Calcium in PDB 3v96: Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)
Enzymatic activity of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)
All present enzymatic activity of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1):
3.4.24.22;
Protein crystallography data
The structure of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1), PDB code: 3v96
was solved by
J.Batra,
A.S.Soares,
E.S.Radisky,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.00 /
1.90
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
231.720,
37.682,
39.523,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
26.6
|
Other elements in 3v96:
The structure of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)
(pdb code 3v96). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1), PDB code: 3v96:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 3v96
Go back to
Calcium Binding Sites List in 3v96
Calcium binding site 1 out
of 3 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:33.9
occ:1.00
|
O
|
B:SER179
|
2.2
|
27.9
|
1.0
|
OE2
|
B:GLU200
|
2.3
|
36.7
|
1.0
|
O
|
B:GLY175
|
2.3
|
39.0
|
1.0
|
OD2
|
B:ASP174
|
2.4
|
37.1
|
1.0
|
O
|
B:GLY177
|
2.4
|
31.6
|
1.0
|
OD2
|
B:ASP197
|
2.5
|
36.2
|
1.0
|
CG
|
B:ASP197
|
3.3
|
39.3
|
1.0
|
C
|
B:SER179
|
3.4
|
25.8
|
1.0
|
CD
|
B:GLU200
|
3.5
|
34.1
|
1.0
|
C
|
B:GLY175
|
3.5
|
39.9
|
1.0
|
C
|
B:GLY177
|
3.6
|
32.8
|
1.0
|
CG
|
B:ASP174
|
3.6
|
36.2
|
1.0
|
N
|
B:GLY177
|
3.8
|
35.6
|
1.0
|
CB
|
B:ASP197
|
3.9
|
35.7
|
1.0
|
N
|
B:GLY175
|
4.0
|
40.1
|
1.0
|
N
|
B:SER179
|
4.0
|
26.6
|
1.0
|
OE1
|
B:GLU200
|
4.1
|
34.8
|
1.0
|
C
|
B:PRO176
|
4.1
|
37.4
|
1.0
|
C
|
B:ASP174
|
4.2
|
40.1
|
1.0
|
CA
|
B:SER179
|
4.2
|
25.1
|
0.5
|
CA
|
B:SER179
|
4.2
|
25.4
|
0.5
|
OD1
|
B:ASP197
|
4.2
|
40.7
|
1.0
|
OD1
|
B:ASP174
|
4.3
|
34.6
|
1.0
|
CA
|
B:GLY177
|
4.3
|
34.3
|
1.0
|
N
|
B:LEU180
|
4.3
|
25.5
|
1.0
|
N
|
B:ASP174
|
4.3
|
37.6
|
1.0
|
OG
|
B:SER179
|
4.3
|
24.9
|
0.5
|
CA
|
B:GLY175
|
4.4
|
41.1
|
1.0
|
N
|
B:PRO176
|
4.4
|
40.4
|
1.0
|
CA
|
B:PRO176
|
4.4
|
39.3
|
1.0
|
CA
|
B:LEU180
|
4.5
|
27.0
|
1.0
|
C
|
B:HIS178
|
4.5
|
28.4
|
1.0
|
CG
|
B:GLU200
|
4.6
|
35.6
|
1.0
|
O
|
B:ASP174
|
4.6
|
39.8
|
1.0
|
O
|
B:PRO176
|
4.6
|
38.1
|
1.0
|
N
|
B:HIS178
|
4.6
|
31.0
|
1.0
|
CA
|
B:ASP174
|
4.7
|
39.1
|
1.0
|
CB
|
B:ASP174
|
4.7
|
37.2
|
1.0
|
CB
|
B:HIS178
|
4.8
|
32.1
|
1.0
|
CD2
|
B:LEU180
|
4.9
|
25.4
|
1.0
|
CA
|
B:HIS178
|
4.9
|
29.4
|
1.0
|
CB
|
B:SER179
|
4.9
|
25.6
|
0.5
|
CB
|
B:SER179
|
5.0
|
25.6
|
0.5
|
|
Calcium binding site 2 out
of 3 in 3v96
Go back to
Calcium Binding Sites List in 3v96
Calcium binding site 2 out
of 3 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca304
b:49.2
occ:1.00
|
O
|
B:HOH449
|
2.2
|
53.3
|
1.0
|
O
|
B:ASP157
|
2.3
|
48.9
|
1.0
|
O
|
B:HOH447
