Zinc in PDB 9g5j: Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans
Protein crystallography data
The structure of Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans, PDB code: 9g5j
was solved by
B.Claushuis,
F.Wojtalla,
H.Van Leeuwen,
J.Corver,
U.Baumann,
P.Hensbergen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.71 /
2.00
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.43,
95.41,
126.81,
90,
90,
90
|
|
R / Rfree (%)
|
19 /
22.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans
(pdb code 9g5j). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans, PDB code: 9g5j:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 9g5j
Go back to
Zinc Binding Sites List in 9g5j
Zinc binding site 1 out
of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn701
b:18.7
occ:0.41
|
O
|
E:PRO4
|
1.9
|
21.6
|
1.0
|
|
OE1
|
A:GLU197
|
2.0
|
20.4
|
1.0
|
|
OE2
|
A:GLU197
|
2.1
|
26.1
|
1.0
|
|
NE2
|
A:HIS157
|
2.3
|
23.6
|
1.0
|
|
CD
|
A:GLU197
|
2.3
|
18.6
|
1.0
|
|
NE2
|
A:HIS153
|
2.3
|
23.3
|
1.0
|
|
CE1
|
A:HIS157
|
3.0
|
21.9
|
1.0
|
|
HE1
|
A:HIS157
|
3.1
|
26.4
|
1.0
|
|
C
|
E:PRO4
|
3.1
|
26.3
|
1.0
|
|
HA
|
E:PRO5
|
3.1
|
26.5
|
1.0
|
|
CD2
|
A:HIS153
|
3.2
|
21.7
|
1.0
|
|
CE1
|
A:HIS153
|
3.3
|
21.9
|
1.0
|
|
HD2
|
A:HIS153
|
3.4
|
26.2
|
1.0
|
|
CD2
|
A:HIS157
|
3.4
|
21.1
|
1.0
|
|
HE1
|
A:HIS153
|
3.5
|
26.3
|
1.0
|
|
HE2
|
A:PHE190
|
3.5
|
25.4
|
1.0
|
|
HD2
|
A:HIS157
|
3.7
|
25.4
|
1.0
|
|
CA
|
E:PRO5
|
3.7
|
22.0
|
1.0
|
|
HB3
|
E:LEU3
|
3.8
|
31.4
|
1.0
|
|
CG
|
A:GLU197
|
3.8
|
20.8
|
1.0
|
|
HA
|
A:GLU197
|
3.8
|
23.8
|
1.0
|
|
N
|
E:PRO5
|
3.8
|
22.5
|
1.0
|
|
HD3
|
E:PRO6
|
3.8
|
27.2
|
1.0
|
|
C
|
E:PRO5
|
4.0
|
22.8
|
1.0
|
|
HZ
|
A:PHE190
|
4.0
|
25.3
|
1.0
|
|
HD2
|
E:PRO4
|
4.1
|
25.5
|
1.0
|
|
N
|
E:PRO4
|
4.1
|
25.4
|
1.0
|
|
HH22
|
A:ARG111
|
4.1
|
47.9
|
1.0
|
|
HB3
|
A:ALA200
|
4.1
|
25.1
|
1.0
|
|
HG2
|
A:GLU197
|
4.2
|
25.1
|
1.0
|
|
CA
|
E:PRO4
|
4.2
|
21.2
|
1.0
|
|
ND1
|
A:HIS157
|
4.2
|
23.8
|
1.0
|
|
HG3
|
A:GLU197
|
4.3
|
25.1
|
1.0
|
|
