Zinc in PDB 4h49: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.:
3.4.24.65;
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor., PDB code: 4h49
was solved by
C.Antoni,
E.A.Stura,
L.Vera,
E.Nuti,
L.Carafa,
E.Cassar-Lajeunesse,
V.Dive,
A.Rossello,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.26 /
2.16
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.440,
106.490,
65.880,
90.00,
94.96,
90.00
|
R / Rfree (%)
|
16.7 /
24.1
|
Other elements in 4h49:
The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
(pdb code 4h49). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor., PDB code: 4h49:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 1 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:14.2
occ:1.00
|
NE2
|
A:HIS228
|
2.0
|
13.9
|
1.0
|
NE2
|
A:HIS222
|
2.1
|
17.8
|
1.0
|
NE2
|
A:HIS218
|
2.1
|
12.4
|
1.0
|
O23
|
B:L29601
|
2.2
|
15.2
|
1.0
|
O22
|
B:L29601
|
2.5
|
20.9
|
1.0
|
CD2
|
A:HIS218
|
2.9
|
12.1
|
1.0
|
C21
|
B:L29601
|
3.0
|
15.2
|
1.0
|
CD2
|
A:HIS228
|
3.0
|
17.1
|
1.0
|
CE1
|
A:HIS228
|
3.0
|
16.3
|
1.0
|
CE1
|
A:HIS222
|
3.1
|
13.4
|
1.0
|
CD2
|
A:HIS222
|
3.1
|
12.0
|
1.0
|
CE1
|
A:HIS218
|
3.1
|
13.0
|
1.0
|
N22
|
B:L29601
|
3.2
|
20.0
|
1.0
|
ND1
|
A:HIS228
|
4.1
|
11.3
|
1.0
|
CG
|
A:HIS218
|
4.1
|
11.0
|
1.0
|
CG
|
A:HIS228
|
4.1
|
15.7
|
1.0
|
ND1
|
A:HIS218
|
4.2
|
10.3
|
1.0
|
ND1
|
A:HIS222
|
4.2
|
14.9
|
1.0
|
CG
|
A:HIS222
|
4.2
|
15.9
|
1.0
|
O
|
B:HOH729
|
4.2
|
14.8
|
1.0
|
C17
|
B:L29601
|
4.4
|
13.3
|
1.0
|
OE2
|
A:GLU219
|
4.5
|
17.4
|
1.0
|
C11
|
B:L29601
|
4.7
|
10.0
|
1.0
|
O
|
A:HOH418
|
4.8
|
22.7
|
1.0
|
C24
|
B:L29601
|
4.8
|
18.3
|
1.0
|
CE
|
A:MET236
|
4.9
|
8.6
|
1.0
|
C12
|
B:L29601
|
4.9
|
13.2
|
1.0
|
N16
|
B:L29601
|
4.9
|
18.9
|
1.0
|
OE1
|
A:GLU219
|
5.0
|
17.2
|
1.0
|
C10
|
B:L29601
|
5.0
|
11.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 2 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:14.4
occ:1.00
|
NE2
|
A:HIS183
|
1.9
|
15.3
|
1.0
|
NE2
|
