Calcium in PDB 5d2b: Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470
Enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470
All present enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470:
3.4.24.65;
Protein crystallography data
The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470, PDB code: 5d2b
was solved by
C.Rouanet-Mehouas,
L.Devel,
V.Dive,
E.A.Stura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.45 /
1.20
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.900,
63.100,
36.790,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.4 /
17.5
|
Other elements in 5d2b:
The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470
(pdb code 5d2b). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470, PDB code: 5d2b:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 5d2b
Go back to
Calcium Binding Sites List in 5d2b
Calcium binding site 1 out
of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470
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 A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:14.2
occ:1.00
|
O
|
A:GLY190
|
2.3
|
16.4
|
1.0
|
O
|
A:GLY192
|
2.3
|
13.7
|
1.0
|
O
|
A:HOH441
|
2.3
|
16.4
|
1.0
|
O
|
A:ASP158
|
2.3
|
11.9
|
1.0
|
O
|
A:HOH456
|
2.4
|
16.3
|
1.0
|
OD2
|
A:ASP194
|
2.4
|
12.9
|
1.0
|
CG
|
A:ASP194
|
3.4
|
13.0
|
1.0
|
C
|
A:ASP158
|
3.5
|
11.5
|
1.0
|
C
|
A:GLY190
|
3.5
|
16.4
|
1.0
|
C
|
A:GLY192
|
3.5
|
13.3
|
1.0
|
OD1
|
A:ASP194
|
3.8
|
14.2
|
1.0
|
C
|
A:ILE191
|
3.9
|
14.7
|
0.6
|
C
|
A:ILE191
|
4.0
|
15.2
|
0.4
|
N
|
A:GLY192
|
4.0
|
14.6
|
1.0
|
O
|
A:ILE191
|
4.2
|
15.1
|
0.4
|
O
|
A:ILE191
|
4.2
|
14.0
|
0.6
|
N
|
A:ASP194
|
4.3
|
11.5
|
1.0
|
O
|
A:ALA157
|
4.3
|
15.1
|
1.0
|
CA
|
A:ASP158
|
4.3
|
12.0
|
1.0
|
CA
|
A:GLY192
|
4.3
|
14.2
|
1.0
|
CA
|
A:ILE191
|
4.3
|
16.2
|
0.6
|
N
|
A:ILE191
|
4.3
|
16.4
|
0.6
|
N
|
A:ILE191
|
4.4
|
16.4
|
0.4
|
O
|
A:GLY188
|
4.4
|
18.0
|
1.0
|
CA
|
A:GLY190
|
4.4
|
17.7
|
1.0
|
N
|
A:ILE159
|
4.4
|
11.0
|
1.0
|
CA
|
A:ILE191
|
4.4
|
16.4
|
0.4
|
N
|
A:GLY190
|
4.4
|
18.6
|
1.0
|
N
|
A:GLY193
|
4.4
|
13.0
|
1.0
|
O
|
A:HOH644
|
4.5
|
28.5
|
1.0
|
CA
|
A:ILE159
|
4.5
|
11.0
|
1.0
|
CA
|
A:GLY193
|
4.5
|
12.6
|
1.0
|
N
|
A:LEU160
|
4.6
|
11.2
|
0.4
|
C
|
A:GLY193
|
4.6
|
11.5
|
1.0
|
N
|
A:LEU160
|
4.6
|
11.2
|
0.6
|
CB
|
A:ASP194
|
4.6
|
12.4
|
1.0
|
O
|
A:HOH437
|
4.7
|
26.4
|
1.0
|
C
|
A:SER189
|
4.8
|
18.9
|
1.0
|
CA
|
A:ASP194
|
4.8
|
11.5
|
1.0
|
O
|
A:HOH450
|
4.8
|
16.9
|
1.0
|
CH2
|
A:TRP109
|
4.9
|
14.8
|
1.0
|
CE
|
A:MET156
|
4.9
|
25.7
|
0.3
|
CG
|
A:LEU160
|
5.0
|
12.7
|
0.4
|
|
Calcium binding site 2 out
of 3 in 5d2b
Go back to
Calcium Binding Sites List in 5d2b
Calcium binding site 2 out
of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470
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 A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:14.8
occ:1.00
|
OE2
|
A:GLU199
|
2.3
|
14.1
|
1.0
|
O
|
A:GLU199
|
2.4
|
13.9
|
1.0
|
OD2
|
A:ASP124
|
2.4
|
14.9
|
1.0
|
O
|
A:HOH552
|
2.4
|
19.3
|
1.0
|
O
|
A:GLU201
|
2.4
|
14.6
|
