Chlorine in PDB 7zbv: Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
Enzymatic activity of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
All present enzymatic activity of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor:
3.4.24.3;
Protein crystallography data
The structure of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor, PDB code: 7zbv
was solved by
E.Schoenauer,
H.Brandstetter,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
60.76 /
1.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.267,
77.787,
97.319,
90,
90,
90
|
R / Rfree (%)
|
18.7 /
22.9
|
Other elements in 7zbv:
The structure of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
(pdb code 7zbv). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor, PDB code: 7zbv:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 7zbv
Go back to
Chlorine Binding Sites List in 7zbv
Chlorine binding site 1 out
of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl802
b:52.9
occ:1.00
|
CL
|
A:ITO802
|
0.0
|
52.9
|
1.0
|
C3
|
A:ITO802
|
1.7
|
62.0
|
1.0
|
C2
|
A:ITO802
|
2.7
|
56.4
|
1.0
|
C4
|
A:ITO802
|
2.7
|
70.1
|
1.0
|
H2
|
A:ITO802
|
2.8
|
67.8
|
1.0
|
CL1
|
A:ITO802
|
3.2
|
56.1
|
1.0
|
C1
|
A:ITO802
|
4.0
|
63.3
|
1.0
|
C5
|
A:ITO802
|
4.0
|
57.0
|
1.0
|
C6
|
A:ITO802
|
4.5
|
60.9
|
1.0
|
H3
|
A:ITO802
|
4.9
|
68.5
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 7zbv
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Chlorine Binding Sites List in 7zbv
Chlorine binding site 2 out
of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl802
b:56.1
occ:1.00
|
CL1
|
A:ITO802
|
0.0
|
56.1
|
1.0
|
C4
|
A:ITO802
|
1.7
|
70.1
|
1.0
|
C5
|
A:ITO802
|
2.7
|
57.0
|
1.0
|
C3
|
A:ITO802
|
2.7
|
62.0
|
1.0
|
H3
|
A:ITO802
|
2.8
|
68.5
|
1.0
|
CL
|
A:ITO802
|
3.2
|
52.9
|
1.0
|
C6
|
A:ITO802
|
4.0
|
60.9
|
1.0
|
C2
|
A:ITO802
|
4.0
|
56.4
|
1.0
|
C1
|
A:ITO802
|
4.5
|
63.3
|
1.0
|
H2
|
A:ITO802
|
4.9
|
67.8
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 7zbv
Go back to
Chlorine Binding Sites List in 7zbv
Chlorine binding site 3 out
of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl804
b:83.1
occ:0.70
|
CL
|
A:ITO804
|
0.0
|
83.1
|
0.7
|
C3
|
A:ITO804
|
1.7
|
72.3
|
0.7
|
C2
|
A:ITO804
|
2.7
|
74.4
|
0.7
|
C4
|
A:ITO804
|
2.7
|
66.9
|
0.7
|
H2
|
A:ITO804
|
2.8
|
89.3
|
0.7
|
HH22
|
A:ARG573
|
3.0
|
41.8
|
1.0
|
CG
|
A:PHE515
|
3.1
|
62.1
|
1.0
|
HA
|
A:LEU520
|
3.2
|
30.7
|
1.0
|
CL1
|
A:ITO804
|
3.2
|
79.8
|
0.7
|
HB3
|
A:PHE515
|
3.2
|
55.7
|
1.0
|
CD2
|
A:PHE515
|
3.2
|
55.6
|
1.0
|
CD1
|
A:PHE515
|
3.4
|
68.9
|
1.0
|
HD2
|
A:PHE515
|
3.6
|
66.8
|
1.0
|
NH2
|
A:ARG573
|
3.6
|
34.8
|
1.0
|
HG2
|
A:GLU519
|
3.6
|
45.6
|
1.0
|
HH21
|
A:ARG573
|
3.6
|
41.8
|
1.0
|
CE2
|
A:PHE515
|
3.7
|
69.7
|
1.0
|
CB
|
A:PHE515
|
3.7
|
46.4
|
1.0
|
HD12
|
A:LEU520
|
3.8
|
53.9
|
1.0
|
CE1
|
A:PHE515
|
3.8
|
63.2
|
1.0
|
HD1
|
A:PHE515
|
3.9
|
82.7
|
1.0
|
HB2
|
A:LEU520
|
3.9
|
33.7
|
1.0
|
CZ
|
A:PHE515
|
3.9
|
73.4
|
1.0
|
C5
|
A:ITO804
|
4.0
|
60.7
|
0.7
|
C1
|
A:ITO804
|
4.0
|
71.7
|
0.7
|
HB2
|
A:PHE515