A:HIS168
|
1.9
|
14.8
|
1.0
|
OD2
|
A:ASP170
|
2.0
|
17.6
|
1.0
|
ND1
|
A:HIS196
|
2.2
|
12.5
|
1.0
|
CE1
|
A:HIS183
|
2.8
|
15.7
|
1.0
|
CE1
|
A:HIS168
|
2.9
|
14.9
|
1.0
|
CG
|
A:ASP170
|
2.9
|
22.2
|
1.0
|
CD2
|
A:HIS168
|
3.0
|
16.6
|
1.0
|
CD2
|
A:HIS183
|
3.0
|
14.9
|
1.0
|
CE1
|
A:HIS196
|
3.2
|
10.3
|
1.0
|
OD1
|
A:ASP170
|
3.2
|
18.0
|
1.0
|
CG
|
A:HIS196
|
3.2
|
14.7
|
1.0
|
CB
|
A:HIS196
|
3.5
|
12.6
|
1.0
|
ND1
|
A:HIS183
|
4.0
|
13.5
|
1.0
|
ND1
|
A:HIS168
|
4.0
|
14.4
|
1.0
|
CG
|
A:HIS168
|
4.1
|
21.4
|
1.0
|
CG
|
A:HIS183
|
4.1
|
17.6
|
1.0
|
O
|
A:HIS172
|
4.2
|
18.1
|
1.0
|
CB
|
A:ASP170
|
4.3
|
22.7
|
1.0
|
NE2
|
A:HIS196
|
4.3
|
10.6
|
1.0
|
CD2
|
A:HIS196
|
4.3
|
9.2
|
1.0
|
CE2
|
A:PHE185
|
4.4
|
25.2
|
1.0
|
CZ
|
A:PHE174
|
4.6
|
9.2
|
1.0
|
CE2
|
A:PHE174
|
4.7
|
9.1
|
1.0
|
CZ
|
A:PHE185
|
4.7
|
14.1
|
1.0
|
CB
|
A:HIS172
|
5.0
|
21.1
|
1.0
|
|
Zinc binding site 3 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 3 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn602
b:16.2
occ:1.00
|
NE2
|
B:HIS228
|
2.0
|
17.1
|
1.0
|
O62
|
B:L29601
|
2.1
|
18.0
|
1.0
|
NE2
|
B:HIS222
|
2.1
|
18.4
|
1.0
|
NE2
|
B:HIS218
|
2.2
|
12.4
|
1.0
|
O61
|
B:L29601
|
2.3
|
21.9
|
1.0
|
C60
|
B:L29601
|
2.9
|
21.9
|
1.0
|
CD2
|
B:HIS228
|
3.0
|
17.1
|
1.0
|
CD2
|
B:HIS218
|
3.0
|
11.0
|
1.0
|
CE1
|
B:HIS228
|
3.0
|
16.5
|
1.0
|
N61
|
B:L29601
|
3.1
|
19.7
|
1.0
|
CD2
|
B:HIS222
|
3.1
|
9.6
|
1.0
|
CE1
|
B:HIS222
|
3.1
|
16.6
|
1.0
|
CE1
|
B:HIS218
|
3.3
|
11.3
|
1.0
|
ND1
|
B:HIS228
|
4.1
|
15.5
|
1.0
|
CG
|
B:HIS228
|
4.2
|
17.3
|
1.0
|
O
|
B:HOH728
|
4.2
|
18.1
|
1.0
|
CG
|
B:HIS218
|
4.2
|
11.3
|
1.0
|
CG
|
B:HIS222
|
4.2
|
13.4
|
1.0
|
ND1
|
B:HIS222
|
4.2
|
18.2
|
1.0
|
ND1
|
B:HIS218
|
4.3
|
15.6
|
1.0
|
C56
|
B:L29601
|
4.3
|
22.1
|
1.0
|
OE2
|
B:GLU219
|
4.6
|
18.1
|
1.0
|
C39
|
B:L29601
|
4.7
|
16.9
|
1.0
|
C59
|
B:L29601
|
4.8
|
16.1
|
1.0
|
OE1
|
B:GLU219
|
4.9
|
19.1
|
1.0
|
C5A
|
B:L29601
|
4.9
|
10.6
|
1.0
|
CE
|
B:MET236
