Calcium in PDB 8h78: Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Enzymatic activity of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
All present enzymatic activity of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor:
3.4.24.24;
Protein crystallography data
The structure of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 8h78
was solved by
M.Kamitani,
T.Takeuchi,
M.Mima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
21.78 /
2.40
|
Space group
|
I 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.683,
79.683,
127.434,
90,
90,
90
|
R / Rfree (%)
|
26.5 /
31.9
|
Other elements in 8h78:
The structure of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
(pdb code 8h78). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor, PDB code: 8h78:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 8h78
Go back to
Calcium Binding Sites List in 8h78
Calcium binding site 1 out
of 6 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:23.6
occ:1.00
|
O
|
A:GLY78
|
2.0
|
18.1
|
1.0
|
OE2
|
A:GLU103
|
2.2
|
21.7
|
1.0
|
O
|
A:ASP80
|
2.2
|
14.7
|
1.0
|
OD2
|
A:ASP100
|
2.3
|
18.2
|
1.0
|
O
|
A:LEU82
|
2.3
|
18.1
|
1.0
|
OD1
|
A:ASP77
|
2.7
|
13.6
|
1.0
|
C
|
A:GLY78
|
3.3
|
19.5
|
1.0
|
CG
|
A:ASP100
|
3.3
|
18.5
|
1.0
|
CD
|
A:GLU103
|
3.5
|
23.5
|
1.0
|
C
|
A:ASP80
|
3.5
|
16.4
|
1.0
|
C
|
A:LEU82
|
3.5
|
17.2
|
1.0
|
CG
|
A:ASP77
|
3.7
|
13.5
|
1.0
|
N
|
A:ASP80
|
3.8
|
17.3
|
1.0
|
N
|
A:GLY78
|
3.9
|
16.1
|
1.0
|
CB
|
A:ASP100
|
3.9
|
18.3
|
1.0
|
N
|
A:LEU82
|
4.0
|
17.9
|
1.0
|
C
|
A:ASP77
|
4.0
|
15.4
|
1.0
|
C
|
A:LYS79
|
4.1
|
20.4
|
1.0
|
N
|
A:ASP77
|
4.1
|
17.1
|
1.0
|
CA
|
A:GLY78
|
4.2
|
17.3
|
1.0
|
OD1
|
A:ASP100
|
4.2
|
16.9
|
1.0
|
N
|
A:LYS79
|
4.2
|
21.9
|
1.0
|
CA
|
A:LEU82
|
4.2
|
17.7
|
1.0
|
OD2
|
A:ASP77
|
4.2
|
11.6
|
1.0
|
CA
|
A:ASP80
|
4.2
|
16.4
|
1.0
|
OE1
|
A:GLU103
|
4.2
|
24.0
|
1.0
|
C
|
A:GLY81
|
4.4
|
16.9
|
1.0
|
O
|
A:ASP77
|
4.4
|
15.2
|
1.0
|
CA
|
A:LYS79
|
4.4
|
22.1
|
1.0
|
CG
|
A:GLU103
|
4.4
|
23.2
|
1.0
|
CA
|
A:ASP77
|
4.5
|
15.2
|
1.0
|
N
|
A:GLY81
|
4.5
|
17.0
|
1.0
|
N
|
A:LEU83
|
4.5
|
15.6
|
1.0
|
O
|
A:LYS79
|
4.5
|
20.7
|
1.0
|
CB
|
A:LEU82
|
4.6
|
17.8
|
1.0
|
CB
|
A:ASP77
|
4.7
|
14.4
|
1.0
|
CA
|
A:GLY81
|
4.8
|
16.8
|
1.0
|
CA
|
A:LEU83
|
4.8
|
15.2
|
1.0
|
O
|
A:HOH310
|
4.9
|
7.3
|
1.0
