Zinc in PDB 9hlw: Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7

All present enzymatic activity of Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7:
3.4.17.21;

The structure of Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7 (pdb code 9hlw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7, PDB code: 9hlw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:160.3 occ:1.00 OE2 A:GLU425 2.0 76.1 1.0 OE1 A:GLU425 2.2 77.1 1.0 OD2 A:ASP387 2.2 81.9 1.0 NE2 A:HIS553 2.3 75.8 1.0 CD A:GLU425 2.4 76.3 1.0 CE1 A:HIS553 3.2 75.2 1.0 CD2 A:HIS553 3.3 74.8 1.0 CG A:ASP387 3.4 81.2 1.0 OH A:TYR552 3.6 77.5 1.0 ZN A:ZN806 3.8 125.2 1.0 CG A:GLU425 3.9 76.5 1.0 CE1 A:TYR552 4.0 76.8 1.0 OD1 A:ASP387 4.0 82.6 1.0 CZ A:TYR552 4.2 77.1 1.0 ND1 A:HIS553 4.4 74.2 1.0 CB A:ASP387 4.4 79.7 1.0 OE1 A:GLU424 4.4 74.7 1.0 CG A:HIS553 4.4 74.3 1.0 NE2 A:HIS377 4.7 69.1 1.0 CB A:GLU425 4.7 75.9 1.0 NE1 A:TRP381 4.8 73.2 1.0

Zinc binding site 2 out of 4 in the Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:125.2 occ:1.00 OD1 A:ASP387 2.0 82.6 1.0 CE1 A:HIS377 2.0 69.8 1.0 NE2 A:HIS377 2.3 69.1 1.0 OD2 A:ASP453 2.7 98.4 1.0 CG A:ASP387 2.7 81.2 1.0 OD2 A:ASP387 2.8 81.9 1.0 OD1 A:ASP453 3.1 97.8 1.0 CG A:ASP453 3.2 97.7 1.0 ND1 A:HIS377 3.3 70.1 1.0 OE1 A:GLU424 3.5 74.7 1.0 CD2 A:HIS377 3.6 68.5 1.0 ZN A:ZN805 3.8 160.3 1.0 OE2 A:GLU425 3.8 76.1 1.0 CD A:GLU424 4.1 72.8 1.0 CG A:HIS377 4.1 69.7 1.0 OE2 A:GLU424 4.1 73.6 1.0 CB A:ASP387 4.2 79.7 1.0 CB A:PRO388 4.4 69.0 1.0 OG A:SER454 4.5 77.7 1.0 OD1 A:ASN519 4.5 70.6 1.0 CB A:ASP453 4.5 97.9 1.0 ND2 A:ASN519 4.6 69.1 1.0 CD A:GLU425 4.6 76.3 1.0 CA A:ASP387 4.8 79.5 1.0 CA A:PRO388 4.9 68.7 1.0 CG A:ASN519 5.0 68.9 1.0

Zinc binding site 3 out of 4 in the Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn805 b:156.3 occ:1.00 OE2 E:GLU425 2.0 77.0 1.0 OE1 E:GLU425 2.2 77.8 1.0 OD2 E:ASP387 2.2 80.1 1.0 NE2 E:HIS553 2.3 78.7 1.0 CD E:GLU425 2.4 77.1 1.0 CE1 E:HIS553 3.2 78.3 1.0 CD2 E:HIS553 3.3 77.8 1.0 CG E:ASP387 3.3 79.4 1.0 OH E:TYR552 3.5 79.9 1.0 ZN E:ZN806 3.8 118.5 1.0 CG E:GLU425 3.9 77.2 1.0 CE1 E:TYR552 4.0 79.2 1.0 OD1 E:ASP387 4.0 80.8 1.0 CZ E:TYR552 4.2 79.5 1.0 ND1 E:HIS553 4.4 77.4 1.0 CB E:ASP387 4.4 78.0 1.0 OE1 E:GLU424 4.4 76.6 1.0 CG E:HIS553 4.4 77.5 1.0 NE2 E:HIS377 4.7 68.2 1.0 CB E:GLU425 4.7 76.7 1.0 NE1 E:TRP381 4.8 71.3 1.0 CD1 E:TRP381 5.0 71.4 1.0

Zinc binding site 4 out of 4 in the Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Prostate Specific Membrane Antigen (Psma) in Complex with NANOBODY7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn806 b:118.5 occ:1.00 CE1 E:HIS377 2.0 68.7 1.0 OD1 E:ASP387 2.0 80.8 1.0 NE2 E:HIS377 2.3 68.2 1.0 OD2 E:ASP453 2.7 92.0 1.0 CG E:ASP387 2.7 79.4 1.0 OD2 E:ASP387 2.8 80.1 1.0 OD1 E:ASP453 3.1 91.3 1.0 CG E:ASP453 3.2 91.1 1.0 ND1 E:HIS377 3.3 68.9 1.0 OE1 E:GLU424 3.5 76.6 1.0 CD2 E:HIS377 3.6 67.7 1.0 ZN E:ZN805 3.8 156.3 1.0 OE2 E:GLU425 3.8 77.0 1.0 CD E:GLU424 4.1 74.9 1.0 CG E:HIS377 4.1 68.7 1.0 OE2 E:GLU424 4.1 75.6 1.0 CB E:ASP387 4.2 78.0 1.0 CB E:PRO388 4.4 70.3 1.0 OG E:SER454 4.4 77.0 1.0 CB E:ASP453 4.5 91.2 1.0 OD1 E:ASN519 4.6 71.1 1.0 CD E:GLU425 4.6 77.1 1.0 ND2 E:ASN519 4.6 69.8 1.0 CA E:ASP387 4.8 78.1 1.0 CA E:PRO388 4.9 70.2 1.0

G.Alon-Zchut, R.Zalk, T.T.Huynh, M.R.Zalutsky, Y.Weizmann, R.Zarivach, N.Papo. Structural Analysis of Nanobody Interactions with Their Prostate-Specific Membrane Antigen Binding Epitopes. Int.J.Biol.Macromol. 45693 2025.
ISSN: ISSN 0141-8130
PubMed: 40609945
DOI: 10.1016/J.IJBIOMAC.2025.145693