O
|
E:HOH103
|
4.3
|
24.1
|
1.0
|
|
HG2
|
E:PRO4
|
4.3
|
28.6
|
1.0
|
|
CE2
|
A:PHE190
|
4.3
|
21.1
|
1.0
|
|
ND1
|
A:HIS153
|
4.4
|
21.0
|
1.0
|
|
HB3
|
A:GLU197
|
4.4
|
24.8
|
1.0
|
|
CG
|
A:HIS153
|
4.4
|
19.9
|
1.0
|
|
C
|
E:LEU3
|
4.4
|
24.3
|
1.0
|
|
N
|
E:PRO6
|
4.4
|
24.8
|
1.0
|
|
CG
|
A:HIS157
|
4.4
|
19.9
|
1.0
|
|
O
|
E:PRO5
|
4.4
|
19.1
|
1.0
|
|
CB
|
A:GLU197
|
4.5
|
20.6
|
1.0
|
|
CD
|
E:PRO6
|
4.5
|
22.6
|
1.0
|
|
CD
|
E:PRO4
|
4.5
|
21.2
|
1.0
|
|
CZ
|
A:PHE190
|
4.6
|
21.1
|
1.0
|
|
CA
|
A:GLU197
|
4.6
|
19.8
|
1.0
|
|
HH12
|
A:ARG111
|
4.6
|
35.3
|
1.0
|
|
O
|
E:LEU3
|
4.6
|
21.8
|
1.0
|
|
CB
|
E:LEU3
|
4.7
|
26.1
|
1.0
|
|
HB1
|
A:ALA200
|
4.8
|
25.1
|
1.0
|
|
HD2
|
E:PRO6
|
4.8
|
27.2
|
1.0
|
|
CB
|
A:ALA200
|
4.8
|
20.9
|
1.0
|
|
CG
|
E:PRO4
|
4.8
|
23.7
|
1.0
|
|
HA
|
E:PRO4
|
4.8
|
25.6
|
1.0
|
|
HB2
|
A:ALA200
|
4.9
|
25.1
|
1.0
|
|
HD1
|
A:HIS157
|
5.0
|
28.6
|
1.0
|
|
NH2
|
A:ARG111
|
5.0
|
39.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 9g5j
Go back to
Zinc Binding Sites List in 9g5j
Zinc binding site 2 out
of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn701
b:23.3
occ:0.38
|
OE1
|
B:GLU197
|
2.0
|
26.2
|
1.0
|
|
OE2
|
B:GLU197
|
2.1
|
33.0
|
1.0
|
|
O
|
F:PRO4
|
2.2
|
33.9
|
1.0
|
|
NE2
|
B:HIS153
|
2.3
|
27.0
|
1.0
|
|
NE2
|
B:HIS157
|
2.3
|
32.1
|
1.0
|
|
CD
|
B:GLU197
|
2.3
|
21.7
|
1.0
|
|
HA
|
F:PRO5
|
2.5
|
37.0
|
1.0
|
|
CD2
|
B:HIS153
|
3.1
|
24.5
|
1.0
|
|
HD2
|
B:HIS153
|
3.1
|
29.4
|
1.0
|
|
CD2
|
B:HIS157
|
3.1
|
31.8
|
1.0
|
|
C
|
F:PRO4
|
3.2
|
32.5
|
1.0
|
|
HD2
|
B:HIS157
|
3.2
|
38.2
|
1.0
|
|
CA
|
F:PRO5
|
3.3
|
30.8
|
1.0
|
|
CE1
|
B:HIS157
|
3.4
|
34.8
|
1.0
|
|
CE1
|
B:HIS153
|
3.4
|
23.0
|
1.0
|
|
N
|
F:PRO5
|
3.6
|
31.9
|
1.0
|
|
HD3
|
F:PRO6
|
3.6
|
32.6
|
1.0
|
|
HE2
|
B:PHE190
|
3.6
|
29.9
|
1.0
|
|
HE1
|
B:HIS157
|
3.6
|
41.8
|
1.0
|
|
HE1
|
B:HIS153
|
3.6
|
27.6
|
1.0
|
|
CG
|
B:GLU197
|
3.8
|
26.6
|
1.0
|
|
C
|
F:PRO5
|
3.8
|
27.1
|
1.0
|
|
HA
|
B:GLU197
|
3.9
|
32.9
|
1.0
|
|
HB3
|
F:LEU3
|
4.1
|
86.9
|
1.0
|
|