|
4.0
|
55.7
|
1.0
|
CA
|
A:LEU520
|
4.0
|
25.5
|
1.0
|
HD13
|
A:LEU520
|
4.0
|
53.9
|
1.0
|
HE2
|
A:PHE515
|
4.2
|
83.7
|
1.0
|
HB2
|
A:HIS523
|
4.2
|
32.6
|
1.0
|
N
|
A:LEU520
|
4.3
|
24.3
|
1.0
|
HB3
|
A:HIS523
|
4.3
|
32.6
|
1.0
|
O
|
A:GLU519
|
4.3
|
26.7
|
1.0
|
CD1
|
A:LEU520
|
4.3
|
44.9
|
1.0
|
C
|
A:GLU519
|
4.4
|
26.0
|
1.0
|
HE1
|
A:PHE515
|
4.4
|
75.9
|
1.0
|
CB
|
A:LEU520
|
4.5
|
28.1
|
1.0
|
C6
|
A:ITO804
|
4.5
|
65.6
|
0.7
|
CG
|
A:GLU519
|
4.5
|
38.0
|
1.0
|
HZ
|
A:PHE515
|
4.6
|
88.1
|
1.0
|
HB3
|
A:GLU519
|
4.6
|
31.6
|
1.0
|
H
|
A:LEU520
|
4.6
|
29.2
|
1.0
|
CB
|
A:HIS523
|
4.7
|
27.1
|
1.0
|
CZ
|
A:ARG573
|
4.7
|
31.0
|
1.0
|
HD1
|
A:HIS523
|
4.7
|
37.4
|
1.0
|
HH12
|
A:ARG573
|
4.7
|
33.3
|
1.0
|
OE1
|
A:GLU559
|
4.8
|
39.5
|
1.0
|
H3
|
A:ITO804
|
4.8
|
73.0
|
0.7
|
|
Chlorine binding site 4 out
of 4 in 7zbv
Go back to
Chlorine Binding Sites List in 7zbv
Chlorine binding site 4 out
of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl804
b:79.8
occ:0.70
|
CL1
|
A:ITO804
|
0.0
|
79.8
|
0.7
|
C4
|
A:ITO804
|
1.7
|
66.9
|
0.7
|
C5
|
A:ITO804
|
2.7
|
60.7
|
0.7
|
C3
|
A:ITO804
|
2.7
|
72.3
|
0.7
|
HD11
|
A:ILE576
|
2.8
|
45.6
|
1.0
|
HH22
|
A:ARG573
|
2.8
|
41.8
|
1.0
|
OE1
|
A:GLU559
|
2.8
|
39.5
|
1.0
|
OE2
|
A:GLU559
|
2.8
|
47.1
|
1.0
|
H3
|
A:ITO804
|
2.8
|
73.0
|
0.7
|
CD
|
A:GLU559
|
3.1
|
42.2
|
1.0
|
CL
|
A:ITO804
|
3.2
|
83.1
|
0.7
|
HZ
|
A:PHE515
|
3.3
|
88.1
|
1.0
|
CZ
|
A:PHE515
|
3.4
|
73.4
|
1.0
|
HH12
|
A:ARG573
|
3.5
|
33.3
|
1.0
|
O
|
A:HOH902
|
3.6
|
40.1
|
1.0
|
CD1
|
A:ILE576
|
3.6
|
38.0
|
1.0
|
NH2
|
A:ARG573
|
3.6
|
34.8
|
1.0
|
HD13
|
A:ILE576
|
3.7
|
45.6
|
1.0
|
CE2
|
A:PHE515
|
3.8
|
69.7
|
1.0
|
HD1
|
A:HIS523
|
3.9
|
37.4
|
1.0
|
HE2
|
A:PHE515
|
3.9
|
83.7
|
1.0
|
HD12
|
A:ILE576
|
3.9
|
45.6
|
1.0
|
CE1
|
A:PHE515
|
3.9
|
63.2
|
1.0
|
C2
|
A:ITO804
|
3.9
|
74.4
|
0.7
|
C6
|
A:ITO804
|
4.0
|
65.6
|
0.7
|
HH21
|
A:ARG573
|
4.1
|
41.8
|
1.0
|
NH1
|
A:ARG573
|
4.2
|
27.7
|
1.0
|
HE1
|
A:PHE515
|
4.2
|
75.9
|
1.0
|
ND1
|
A:HIS523
|
4.4
|
31.1
|
1.0
|
CZ
|
A:ARG573
|
4.4
|
31.0
|
1.0
|
C1
|
A:ITO804
|
4.5
|
71.7
|
0.7
|
HE2
|
A:TYR579
|
4.5
|
57.7
|
1.0
|
CD2
|
A:PHE515
|
4.5
|
55.6
|
1.0
|
CG
|
A:GLU559
|
4.6
|
27.4
|
1.0
|
CD1
|
A:PHE515
|
4.7
|
68.9
|
1.0
|
HE1
|
A:HIS523
|
4.7
|
41.8
|
1.0
|
CG1
|
A:ILE576
|
4.7
|
27.6
|
1.0
|
HD2
|
A:TYR607
|
4.7
|
49.5
|
1.0
|
HG12
|
A:ILE576
|
4.7
|
33.2
|
1.0
|
H2
|
A:ITO804
|
4.8
|
89.3
|
0.7
|
CE1
|
A:HIS523
|
4.8
|
34.8
|
1.0
|
HG13
|
A:ILE576
|
4.9
|
33.2
|
1.0
|
HH11
|
A:ARG573
|
4.9
|
33.3
|
1.0
|
CG
|
A:PHE515
|
4.9
|
62.1
|
1.0
|
HG3
|
A:GLU559
|
5.0
|
32.9
|
1.0
|
|
Reference:
A.Alhayek,
A.S.Abdelsamie,
E.Schonauer,
V.Camberlein,
E.Hutterer,
G.Posselt,
J.Serwanja,
C.Blochl,
C.G.Huber,
J.Haupenthal,
H.Brandstetter,
S.Wessler,
A.K.H.Hirsch.
Discovery and Characterization of Synthesized and Fda-Approved Inhibitors of Clostridial and Bacillary Collagenases. J.Med.Chem. V. 65 12933 2022.
ISSN: ISSN 0022-2623
PubMed: 36154055
DOI: 10.1021/ACS.JMEDCHEM.2C00785
Page generated: Tue Jul 30 06:10:52 2024
|