|
2.3
|
56.1
|
1.0
|
O
|
B:GLY189
|
2.4
|
52.2
|
1.0
|
O
|
B:TYR191
|
2.5
|
43.2
|
1.0
|
OD1
|
B:ASP193
|
2.6
|
45.4
|
1.0
|
CG
|
B:ASP193
|
3.4
|
42.8
|
1.0
|
C
|
B:ASP157
|
3.5
|
48.8
|
1.0
|
C
|
B:TYR191
|
3.6
|
42.2
|
1.0
|
C
|
B:GLY189
|
3.6
|
54.0
|
1.0
|
OD2
|
B:ASP193
|
3.7
|
48.1
|
1.0
|
O
|
B:LEU190
|
3.9
|
46.7
|
1.0
|
O
|
B:ALA156
|
3.9
|
56.4
|
1.0
|
C
|
B:LEU190
|
4.0
|
47.9
|
1.0
|
N
|
B:ASP193
|
4.2
|
37.5
|
1.0
|
CA
|
B:ASP157
|
4.2
|
51.3
|
1.0
|
CA
|
B:GLY192
|
4.3
|
37.1
|
1.0
|
N
|
B:TYR191
|
4.3
|
47.2
|
1.0
|
OE1
|
B:GLU155
|
4.4
|
70.4
|
1.0
|
O
|
B:GLY187
|
4.4
|
44.7
|
1.0
|
N
|
B:GLY192
|
4.4
|
38.7
|
1.0
|
C
|
B:GLY192
|
4.4
|
36.5
|
1.0
|
N
|
B:ILE158
|
4.5
|
47.9
|
1.0
|
O
|
B:HOH437
|
4.5
|
57.5
|
1.0
|
N
|
B:LEU190
|
4.5
|
54.5
|
1.0
|
CA
|
B:LEU190
|
4.6
|
52.0
|
1.0
|
CA
|
B:GLY189
|
4.6
|
57.5
|
1.0
|
CA
|
B:TYR191
|
4.6
|
44.3
|
1.0
|
CB
|
B:ASP193
|
4.6
|
41.1
|
1.0
|
N
|
B:GLY189
|
4.6
|
55.4
|
1.0
|
N
|
B:MET159
|
4.6
|
47.4
|
1.0
|
C
|
B:PRO188
|
4.7
|
52.7
|
1.0
|
CG
|
B:MET159
|
4.7
|
57.3
|
1.0
|
CA
|
B:ASP193
|
4.8
|
37.7
|
1.0
|
CA
|
B:ILE158
|
4.8
|
44.3
|
1.0
|
C
|
B:ALA156
|
4.9
|
57.4
|
1.0
|
O
|
B:HOH427
|
4.9
|
60.5
|
1.0
|
O
|
B:PRO188
|
5.0
|
48.5
|
1.0
|
|
Calcium binding site 3 out
of 3 in 3v96
Go back to
Calcium Binding Sites List in 3v96
Calcium binding site 3 out
of 3 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca305
b:56.4
occ:1.00
|
OD1
|
B:ASP198
|
2.3
|
50.2
|
1.0
|
O
|
B:GLU200
|
2.3
|
45.1
|
1.0
|
O
|
B:ASP198
|
2.3
|
44.0
|
1.0
|
OD2
|
B:ASP123
|
2.5
|
47.8
|
1.0
|
C
|
B:ASP198
|
3.1
|
43.4
|
1.0
|
OD1
|
B:ASP123
|
3.1
|
55.7
|
1.0
|
CG
|
B:ASP123
|
3.2
|
48.6
|
1.0
|
CG
|
B:ASP198
|
3.2
|
49.3
|
1.0
|
C
|
B:GLU200
|
3.5
|
43.0
|
1.0
|
CA
|
B:ASP198
|
3.5
|
42.8
|
1.0
|
CB
|
B:ASP198
|
3.8
|
45.5
|
1.0
|
OG1
|
B:THR121
|
4.0
|
51.5
|
1.0
|
OD2
|
B:ASP198
|
4.2
|
59.5
|
1.0
|
N
|
B:GLU200
|
4.2
|
39.8
|
1.0
|
CD1
|
B:TRP202
|
4.2
|
43.5
|
1.0
|
N
|
B:ASP199
|
4.2
|
43.1
|
1.0
|
CA
|
B:LYS201
|
4.2
|
46.3
|
1.0
|
N
|
B:LYS201
|
4.3
|
44.3
|
1.0
|
C
|
B:ASP199
|
4.4
|
42.1
|
1.0
|
CA
|
B:GLU200
|
4.5
|
40.2
|
1.0
|
CA
|
B:ASP199
|
4.5
|
43.6
|
1.0
|
CB
|
B:ASP123
|
4.6
|
52.1
|
1.0
|
NE1
|
B:TRP202
|
4.6
|
41.4
|
1.0
|
N
|
B:TRP202
|
4.8
|
45.3
|
1.0
|
O
|
B:ASP197
|
4.8
|
38.5
|
1.0
|
N
|
B:ASP198
|
4.9
|
40.2
|
1.0
|
O
|
B:HOH439
|
5.0
|
66.6
|
1.0
|
O
|
B:ASP199
|
5.0
|
42.1
|
1.0
|
|
Reference:
J.Batra,
J.Robinson,
A.S.Soares,
A.P.Fields,
D.C.Radisky,
E.S.Radisky.
Matrix Metalloproteinase-10 (Mmp-10) Interaction with Tissue Inhibitors of Metalloproteinases Timp-1 and Timp-2: Binding Studies and Crystal Structure. J.Biol.Chem. V. 287 15935 2012.
ISSN: ISSN 0021-9258
PubMed: 22427646
DOI: 10.1074/JBC.M112.341156
Page generated: Sat Jul 13 20:36:24 2024
|