HG2
|
B:GLU197
|
4.2
|
32.0
|
1.0
|
|
CD
|
F:PRO6
|
4.2
|
27.1
|
1.0
|
|
HZ
|
B:PHE190
|
4.2
|
27.5
|
1.0
|
|
N
|
F:PRO6
|
4.2
|
24.1
|
1.0
|
|
HG3
|
B:GLU197
|
4.3
|
32.0
|
1.0
|
|
HB3
|
B:ALA200
|
4.3
|
27.4
|
1.0
|
|
CG
|
B:HIS153
|
4.3
|
24.7
|
1.0
|
|
CG
|
B:HIS157
|
4.3
|
28.6
|
1.0
|
|
HD2
|
F:PRO6
|
4.3
|
32.6
|
1.0
|
|
ND1
|
B:HIS153
|
4.4
|
23.1
|
1.0
|
|
ND1
|
B:HIS157
|
4.4
|
36.0
|
1.0
|
|
CA
|
F:PRO4
|
4.4
|
33.6
|
1.0
|
|
CE2
|
B:PHE190
|
4.4
|
24.8
|
1.0
|
|
O
|
F:LEU3
|
4.4
|
42.1
|
1.0
|
|
HB3
|
B:GLU197
|
4.5
|
31.3
|
1.0
|
|
O
|
F:PRO5
|
4.5
|
25.9
|
1.0
|
|
HB3
|
F:PRO5
|
4.5
|
36.4
|
1.0
|
|
CB
|
F:PRO5
|
4.5
|
30.3
|
1.0
|
|
CB
|
B:GLU197
|
4.6
|
26.0
|
1.0
|
|
N
|
F:PRO4
|
4.6
|
40.9
|
1.0
|
|
C
|
F:LEU3
|
4.6
|
44.2
|
1.0
|
|
CA
|
B:GLU197
|
4.7
|
27.4
|
1.0
|
|
CZ
|
B:PHE190
|
4.7
|
22.8
|
1.0
|
|
HA
|
F:PRO4
|
4.8
|
39.9
|
1.0
|
|
HB1
|
B:ALA200
|
4.8
|
27.4
|
1.0
|
|
CD
|
F:PRO5
|
4.9
|
31.0
|
1.0
|
|
CB
|
B:ALA200
|
4.9
|
22.7
|
1.0
|
|
CB
|
F:LEU3
|
5.0
|
72.3
|
1.0
|
|
HD3
|
F:PRO5
|
5.0
|
37.3
|
1.0
|
|
HB2
|
B:ALA200
|
5.0
|
27.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 9g5j
Go back to
Zinc Binding Sites List in 9g5j
Zinc binding site 3 out
of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn701
b:25.4
occ:0.31
|
OE1
|
C:GLU197
|
2.0
|
26.2
|
1.0
|
|
OE2
|
C:GLU197
|
2.0
|
35.6
|
1.0
|
|
O
|
G:PRO4
|
2.1
|
28.3
|
1.0
|
|
CD
|
C:GLU197
|
2.3
|
27.9
|
1.0
|
|
NE2
|
C:HIS153
|
2.3
|
26.4
|
1.0
|
|
NE2
|
C:HIS157
|
2.3
|
27.4
|
0.5
|
|
HA
|
G:PRO5
|
2.4
|
34.3
|
1.0
|
|
HD2
|
C:HIS157
|
3.0
|
36.7
|
0.5
|
|
C
|
G:PRO4
|
3.0
|
27.6
|
1.0
|
|
CD2
|
C:HIS157
|
3.1
|
28.7
|
0.5
|
|
HD2
|
C:HIS157
|
3.1
|
34.5
|
0.5
|
|
CD2
|
C:HIS153
|
3.2
|
22.3
|
1.0
|
|
CA
|
G:PRO5
|
3.2
|
28.5
|
1.0
|
|
HD2
|
C:HIS153
|
3.2
|
26.8
|
1.0
|
|
CE1
|
C:HIS153
|
3.3
|
26.8
|
1.0
|
|
CE1
|
C:HIS157
|
3.4
|
29.4
|
0.5
|
|
N
|
G:PRO5
|
3.4
|
27.9
|
1.0
|
|
HE1
|
C:HIS153
|
3.6
|
32.2
|
1.0
|
|
HE2
|
C:PHE190
|
3.6
|
26.1
|
1.0
|
|
HE1
|
C:HIS157
|
3.7
|
35.4
|
0.5
|