1.0
|
O
|
A:HOH588
|
2.4
|
18.3
|
1.0
|
OD1
|
A:ASP124
|
2.6
|
16.4
|
1.0
|
CG
|
A:ASP124
|
2.8
|
15.3
|
1.0
|
CD
|
A:GLU199
|
3.4
|
14.1
|
1.0
|
C
|
A:GLU199
|
3.5
|
12.6
|
1.0
|
C
|
A:GLU201
|
3.6
|
13.8
|
1.0
|
CG
|
A:GLU199
|
3.9
|
13.8
|
1.0
|
OG1
|
A:THR122
|
4.1
|
13.7
|
1.0
|
CA
|
A:GLU199
|
4.2
|
12.4
|
1.0
|
CA
|
A:PHE202
|
4.2
|
14.8
|
1.0
|
CD1
|
A:TRP203
|
4.3
|
12.8
|
1.0
|
N
|
A:PHE202
|
4.4
|
13.6
|
1.0
|
CB
|
A:ASP124
|
4.4
|
15.5
|
1.0
|
O
|
A:HOH648
|
4.4
|
35.6
|
1.0
|
N
|
A:GLU201
|
4.4
|
13.4
|
1.0
|
C
|
A:ASP200
|
4.5
|
14.5
|
1.0
|
OE1
|
A:GLU199
|
4.5
|
14.4
|
1.0
|
N
|
A:ASP200
|
4.5
|
12.2
|
1.0
|
O
|
A:HOH428
|
4.6
|
26.9
|
1.0
|
CB
|
A:GLU199
|
4.6
|
13.2
|
1.0
|
O
|
A:HOH445
|
4.6
|
25.9
|
1.0
|
CA
|
A:GLU201
|
4.7
|
13.6
|
1.0
|
CA
|
A:ASP200
|
4.7
|
13.7
|
1.0
|
N
|
A:TRP203
|
4.8
|
13.2
|
1.0
|
NE1
|
A:TRP203
|
4.8
|
12.4
|
1.0
|
O
|
A:HOH677
|
4.9
|
21.7
|
1.0
|
O
|
A:ASP200
|
4.9
|
16.0
|
1.0
|
CD1
|
A:PHE202
|
5.0
|
19.4
|
1.0
|
|
Calcium binding site 3 out
of 3 in 5d2b
Go back to
Calcium Binding Sites List in 5d2b
Calcium binding site 3 out
of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470
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 A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:13.0
occ:1.00
|
OE2
|
A:GLU201
|
2.3
|
16.6
|
1.0
|
O
|
A:ILE180
|
2.3
|
13.3
|
1.0
|
O
|
A:GLY178
|
2.3
|
15.1
|
1.0
|
O
|
A:GLY176
|
2.3
|
14.9
|
1.0
|
OD2
|
A:ASP175
|
2.3
|
13.8
|
1.0
|
OD1
|
A:ASP198
|
2.3
|
12.5
|
1.0
|
CG
|
A:ASP198
|
3.4
|
11.7
|
1.0
|
C
|
A:ILE180
|
3.5
|
12.4
|
1.0
|
CD
|
A:GLU201
|
3.5
|
15.8
|
1.0
|
C
|
A:GLY178
|
3.5
|
15.2
|
1.0
|
CG
|
A:ASP175
|
3.5
|
14.4
|
1.0
|
C
|
A:GLY176
|
3.5
|
14.7
|
1.0
|
N
|
A:GLY178
|
3.9
|
15.9
|
1.0
|
N
|
A:ILE180
|
3.9
|
14.0
|
1.0
|
CB
|
A:ASP198
|
4.0
|
11.3
|
1.0
|
N
|
A:GLY176
|
4.1
|
15.0
|
1.0
|
OD1
|
A:ASP175
|
4.1
|
14.9
|
1.0
|
OE1
|
A:GLU201
|
4.1
|
16.7
|
1.0
|
C
|
A:LYS177
|
4.2
|
16.8
|
1.0
|
C
|
A:GLY179
|
4.2
|
14.4
|
1.0
|
CA
|
A:ILE180
|
4.3
|
14.1
|
1.0
|
N
|
A:ASP175
|
4.3
|
13.8
|
1.0
|
C
|
A:ASP175
|
4.3
|
14.7
|
1.0
|
CA
|
A:GLY178
|
4.3
|
16.1
|
1.0
|
OD2
|
A:ASP198
|
4.3
|
12.0
|
1.0
|
CA
|
A:GLY176
|
4.4
|
15.2
|
1.0
|
N
|
A:LEU181
|
4.4
|
12.0
|
1.0
|
CA
|
A:LYS177
|
4.4
|
16.9
|
1.0
|
N
|
A:LYS177
|
4.5
|
15.8
|
1.0
|
CG2
|
A:ILE180
|
4.5
|
17.9
|
1.0
|
N
|
A:GLY179
|
4.5
|
15.5
|
1.0
|
CG
|
A:GLU201
|
4.5
|
14.2
|
1.0
|
CA
|
A:LEU181
|
4.6
|
11.9
|
1.0
|
CA
|
A:ASP175
|
4.6
|
14.7
|
1.0
|
CA
|
A:GLY179
|
4.6
|
14.7
|
1.0
|
CB
|
A:ASP175
|
4.6
|
14.8
|
1.0
|
O
|
A:ASP175
|
4.7
|
15.5
|
1.0
|
O
|
A:HOH513
|
4.7
|
28.3
|
1.0
|
O
|
A:GLY179
|
4.8
|
15.2
|
1.0
|
O
|
A:LYS177
|
4.8
|
18.3
|
1.0
|
|
Reference:
C.Rouanet-Mehouas,
B.Czarny,
F.Beau,
E.Cassar-Lajeunesse,
E.A.Stura,
V.Dive,
L.Devel.
Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played By the Zinc-Binding Group on Potency and Selectivity. J. Med. Chem. V. 60 403 2017.
ISSN: ISSN 1520-4804
PubMed: 27996256
DOI: 10.1021/ACS.JMEDCHEM.6B01420
Page generated: Sun Jul 14 17:43:48 2024
|