Zinc in PDB 7ufg: Cryo-Em Structure of Papp-A in Complex with IGFBP5

All present enzymatic activity of Cryo-Em Structure of Papp-A in Complex with IGFBP5:
3.4.24.79;

The binding sites of Zinc atom in the Cryo-Em Structure of Papp-A in Complex with IGFBP5 (pdb code 7ufg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Papp-A in Complex with IGFBP5, PDB code: 7ufg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Papp-A in Complex with IGFBP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Papp-A in Complex with IGFBP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4000 b:140.0 occ:1.00 O C:SER143 1.9 141.3 1.0 HE1 A:HIS492 2.1 128.4 1.0 NE2 A:HIS492 2.3 128.4 1.0 NE2 A:HIS486 2.3 118.8 1.0 NE2 A:HIS482 2.3 127.7 1.0 CE1 A:HIS492 2.5 128.4 1.0 O C:THR141 2.8 133.9 1.0 CD2 A:HIS486 3.1 118.8 1.0 HD2 A:HIS486 3.1 118.8 1.0 CE1 A:HIS482 3.1 127.7 1.0 C C:SER143 3.1 141.3 1.0 OH A:TYR558 3.1 144.0 1.0 HE1 A:HIS482 3.1 127.7 1.0 HH A:TYR558 3.3 144.0 1.0 CD2 A:HIS482 3.4 127.7 1.0 CE1 A:HIS486 3.4 118.8 1.0 CD2 A:HIS492 3.7 128.4 1.0 HD2 A:HIS482 3.7 127.7 1.0 HE1 A:HIS486 3.7 118.8 1.0 CZ A:TYR558 3.7 144.0 1.0 C C:THR141 3.8 133.9 1.0 ND1 A:HIS492 3.8 128.4 1.0 O C:LEU140 3.9 142.4 1.0 N C:SER143 4.0 141.3 1.0 HA C:THR141 4.0 133.9 1.0 H C:SER143 4.0 141.3 1.0 CA C:SER143 4.1 141.3 1.0 HD2 A:HIS492 4.2 128.4 1.0 HE1 A:TYR558 4.2 144.0 1.0 CE1 A:TYR558 4.3 144.0 1.0 C C:GLN142 4.3 132.0 1.0 ND1 A:HIS482 4.3 127.7 1.0 CG A:HIS486 4.3 118.8 1.0 HD1 A:HIS492 4.4 128.4 1.0 CG A:HIS492 4.4 128.4 1.0 CE2 A:TYR558 4.4 144.0 1.0 ND1 A:HIS486 4.4 118.8 1.0 HE2 A:TYR558 4.5 144.0 1.0 CA C:THR141 4.5 133.9 1.0 CG A:HIS482 4.5 127.7 1.0 HB2 C:SER143 4.6 141.3 1.0 O C:GLN142 4.7 132.0 1.0 N C:GLN142 4.7 132.0 1.0 HA C:GLN142 4.7 132.0 1.0 HZ A:PHE494 4.7 137.2 1.0 CA C:GLN142 4.8 132.0 1.0 HA C:SER143 4.9 141.3 1.0 CB C:SER143 4.9 141.3 1.0 C C:LEU140 5.0 142.4 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Papp-A in Complex with IGFBP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Papp-A in Complex with IGFBP5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4000 b:71.8 occ:1.00 O D:SER143 1.9 50.2 1.0 HE1 B:HIS492 2.0 38.0 1.0 NE2 B:HIS492 2.3 38.0 1.0 NE2 B:HIS482 2.3 26.9 1.0 NE2 B:HIS486 2.3 23.2 1.0 CE1 B:HIS492 2.4 38.0 1.0 C D:SER143 2.9 50.2 1.0 HD2 B:HIS486 3.0 23.2 1.0 CD2 B:HIS486 3.0 23.2 1.0 CE1 B:HIS482 3.2 26.9 1.0 CD2 B:HIS482 3.3 26.9 1.0 HD2 B:HIS482 3.4 26.9 1.0 HE1 B:HIS482 3.4 26.9 1.0 CE1 B:HIS486 3.4 23.2 1.0 HB3 D:SER143 3.4 50.2 1.0 N D:SER143 3.6 50.2 1.0 CA D:SER143 3.6 50.2 1.0 H D:SER143 3.6 50.2 1.0 CD2 B:HIS492 3.7 38.0 1.0 ND1 B:HIS492 3.7 38.0 1.0 HH B:TYR558 3.7 58.4 1.0 HE1 B:HIS486 3.7 23.2 1.0 CB D:SER143 3.9 50.2 1.0 OH B:TYR558 3.9 58.4 1.0 HB2 D:SER143 4.0 50.2 1.0 C D:GLN142 4.0 37.2 1.0 O D:THR141 4.1 44.1 1.0 HD1 B:HIS492 4.2 38.0 1.0 HD2 B:HIS492 4.2 38.0 1.0 CG B:HIS486 4.3 23.2 1.0 CG B:HIS492 4.3 38.0 1.0 ND1 B:HIS482 4.4 26.9 1.0 CG B:HIS482 4.4 26.9 1.0 O D:GLN142 4.4 37.2 1.0 ND1 B:HIS486 4.4 23.2 1.0 CZ B:TYR558 4.5 58.4 1.0 HA D:SER143 4.5 50.2 1.0 HA D:GLN142 4.5 37.2 1.0 HE1 B:TYR558 4.5 58.4 1.0 C D:THR141 4.6 44.1 1.0 O D:LEU140 4.7 53.6 1.0 CE1 B:TYR558 4.7 58.4 1.0 CA D:GLN142 4.7 37.2 1.0 N D:GLN142 5.0 37.2 1.0

R.A.Judge, J.Sridar, K.Tunyasunvunakool, R.Jain, J.C.K.Wang, C.Ouch, J.Xu, A.Mafi, A.H.Nile, C.Remarcik, C.L.Smith, C.Ghosh, C.Xu, V.Stoll, J.Jumper, A.H.Singh, D.Eaton, Q.Hao. Structure of the Papp-ABP5 Complex Reveals Mechanism of Substrate Recognition Nat Commun V. 13 5500 2022.
ISSN: ESSN 2041-1723
PubMed: 36127359
DOI: 10.1038/S41467-022-33175-2