|
HD3
|
G:PRO6
|
3.7
|
30.4
|
1.0
|
|
CG
|
C:GLU197
|
3.8
|
27.6
|
1.0
|
|
C
|
G:PRO5
|
3.8
|
27.6
|
1.0
|
|
CD2
|
C:HIS157
|
3.8
|
30.5
|
0.5
|
|
HA
|
C:GLU197
|
3.9
|
28.3
|
1.0
|
|
HE2
|
C:HIS157
|
4.1
|
42.9
|
0.5
|
|
HB3
|
G:LEU3
|
4.1
|
58.5
|
1.0
|
|
HG2
|
C:GLU197
|
4.2
|
33.1
|
1.0
|
|
HZ
|
C:PHE190
|
4.2
|
28.0
|
1.0
|
|
HG3
|
C:GLU197
|
4.2
|
33.1
|
1.0
|
|
O
|
G:LEU3
|
4.3
|
41.7
|
1.0
|
|
N
|
G:PRO6
|
4.3
|
25.2
|
1.0
|
|
O
|
G:HOH101
|
4.3
|
28.8
|
1.0
|
|
CA
|
G:PRO4
|
4.3
|
30.0
|
1.0
|
|
CG
|
C:HIS157
|
4.3
|
27.1
|
0.5
|
|
NE2
|
C:HIS157
|
4.4
|
35.7
|
0.5
|
|
CG
|
C:HIS153
|
4.4
|
23.0
|
1.0
|
|
HB3
|
C:ALA200
|
4.4
|
28.7
|
1.0
|
|
CE2
|
C:PHE190
|
4.4
|
21.7
|
1.0
|
|
O
|
G:PRO5
|
4.4
|
21.3
|
1.0
|
|
ND1
|
C:HIS153
|
4.4
|
23.7
|
1.0
|
|
ND1
|
C:HIS157
|
4.4
|
29.2
|
0.5
|
|
CD
|
G:PRO6
|
4.4
|
25.3
|
1.0
|
|
HB3
|
C:GLU197
|
4.4
|
29.8
|
1.0
|
|
HB3
|
G:PRO5
|
4.4
|
37.0
|
1.0
|
|
C
|
G:LEU3
|
4.5
|
46.5
|
1.0
|
|
CB
|
G:PRO5
|
4.5
|
30.8
|
1.0
|
|
N
|
G:PRO4
|
4.5
|
39.0
|
1.0
|
|
CB
|
C:GLU197
|
4.5
|
24.7
|
1.0
|
|
HA
|
G:PRO4
|
4.6
|
36.1
|
1.0
|
|
CA
|
C:GLU197
|
4.7
|
23.5
|
1.0
|
|
CZ
|
C:PHE190
|
4.7
|
23.3
|
1.0
|
|
CD
|
G:PRO5
|
4.7
|
29.1
|
1.0
|
|
HB2
|
G:LEU3
|
4.8
|
58.5
|
1.0
|
|
HD3
|
G:PRO5
|
4.8
|
35.0
|
1.0
|
|
HG3
|
G:PRO6
|
4.9
|
25.7
|
1.0
|
|
CB
|
G:LEU3
|
4.9
|
48.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 9g5j
Go back to
Zinc Binding Sites List in 9g5j
Zinc binding site 4 out
of 4 in the Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn701
b:26.1
occ:0.44
|
O
|
H:PRO4
|
1.9
|
27.4
|
1.0
|
|
OE1
|
D:GLU197
|
2.0
|
23.8
|
1.0
|
|
OE2
|
D:GLU197
|
2.0
|
32.4
|
1.0
|
|
CD
|
D:GLU197
|
2.3
|
26.3
|
1.0
|
|
NE2
|
D:HIS157
|
2.3
|
30.6
|
1.0
|
|
NE2
|
D:HIS153
|
2.3
|
27.2
|
1.0
|
|
CE1
|
D:HIS157
|
3.1
|
29.2
|
1.0
|
|
HE1
|
D:HIS157
|
3.1
|
35.1
|
1.0
|
|
C
|
H:PRO4
|
3.2
|
28.5
|
1.0
|
|
HA
|
H:PRO5
|
3.2
|
29.7
|
1.0
|
|
CD2
|
D:HIS153
|
3.2
|
25.4
|
1.0
|
|
CE1
|
D:HIS153
|
3.3
|
26.2
|
1.0
|
|
HD2
|
D:HIS153
|
3.3
|
30.6
|
1.0