|
4.9
|
14.7
|
1.0
|
N40
|
B:L29601
|
4.9
|
16.5
|
1.0
|
CB
|
B:PRO238
|
5.0
|
17.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 4 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn603
b:26.4
occ:1.00
|
OD1
|
B:ASP170
|
1.9
|
32.9
|
1.0
|
NE2
|
B:HIS168
|
2.0
|
29.8
|
1.0
|
NE2
|
B:HIS183
|
2.1
|
25.2
|
1.0
|
ND1
|
B:HIS196
|
2.1
|
22.0
|
1.0
|
CG
|
B:ASP170
|
2.8
|
39.8
|
1.0
|
CE1
|
B:HIS183
|
2.9
|
24.1
|
1.0
|
CE1
|
B:HIS168
|
3.0
|
32.3
|
1.0
|
CD2
|
B:HIS168
|
3.0
|
31.3
|
1.0
|
OD2
|
B:ASP170
|
3.1
|
30.7
|
1.0
|
CE1
|
B:HIS196
|
3.1
|
21.7
|
1.0
|
CG
|
B:HIS196
|
3.1
|
20.2
|
1.0
|
CD2
|
B:HIS183
|
3.2
|
20.1
|
1.0
|
CB
|
B:HIS196
|
3.4
|
15.9
|
1.0
|
ND1
|
B:HIS183
|
4.1
|
22.6
|
1.0
|
ND1
|
B:HIS168
|
4.1
|
32.3
|
1.0
|
CG
|
B:HIS168
|
4.1
|
39.4
|
1.0
|
O
|
B:HIS172
|
4.2
|
37.2
|
1.0
|
CB
|
B:ASP170
|
4.2
|
38.6
|
1.0
|
NE2
|
B:HIS196
|
4.2
|
22.5
|
1.0
|
CG
|
B:HIS183
|
4.2
|
21.3
|
1.0
|
CD2
|
B:HIS196
|
4.3
|
18.5
|
1.0
|
CE2
|
B:PHE185
|
4.4
|
25.6
|
1.0
|
CZ
|
B:PHE174
|
4.4
|
19.8
|
1.0
|
CZ
|
B:PHE185
|
4.6
|
25.1
|
1.0
|
CE2
|
B:PHE174
|
4.7
|
20.1
|
1.0
|
CA
|
B:HIS196
|
4.9
|
18.7
|
1.0
|
|
Zinc binding site 5 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 5 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:16.5
occ:1.00
|
NE2
|
C:HIS218
|
2.1
|
10.2
|
1.0
|
NE2
|
C:HIS228
|
2.1
|
14.7
|
1.0
|
NE2
|
C:HIS222
|
2.1
|
15.1
|
1.0
|
O23
|
C:L29306
|
2.1
|
21.0
|
1.0
|
O22
|
C:L29306
|
2.2
|
23.9
|
1.0
|
CD2
|
C:HIS218
|
2.9
|
11.8
|
1.0
|
C21
|
C:L29306
|
2.9
|
20.6
|
1.0
|
CE1
|
C:HIS228
|
3.0
|
17.0
|
1.0
|
N22
|
C:L29306
|
3.1
|
20.5
|
1.0
|
CD2
|
C:HIS222
|
3.1
|
12.0
|
1.0
|
CD2
|
C:HIS228
|
3.1
|
13.0
|
1.0
|
CE1
|
C:HIS222
|
3.1
|
16.8
|
1.0
|
CE1
|
C:HIS218
|
3.2
|
11.1
|
1.0
|
CG
|
C:HIS218
|
4.1
|
12.1
|
1.0
|
ND1
|
C:HIS228
|
4.2
|
15.2
|
1.0
|
O
|
C:HOH444
|
4.2
|
16.7
|
1.0
|
CG
|
C:HIS228
|
4.2
|
16.6
|
1.0
|
ND1
|
C:HIS218
|
4.2
|
12.6
|
1.0
|
ND1
|
C:HIS222
|
4.2
|
16.2
|
1.0
|
CG
|
C:HIS222