|
|
Calcium binding site 2 out
of 6 in 8h78
Go back to
Calcium Binding Sites List in 8h78
Calcium binding site 2 out
of 6 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca204
b:39.4
occ:1.00
|
O
|
A:GLY92
|
1.8
|
27.8
|
1.0
|
O
|
A:ASP60
|
2.2
|
19.8
|
1.0
|
OD1
|
A:ASP96
|
2.6
|
21.6
|
1.0
|
C
|
A:GLY92
|
3.0
|
34.5
|
1.0
|
O
|
A:GLY94
|
3.1
|
37.2
|
1.0
|
CG
|
A:ASP96
|
3.4
|
19.1
|
1.0
|
C
|
A:ASP60
|
3.4
|
24.0
|
1.0
|
O
|
A:ALA59
|
3.7
|
26.0
|
1.0
|
OD2
|
A:ASP96
|
3.7
|
18.2
|
1.0
|
N
|
A:GLY94
|
3.7
|
36.6
|
1.0
|
C
|
A:GLY94
|
3.8
|
35.3
|
1.0
|
CA
|
A:GLY92
|
3.9
|
39.3
|
1.0
|
C
|
A:VAL93
|
3.9
|
38.4
|
1.0
|
N
|
A:GLY92
|
4.0
|
40.6
|
1.0
|
N
|
A:VAL93
|
4.0
|
33.2
|
1.0
|
CA
|
A:ASP60
|
4.2
|
26.9
|
1.0
|
CA
|
A:GLY94
|
4.3
|
37.0
|
1.0
|
CA
|
A:VAL93
|
4.3
|
36.5
|
1.0
|
O
|
A:VAL93
|
4.3
|
43.3
|
1.0
|
N
|
A:ILE61
|
4.5
|
24.0
|
1.0
|
O
|
A:GLY90
|
4.5
|
42.2
|
1.0
|
N
|
A:ASP96
|
4.5
|
22.4
|
1.0
|
C
|
A:THR91
|
4.6
|
40.6
|
1.0
|
CB
|
A:ASP96
|
4.6
|
19.9
|
1.0
|
C
|
A:ALA59
|
4.7
|
29.2
|
1.0
|
N
|
A:GLY95
|
4.8
|
30.3
|
1.0
|
N
|
A:MET62
|
4.9
|
23.1
|
1.0
|
CA
|
A:ILE61
|
4.9
|
23.2
|
1.0
|
N
|
A:ASP60
|
4.9
|
28.3
|
1.0
|
CG
|
A:MET62
|
4.9
|
25.9
|
1.0
|
OE2
|
A:GLU58
|
4.9
|
68.5
|
1.0
|
O
|
A:THR91
|
4.9
|
37.1
|
1.0
|
CA
|
A:ASP96
|
4.9
|
20.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 8h78
Go back to
Calcium Binding Sites List in 8h78
Calcium binding site 3 out
of 6 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca205
b:45.9
occ:1.00
|
OD2
|
A:ASP26
|
2.3
|
20.6
|
1.0
|
O
|
A:GLU103
|
2.4
|
20.6
|
1.0
|
O
|
A:ASP101
|
2.5
|
21.3
|
1.0
|
OD1
|
A:ASP101
|
2.7
|
22.1
|
1.0
|
CG
|
A:ASP26
|
3.1
|
21.1
|
1.0
|
O
|
A:HOH321
|
3.1
|
22.3
|
1.0
|
OD1
|
A:ASP26
|
3.2
|
22.3
|
1.0
|
C
|
A:ASP101
|
3.4
|
20.0
|
1.0
|
C
|
A:GLU103
|
3.6
|
19.2
|
1.0
|
CG
|
A:ASP101
|
3.6
|
22.2
|
1.0
|
OG1
|
A:THR24
|
3.6
|
18.8
|
1.0
|
CA
|
A:ASP101
|
3.8
|
19.9
|
1.0
|
CD1
|
A:TRP105
|
4.0
|
12.3
|
1.0
|
CB
|
A:ASP101
|
4.2
|
20.8
|
1.0
|
N
|
A:GLU103
|
4.2
|
22.3
|
1.0
|
N
|
A:ASP102
|
4.4
|
20.6
|
1.0
|
N
|
A:LEU104
|
4.4
|
17.6
|
1.0
|
CA
|
A:LEU104
|
4.5
|
15.8
|
1.0
|
CB
|
A:ASP26
|
4.5
|
21.0
|
1.0
|
C
|
A:ASP102
|
4.5
|
21.4
|
1.0
|
OD2
|
A:ASP101
|
4.5
|
24.9
|
1.0
|
CA
|
A:GLU103
|
4.6
|
21.5
|
1.0
|
NE1
|
A:TRP105
|
4.6
|
12.2
|
1.0
|
N
