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:
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
Go back to
Zinc Binding Sites List in 9hvk
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
Go back to
Zinc Binding Sites List in 9hvk
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
Go back to
Zinc Binding Sites List in 9hvk
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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