|
|
CD2
|
D:HIS157
|
3.4
|
26.5
|
1.0
|
|
HE1
|
D:HIS153
|
3.5
|
31.5
|
1.0
|
|
HB3
|
H:LEU3
|
3.6
|
37.0
|
1.0
|
|
HE2
|
D:PHE190
|
3.6
|
30.0
|
1.0
|
|
HD2
|
D:HIS157
|
3.6
|
31.9
|
1.0
|
|
CG
|
D:GLU197
|
3.8
|
30.7
|
1.0
|
|
CA
|
H:PRO5
|
3.8
|
24.6
|
1.0
|
|
HA
|
D:GLU197
|
3.8
|
34.3
|
1.0
|
|
HD3
|
H:PRO6
|
3.9
|
34.2
|
1.0
|
|
N
|
H:PRO5
|
3.9
|
28.0
|
1.0
|
|
HZ
|
D:PHE190
|
4.0
|
33.5
|
1.0
|
|
HD2
|
H:PRO4
|
4.1
|
38.1
|
1.0
|
|
C
|
H:PRO5
|
4.1
|
24.8
|
1.0
|
|
N
|
H:PRO4
|
4.1
|
28.5
|
1.0
|
|
HG2
|
D:GLU197
|
4.1
|
37.0
|
1.0
|
|
HB3
|
D:ALA200
|
4.2
|
32.7
|
1.0
|
|
ND1
|
D:HIS157
|
4.2
|
28.8
|
1.0
|
|
HG3
|
D:GLU197
|
4.2
|
37.0
|
1.0
|
|
CA
|
H:PRO4
|
4.3
|
28.0
|
1.0
|
|
O
|
H:HOH102
|
4.3
|
27.1
|
1.0
|
|
CE2
|
D:PHE190
|
4.4
|
24.9
|
1.0
|
|
HG2
|
H:PRO4
|
4.4
|
36.6
|
1.0
|
|
HB3
|
D:GLU197
|
4.4
|
27.9
|
1.0
|
|
ND1
|
D:HIS153
|
4.4
|
24.4
|
1.0
|
|
CG
|
D:HIS153
|
4.4
|
23.0
|
1.0
|
|
C
|
H:LEU3
|
4.4
|
28.3
|
1.0
|
|
CG
|
D:HIS157
|
4.4
|
27.7
|
1.0
|
|
N
|
H:PRO6
|
4.5
|
24.9
|
1.0
|
|
CB
|
D:GLU197
|
4.5
|
23.2
|
1.0
|
|
HD22
|
H:LEU3
|
4.5
|
55.6
|
1.0
|
|
O
|
H:PRO5
|
4.5
|
26.1
|
1.0
|
|
CB
|
H:LEU3
|
4.5
|
30.8
|
1.0
|
|
CD
|
H:PRO4
|
4.5
|
31.7
|
1.0
|
|
CD
|
H:PRO6
|
4.6
|
28.4
|
1.0
|
|
CZ
|
D:PHE190
|
4.6
|
27.8
|
1.0
|
|
CA
|
D:GLU197
|
4.6
|
28.5
|
1.0
|
|
O
|
H:LEU3
|
4.7
|
27.2
|
1.0
|
|
HD2
|
H:PRO6
|
4.8
|
34.2
|
1.0
|
|
CB
|
D:ALA200
|
4.9
|
27.2
|
1.0
|
|
HB1
|
D:ALA200
|
4.9
|
32.7
|
1.0
|
|
CG
|
H:PRO4
|
4.9
|
30.5
|
1.0
|
|
HA
|
H:PRO4
|
4.9
|
33.6
|
1.0
|
|
HB2
|
D:ALA200
|
4.9
|
32.7
|
1.0
|
|
HB2
|
H:LEU3
|
4.9
|
37.0
|
1.0
|
|
HD1
|
D:HIS157
|
5.0
|
34.6
|
1.0
|
|
CA
|
H:LEU3
|
5.0
|
29.4
|
1.0
|
|
Reference:
B.Claushuis,
F.Wojtalla,
H.Van Leeuwen,
J.Corver,
U.Baumann,
P.Hensbergen.
Structure of the Pro-Pro Endopeptidase (Ppep-3) E153A Y189F in Complex with Substrate Peptide Ac-Eplpppp-NH2 From Geobacillus Thermodenitrificans To Be Published.
Page generated: Fri Aug 22 17:52:40 2025
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