Zinc in PDB 9hvi: Psma in Complex with Nanobody 8

All present enzymatic activity of Psma in Complex with Nanobody 8:
3.4.17.21;

The structure of Psma in Complex with Nanobody 8 also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Psma in Complex with Nanobody 8 (pdb code 9hvi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Psma in Complex with Nanobody 8, PDB code: 9hvi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Psma in Complex with Nanobody 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Psma in Complex with Nanobody 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:144.9 occ:1.00 NE2 A:HIS553 2.3 89.4 1.0 OE1 A:GLU425 2.3 101.6 1.0 OD2 A:ASP387 2.4 101.5 1.0 CE1 A:HIS553 2.8 87.0 1.0 CD A:GLU425 3.0 98.5 1.0 OE2 A:GLU425 3.1 101.2 1.0 CG A:ASP387 3.4 94.7 1.0 ZN A:ZN806 3.5 158.1 1.0 CD2 A:HIS553 3.5 83.3 1.0 OH A:TYR552 3.6 86.9 1.0 OD1 A:ASP387 3.7 92.7 1.0 OE1 A:GLU424 4.0 103.8 1.0 ND1 A:HIS553 4.1 80.0 1.0 CE1 A:TYR552 4.2 84.3 1.0 CZ A:TYR552 4.3 87.0 1.0 CG A:HIS553 4.5 79.4 1.0 CG A:GLU425 4.5 94.5 1.0 CB A:ASP387 4.7 89.0 1.0 OE2 A:GLU424 4.7 98.5 1.0 CD A:GLU424 4.8 100.3 1.0 OD2 A:ASP453 4.8 112.5 1.0 NE2 A:HIS377 4.9 100.3 1.0

Zinc binding site 2 out of 4 in the Psma in Complex with Nanobody 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Psma in Complex with Nanobody 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:158.1 occ:1.00 OD1 A:ASP387 2.0 92.7 1.0 OD1 A:ASP453 2.2 110.8 1.0 OD2 A:ASP453 2.2 112.5 1.0 NE2 A:HIS377 2.3 100.3 1.0 CG A:ASP453 2.5 108.5 1.0 CG A:ASP387 3.0 94.7 1.0 CD2 A:HIS377 3.3 97.1 1.0 CE1 A:HIS377 3.3 90.4 1.0 OD2 A:ASP387 3.3 101.5 1.0 ZN A:ZN805 3.5 144.9 1.0 OE1 A:GLU424 3.7 103.8 1.0 CB A:ASP453 4.0 106.5 1.0 CB A:PRO388 4.0 90.8 1.0 CD A:GLU424 4.2 100.3 1.0 OE2 A:GLU424 4.2 98.5 1.0 CB A:ASP387 4.3 89.0 1.0 ND1 A:HIS377 4.4 94.4 1.0 CG A:HIS377 4.4 93.3 1.0 OE2 A:GLU425 4.5 101.2 1.0 ND2 A:ASN519 4.6 96.9 1.0 CA A:PRO388 4.6 87.5 1.0 OE1 A:GLU425 4.6 101.6 1.0 OD1 A:ASN519 4.7 100.8 1.0 N A:SER454 4.7 108.9 1.0 CD A:GLU425 4.7 98.5 1.0 CA A:ASP387 4.8 90.2 1.0 CA A:ASP453 4.8 102.0 1.0 N A:PRO388 4.8 84.8 1.0 CG A:PRO388 4.8 88.0 1.0 C A:ASP387 4.9 92.4 1.0

Zinc binding site 3 out of 4 in the Psma in Complex with Nanobody 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Psma in Complex with Nanobody 8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn805 b:140.8 occ:1.00 OE1 E:GLU425 2.3 99.1 1.0 NE2 E:HIS553 2.3 89.0 1.0 OD2 E:ASP387 2.3 102.6 1.0 CE1 E:HIS553 2.9 87.4 1.0 CD E:GLU425 3.0 96.5 1.0 OE2 E:GLU425 3.0 99.5 1.0 CG E:ASP387 3.4 95.1 1.0 ZN E:ZN806 3.5 149.0 1.0 CD2 E:HIS553 3.5 83.3 1.0 OH E:TYR552 3.6 87.6 1.0 OD1 E:ASP387 3.8 93.5 1.0 OE1 E:GLU424 4.0 105.9 1.0 ND1 E:HIS553 4.1 82.9 1.0 CE1 E:TYR552 4.3 84.0 1.0 CZ E:TYR552 4.3 86.8 1.0 CG E:GLU425 4.4 92.4 1.0 CG E:HIS553 4.5 79.5 1.0 OE2 E:GLU424 4.7 98.5 1.0 CB E:ASP387 4.7 90.6 1.0 OD2 E:ASP453 4.8 104.3 1.0 CD E:GLU424 4.8 101.6 1.0 NE2 E:HIS377 4.9 100.2 1.0

Zinc binding site 4 out of 4 in the Psma in Complex with Nanobody 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Psma in Complex with Nanobody 8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn806 b:149.0 occ:1.00 OD1 E:ASP387 2.0 93.5 1.0 OD2 E:ASP453 2.2 104.3 1.0 OD1 E:ASP453 2.3 103.3 1.0 NE2 E:HIS377 2.3 100.2 1.0 CG E:ASP453 2.5 100.9 1.0 CG E:ASP387 3.0 95.1 1.0 OD2 E:ASP387 3.3 102.6 1.0 CD2 E:HIS377 3.3 96.8 1.0 CE1 E:HIS377 3.3 89.7 1.0 ZN E:ZN805 3.5 140.8 1.0 OE1 E:GLU424 3.7 105.9 1.0 CB E:PRO388 4.0 90.0 1.0 CB E:ASP453 4.0 99.2 1.0 CD E:GLU424 4.2 101.6 1.0 OE2 E:GLU424 4.2 98.5 1.0 CB E:ASP387 4.3 90.6 1.0 ND2 E:ASN519 4.4 94.9 1.0 ND1 E:HIS377 4.4 92.9 1.0 CG E:HIS377 4.4 92.7 1.0 OE2 E:GLU425 4.5 99.5 1.0 CA E:PRO388 4.6 87.6 1.0 OE1 E:GLU425 4.6 99.1 1.0 CD E:GLU425 4.7 96.5 1.0 N E:SER454 4.7 103.8 1.0 CA E:ASP387 4.7 91.0 1.0 N E:PRO388 4.8 84.6 1.0 CG E:PRO388 4.8 86.3 1.0 CA E:ASP453 4.9 93.2 1.0 C E:ASP387 4.9 93.5 1.0 OD1 E:ASN519 5.0 100.9 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