|
4.2
|
11.8
|
1.0
|
C17
|
C:L29306
|
4.4
|
22.1
|
1.0
|
OE2
|
C:GLU219
|
4.4
|
20.1
|
1.0
|
CE
|
C:MET236
|
4.8
|
16.4
|
1.0
|
C11
|
C:L29306
|
4.8
|
12.4
|
1.0
|
C24
|
C:L29306
|
4.9
|
15.3
|
1.0
|
C19
|
C:L29306
|
4.9
|
20.8
|
1.0
|
N16
|
C:L29306
|
4.9
|
16.8
|
1.0
|
C12
|
C:L29306
|
5.0
|
13.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 6 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn302
b:22.0
occ:1.00
|
NE2
|
C:HIS183
|
2.0
|
22.9
|
1.0
|
OD1
|
C:ASP170
|
2.0
|
29.3
|
1.0
|
NE2
|
C:HIS168
|
2.1
|
17.5
|
1.0
|
ND1
|
C:HIS196
|
2.2
|
19.4
|
1.0
|
CE1
|
C:HIS183
|
2.9
|
17.5
|
1.0
|
CG
|
C:ASP170
|
2.9
|
28.7
|
1.0
|
CD2
|
C:HIS183
|
3.0
|
18.6
|
1.0
|
CE1
|
C:HIS168
|
3.1
|
20.8
|
1.0
|
CD2
|
C:HIS168
|
3.1
|
20.6
|
1.0
|
CG
|
C:HIS196
|
3.1
|
19.3
|
1.0
|
CE1
|
C:HIS196
|
3.2
|
21.5
|
1.0
|
OD2
|
C:ASP170
|
3.2
|
22.8
|
1.0
|
CB
|
C:HIS196
|
3.4
|
18.4
|
1.0
|
ND1
|
C:HIS183
|
4.0
|
23.4
|
1.0
|
CG
|
C:HIS183
|
4.1
|
15.2
|
1.0
|
ND1
|
C:HIS168
|
4.2
|
21.0
|
1.0
|
CE2
|
C:PHE185
|
4.2
|
28.4
|
1.0
|
O
|
C:HIS172
|
4.2
|
26.9
|
1.0
|
CG
|
C:HIS168
|
4.2
|
26.0
|
1.0
|
CB
|
C:ASP170
|
4.3
|
32.9
|
1.0
|
NE2
|
C:HIS196
|
4.3
|
22.2
|
1.0
|
CD2
|
C:HIS196
|
4.3
|
23.2
|
1.0
|
CZ
|
C:PHE185
|
4.5
|
26.3
|
1.0
|
CZ
|
C:PHE174
|
4.6
|
11.5
|
1.0
|
CE2
|
C:PHE174
|
4.7
|
19.3
|
1.0
|
CB
|
C:HIS172
|
4.9
|
28.3
|
1.0
|
CA
|
C:HIS196
|
4.9
|
16.5
|
1.0
|
|
Zinc binding site 7 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 7 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:17.8
occ:1.00
|
NE2
|
D:HIS218
|
2.0
|
17.0
|
1.0
|
NE2
|
D:HIS222
|
2.1
|
26.4
|
1.0
|
O61
|
C:L29306
|
2.2
|
23.7
|
1.0
|
NE2
|
D:HIS228
|
2.2
|
15.5
|
1.0
|
O62
|
C:L29306
|
2.2
|
24.1
|
1.0
|
C60
|
C:L29306
|
2.9
|
18.4
|
1.0
|
N61
|
C:L29306
|
2.9
|
20.5
|
1.0
|
CD2
|
D:HIS218
|
2.9
|
14.4
|
1.0
|
CD2
|
D:HIS222
|
3.0
|
16.8
|
1.0
|
CE1
|
D:HIS218
|
3.0
|
15.2
|
1.0
|
CD2
|
D:HIS228
|
3.2
|
16.4
|
1.0
|
CE1
|
D:HIS228
|
3.2
|
18.4
|
1.0
|
CE1