|
A:TRP105
|
4.7
|
13.2
|
1.0
|
CA
|
A:ASP102
|
4.7
|
20.6
|
1.0
|
NH2
|
A:ARG67
|
4.8
|
23.8
|
1.0
|
CB
|
A:THR24
|
4.9
|
22.4
|
1.0
|
O
|
A:ASP100
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 4 out
of 6 in 8h78
Go back to
Calcium Binding Sites List in 8h78
Calcium binding site 4 out
of 6 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:48.8
occ:1.00
|
OE2
|
B:GLU103
|
2.1
|
24.7
|
1.0
|
O
|
B:GLY78
|
2.2
|
53.1
|
1.0
|
O
|
B:ASP80
|
2.2
|
60.3
|
1.0
|
O
|
B:LEU82
|
2.3
|
67.1
|
1.0
|
OD1
|
B:ASP77
|
2.5
|
25.5
|
1.0
|
OD2
|
B:ASP100
|
2.6
|
44.0
|
1.0
|
CD
|
B:GLU103
|
3.4
|
32.8
|
1.0
|
C
|
B:ASP80
|
3.4
|
53.7
|
1.0
|
C
|
B:GLY78
|
3.4
|
48.8
|
1.0
|
C
|
B:LEU82
|
3.5
|
55.8
|
1.0
|
CG
|
B:ASP100
|
3.5
|
50.0
|
1.0
|
CG
|
B:ASP77
|
3.7
|
29.2
|
1.0
|
N
|
B:GLY78
|
3.9
|
40.5
|
1.0
|
CB
|
B:ASP100
|
4.0
|
51.7
|
1.0
|
N
|
B:ASP80
|
4.0
|
60.4
|
1.0
|
C
|
B:LYS79
|
4.0
|
59.7
|
1.0
|
N
|
B:LEU82
|
4.0
|
56.3
|
1.0
|
C
|
B:ASP77
|
4.1
|
35.8
|
1.0
|
OE1
|
B:GLU103
|
4.2
|
38.5
|
1.0
|
CA
|
B:ASP80
|
4.2
|
54.0
|
1.0
|
C
|
B:GLY81
|
4.2
|
59.2
|
1.0
|
CA
|
B:LEU82
|
4.2
|
54.1
|
1.0
|
N
|
B:ASP77
|
4.3
|
38.3
|
1.0
|
CA
|
B:GLY78
|
4.3
|
45.5
|
1.0
|
O
|
B:LYS79
|
4.3
|
50.0
|
1.0
|
CG
|
B:GLU103
|
4.3
|
32.9
|
1.0
|
N
|
B:LYS79
|
4.3
|
54.9
|
1.0
|
N
|
B:GLY81
|
4.4
|
53.8
|
1.0
|
OD1
|
B:ASP100
|
4.4
|
48.2
|
1.0
|
OD2
|
B:ASP77
|
4.5
|
29.7
|
1.0
|
O
|
B:ASP77
|
4.5
|
37.9
|
1.0
|
N
|
B:LEU83
|
4.5
|
55.3
|
1.0
|
CA
|
B:GLY81
|
4.5
|
55.1
|
1.0
|
CA
|
B:LYS79
|
4.5
|
57.6
|
1.0
|
CB
|
B:LEU82
|
4.6
|
53.5
|
1.0
|
CA
|
B:ASP77
|
4.6
|
36.3
|
1.0
|
O
|
B:GLY81
|
4.7
|
61.2
|
1.0
|
CA
|
B:LEU83
|
4.7
|
51.2
|
1.0
|
CB
|
B:ASP77
|
4.8
|
32.5
|
1.0
|
|
Calcium binding site 5 out
of 6 in 8h78
Go back to
Calcium Binding Sites List in 8h78
Calcium binding site 5 out
of 6 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca204
b:15.9
occ:1.00
|
O
|
B:ASP60
|
2.1
|
16.6
|
1.0
|
O
|
B:GLY92
|
2.3
|
18.4
|
1.0
|
OD1
|
B:ASP96
|
2.4
|
24.9
|
1.0
|
O
|
B:HOH302
|
2.4
|
10.0
|
1.0
|
O
|
B:HOH304
|
2.5
|
11.6
|
1.0
|
O
|
B:GLY94
|
2.6
|
21.5
|
1.0
|
CG
|
B:ASP96
|
3.3
|
26.4
|
1.0
|
C
|
B:ASP60
|
3.3
|
17.4
|
1.0
|
C
|
B:GLY94
|
3.5
|
20.9
|
1.0
|
C
|
B:GLY92
|
3.5
|
20.0
|
1.0
|
OD2
|
B:ASP96
|
3.8
|
26.7
|
1.0
|
N
|
B:GLY94
|
3.8
|
22.6
|
1.0
|
C
|
B:VAL93
|
3.9
