 4.0 53.0 1.0 ND1 A:HIS198 4.0 14.2 1.0 ND1 A:HIS194 4.0 61.1 1.0 HG23 A:VAL69 4.1 41.1 1.0 CG A:HIS194 4.2 63.4 1.0 CG A:HIS204 4.2 31.1 1.0 CG A:HIS198 4.2 4.4 1.0 CG2 A:VAL69 4.2 44.5 1.0 H A:VAL69 4.5 62.5 1.0 CB A:VAL69 4.5 4.3 1.0 CA A:CYS67 4.6 21.1 1.0 HD1 A:HIS204 4.6 54.1 1.0 HH21 A:ARG66 4.6 41.5 1.0 HG2 A:ARG66 4.7 1.1 1.0 HB3 A:MET212 4.7 52.0 1.0 NH2 A:ARG66 4.7 21.3 1.0 HE2 A:MET212 4.7 45.3 1.0 HE A:ARG66 4.7 11.4 1.0 CZ A:ARG66 4.8 13.2 1.0 NE A:ARG66 4.8 20.1 1.0 HD1 A:HIS198 4.9 43.1 1.0 HD1 A:HIS194 4.9 50.3 1.0 HA A:CYS67 4.9 61.2 1.0 HD2 A:ARG66 5.0 11.4 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