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Zinc in PDB 9hvk: Psma in Complex with Nanobody 7 and 8

Enzymatic activity of Psma in Complex with Nanobody 7 and 8

All present enzymatic activity of Psma in Complex with Nanobody 7 and 8:
3.4.17.21;

Other elements in 9hvk:

The structure of Psma in Complex with Nanobody 7 and 8 also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Psma in Complex with Nanobody 7 and 8 (pdb code 9hvk). 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 7 and 8, PDB code: 9hvk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9hvk

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Zinc binding site 1 out of 4 in the Psma in Complex with Nanobody 7 and 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 7 and 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:249.8
occ:1.00
O A:ARG255 2.1 152.6 1.0
ND1 A:HIS553 2.3 156.4 1.0
CA A:GLY256 2.5 164.2 1.0
CE1 A:HIS553 2.5 155.7 1.0
C A:ARG255 2.9 151.1 1.0
N A:GLY256 3.1 164.6 1.0
OE1 A:GLU425 3.2 141.9 1.0
NE1 A:TRP381 3.2 135.6 1.0
CG A:HIS553 3.5 154.8 1.0
NH2 A:ARG210 3.6 157.6 1.0
CZ2 A:TRP381 3.7 134.3 1.0
CE2 A:TRP381 3.7 133.8 1.0
NE2 A:HIS553 3.7 153.8 1.0
CZ A:ARG210 3.8 159.1 1.0
C A:GLY256 3.8 163.2 1.0
NH1 A:ARG210 4.0 159.1 1.0
N A:ASN257 4.1 136.9 1.0
CD2 A:HIS553 4.2 155.2 1.0
CA A:ARG255 4.3 148.3 1.0
CD1 A:TRP381 4.3 131.8 1.0
NE A:ARG210 4.4 158.5 1.0
CD A:GLU425 4.4 139.6 1.0
CB A:HIS553 4.4 153.4 1.0
OH A:TYR552 4.6 164.4 1.0
CE2 A:TYR552 4.7 162.9 1.0
O A:GLY256 4.8 162.7 1.0
CB A:ARG255 4.8 149.1 1.0
N A:ARG255 4.9 148.6 1.0
CH2 A:TRP381 4.9 132.8 1.0
OE2 A:GLU425 4.9 136.5 1.0
CD2 A:TRP381 5.0 130.4 1.0

Zinc binding site 2 out of 4 in 9hvk

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Zinc binding site 2 out of 4 in the Psma in Complex with Nanobody 7 and 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 7 and 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn806

b:137.0
occ:1.00
OD2 A:ASP453 2.1 151.5 1.0
NE2 A:HIS377 2.3 132.6 1.0
OD1 A:ASP387 2.4 133.8 1.0
CE1 A:HIS377 2.8 129.8 1.0
CG A:ASP453 3.1 153.0 1.0
CG A:ASP387 3.2 133.1 1.0
OD2 A:ASP387 3.2 131.8 1.0
OD1 A:ASP453 3.4 154.7 1.0
CD2 A:HIS377 3.5 133.2 1.0
OE2 A:GLU425 3.7 136.5 1.0
OE2 A:GLU424 3.8 138.1 1.0
OE1 A:GLU424 3.9 141.2 1.0
ND1 A:HIS377 4.0 130.3 1.0
CD A:GLU424 4.2 138.3 1.0
CG A:HIS377 4.3 131.2 1.0
CB A:ASP453 4.5 153.3 1.0
OG A:SER454 4.5 141.4 1.0
CB A:ASP387 4.6 133.5 1.0
CB A:PRO388 4.8 135.1 1.0
CD A:GLU425 4.8 139.6 1.0
NE2 A:HIS553 4.9 153.8 1.0
OD1 A:ASN519 4.9 133.8 1.0

Zinc binding site 3 out of 4 in 9hvk

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Zinc binding site 3 out of 4 in the Psma in Complex with Nanobody 7 and 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 7 and 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn805

b:248.8
occ:1.00
O E:ARG255 2.1 156.7 1.0
ND1 E:HIS553 2.3 155.0 1.0
CA E:GLY256 2.8 154.2 1.0
C E:ARG255 2.8 154.5 1.0
NH1 E:ARG210 3.0 156.8 1.0
CE1 E:HIS553 3.1 153.3 1.0
N E:GLY256 3.1 154.7 1.0
CZ E:ARG210 3.1 156.4 1.0
NH2 E:ARG210 3.4 154.3 1.0
CG E:HIS553 3.4 153.1 1.0
CB E:HIS553 3.8 151.7 1.0
NE E:ARG210 3.8 155.2 1.0
NE2 E:GLN254 4.0 145.9 1.0
CA E:ARG255 4.1 151.8 1.0
CG E:GLN254 4.2 147.0 1.0
C E:GLY256 4.2 153.3 1.0
N E:ARG255 4.2 151.6 1.0
NE1 E:TRP381 4.3 132.8 1.0
NE2 E:HIS553 4.3 150.8 1.0
CD E:ARG210 4.4 155.6 1.0
CD2 E:HIS553 4.4 153.0 1.0
OE1 E:GLU425 4.6 144.8 1.0
CD E:GLN254 4.6 147.3 1.0
N E:ASN257 4.7 141.7 1.0
CE2 E:TYR552 4.8 167.2 1.0
CE2 E:TRP381 4.9 130.3 1.0
CZ2 E:TRP381 5.0 130.9 1.0

Zinc binding site 4 out of 4 in 9hvk

Go back to Zinc Binding Sites List in 9hvk
Zinc binding site 4 out of 4 in the Psma in Complex with Nanobody 7 and 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 7 and 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn806

b:152.8
occ:1.00
OD2 E:ASP453 2.1 150.1 1.0
NE2 E:HIS377 2.3 137.5 1.0
CE1 E:HIS377 3.0 134.2 1.0
CG E:ASP453 3.1 151.4 1.0
OD1 E:ASP453 3.3 153.8 1.0
CD2 E:HIS377 3.4 136.6 1.0
OE2 E:GLU425 3.6 141.1 1.0
OE1 E:GLU424 3.8 141.9 1.0
OE2 E:GLU424 3.9 138.0 1.0
OD2 E:ASP387 4.1 158.6 1.0
ND1 E:HIS377 4.1 133.8 1.0
CD E:GLU424 4.2 138.9 1.0
CG E:HIS377 4.4 134.1 1.0
CB E:ASP453 4.4 150.6 1.0
NE2 E:HIS553 4.6 150.8 1.0
CB E:ASP387 4.7 158.4 1.0
CD E:GLU425 4.7 143.0 1.0
CG E:ASP387 4.9 160.0 1.0
OH E:TYR552 4.9 168.8 1.0
CB E:PRO388 4.9 132.6 1.0

Reference:

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
Page generated: Fri Aug 22 18:06:41 2025

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