|
22.3
|
1.0
|
O
|
B:VAL93
|
4.2
|
23.4
|
1.0
|
CA
|
B:ASP60
|
4.2
|
18.8
|
1.0
|
O
|
B:ALA59
|
4.2
|
18.5
|
1.0
|
CA
|
B:GLY94
|
4.2
|
21.7
|
1.0
|
N
|
B:ASP96
|
4.2
|
24.5
|
1.0
|
N
|
B:ILE61
|
4.3
|
15.8
|
1.0
|
CA
|
B:VAL93
|
4.3
|
22.8
|
1.0
|
N
|
B:VAL93
|
4.4
|
21.7
|
1.0
|
CA
|
B:ILE61
|
4.4
|
16.8
|
1.0
|
O
|
B:GLY90
|
4.4
|
21.8
|
1.0
|
N
|
B:GLY95
|
4.5
|
22.6
|
1.0
|
CB
|
B:ASP96
|
4.5
|
26.4
|
1.0
|
O
|
B:HOH310
|
4.5
|
18.4
|
1.0
|
CA
|
B:GLY92
|
4.5
|
19.8
|
1.0
|
N
|
B:MET62
|
4.5
|
18.1
|
1.0
|
N
|
B:GLY92
|
4.7
|
20.7
|
1.0
|
CA
|
B:ASP96
|
4.7
|
25.3
|
1.0
|
C
|
B:GLY95
|
4.7
|
24.8
|
1.0
|
CA
|
B:GLY95
|
4.7
|
24.0
|
1.0
|
C
|
B:THR91
|
4.8
|
22.6
|
1.0
|
O
|
B:THR91
|
4.8
|
26.1
|
1.0
|
CG
|
B:MET62
|
4.9
|
19.8
|
1.0
|
CH2
|
B:TRP11
|
4.9
|
25.9
|
1.0
|
C
|
B:ALA59
|
5.0
|
20.3
|
1.0
|
|
Calcium binding site 6 out
of 6 in 8h78
Go back to
Calcium Binding Sites List in 8h78
Calcium binding site 6 out
of 6 in the Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Human Mmp-2 Catalytic Domain in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca205
b:48.8
occ:1.00
|
OD2
|
B:ASP26
|
2.2
|
43.6
|
1.0
|
OD1
|
B:ASP101
|
2.5
|
40.0
|
1.0
|
O
|
B:ASP101
|
2.8
|
40.1
|
1.0
|
CG
|
B:ASP26
|
2.8
|
42.5
|
1.0
|
O
|
B:GLU103
|
2.9
|
40.5
|
1.0
|
OD1
|
B:ASP26
|
3.0
|
43.7
|
1.0
|
OG1
|
B:THR24
|
3.2
|
53.5
|
1.0
|
CG
|
B:ASP101
|
3.5
|
39.8
|
1.0
|
C
|
B:ASP101
|
3.8
|
40.0
|
1.0
|
CD1
|
B:TRP105
|
3.9
|
33.4
|
1.0
|
CA
|
B:ASP101
|
4.1
|
39.9
|
1.0
|
C
|
B:GLU103
|
4.1
|
41.5
|
1.0
|
CB
|
B:ASP26
|
4.1
|
44.6
|
1.0
|
CB
|
B:ASP101
|
4.3
|
39.7
|
1.0
|
OD2
|
B:ASP101
|
4.4
|
42.9
|
1.0
|
NE1
|
B:TRP105
|
4.5
|
32.0
|
1.0
|
CB
|
B:THR24
|
4.5
|
57.0
|
1.0
|
CA
|
B:LEU104
|
4.6
|
44.5
|
1.0
|
N
|
B:TRP105
|
4.6
|
52.5
|
1.0
|
N
|
B:LEU104
|
4.8
|
43.2
|
1.0
|
CG
|
B:TRP105
|
4.9
|
36.1
|
1.0
|
N
|
B:ASP102
|
4.9
|
39.1
|
1.0
|
|
Reference:
T.Takeuchi,
Y.Nomura,
T.Tamita,
R.Nishikawa,
H.Kakinuma,
N.Kojima,
K.Hitaka,
Y.Tamura,
M.Kamitani,
M.Mima,
A.Nozoe,
M.Hayashi.
Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with A Phenylbenzamide-Pentapeptide Hybrid Scaffold. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 36595440
DOI: 10.1021/ACS.JMEDCHEM.2C01698
Page generated: Fri Jul 19 09:22:02 2024
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