|
D:HIS222
|
3.2
|
23.1
|
1.0
|
ND1
|
D:HIS218
|
4.1
|
12.1
|
1.0
|
CG
|
D:HIS218
|
4.1
|
13.0
|
1.0
|
CG
|
D:HIS222
|
4.2
|
17.6
|
1.0
|
O
|
D:HOH415
|
4.2
|
16.5
|
1.0
|
ND1
|
D:HIS222
|
4.3
|
19.2
|
1.0
|
ND1
|
D:HIS228
|
4.3
|
14.3
|
1.0
|
OE2
|
D:GLU219
|
4.3
|
22.4
|
1.0
|
CG
|
D:HIS228
|
4.3
|
16.7
|
1.0
|
C56
|
C:L29306
|
4.3
|
14.4
|
1.0
|
O
|
D:HOH428
|
4.8
|
27.9
|
1.0
|
C5A
|
C:L29306
|
4.8
|
15.5
|
1.0
|
C39
|
C:L29306
|
4.8
|
21.4
|
1.0
|
C58
|
C:L29306
|
4.8
|
22.0
|
1.0
|
OE1
|
D:GLU219
|
4.9
|
24.1
|
1.0
|
C45
|
C:L29306
|
4.9
|
13.6
|
1.0
|
CD
|
D:GLU219
|
5.0
|
21.5
|
1.0
|
C49
|
C:L29306
|
5.0
|
13.4
|
1.0
|
|
Zinc binding site 8 out
of 8 in 4h49
Go back to
Zinc Binding Sites List in 4h49
Zinc binding site 8 out
of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:24.3
occ:1.00
|
OD1
|
D:ASP170
|
1.9
|
24.4
|
1.0
|
NE2
|
D:HIS183
|
1.9
|
15.4
|
1.0
|
NE2
|
D:HIS168
|
2.1
|
24.7
|
1.0
|
ND1
|
D:HIS196
|
2.2
|
17.2
|
1.0
|
CE1
|
D:HIS183
|
2.7
|
21.5
|
1.0
|
CG
|
D:ASP170
|
2.9
|
30.5
|
1.0
|
CD2
|
D:HIS168
|
3.1
|
23.5
|
1.0
|
CE1
|
D:HIS168
|
3.1
|
25.5
|
1.0
|
CD2
|
D:HIS183
|
3.1
|
21.3
|
1.0
|
CE1
|
D:HIS196
|
3.2
|
21.6
|
1.0
|
CG
|
D:HIS196
|
3.2
|
21.7
|
1.0
|
OD2
|
D:ASP170
|
3.3
|
25.0
|
1.0
|
CB
|
D:HIS196
|
3.5
|
16.8
|
1.0
|
ND1
|
D:HIS183
|
3.9
|
22.4
|
1.0
|
CG
|
D:HIS183
|
4.1
|
17.1
|
1.0
|
ND1
|
D:HIS168
|
4.2
|
29.2
|
1.0
|
CG
|
D:HIS168
|
4.2
|
30.4
|
1.0
|
CE2
|
D:PHE185
|
4.2
|
29.7
|
1.0
|
CB
|
D:ASP170
|
4.3
|
24.6
|
1.0
|
NE2
|
D:HIS196
|
4.3
|
16.7
|
1.0
|
CD2
|
D:HIS196
|
4.3
|
22.7
|
1.0
|
O
|
D:HIS172
|
4.3
|
30.1
|
1.0
|
CZ
|
D:PHE185
|
4.4
|
26.3
|
1.0
|
CZ
|
D:PHE174
|
4.6
|
18.1
|
1.0
|
CE2
|
D:PHE174
|
4.7
|
21.0
|
1.0
|
CB
|
D:HIS172
|
5.0
|
36.1
|
1.0
|
CA
|
D:HIS196
|
5.0
|
16.5
|
1.0
|
|
Reference:
C.Antoni,
L.Vera,
L.Devel,
M.P.Catalani,
B.Czarny,
E.Cassar-Lajeunesse,
E.Nuti,
A.Rossello,
V.Dive,
E.A.Stura.
Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sat Oct 26 23:53:37 2024
|