Zinc in PDB 4h2e: Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
Enzymatic activity of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
All present enzymatic activity of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains:
3.4.24.35;
Protein crystallography data
The structure of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains, PDB code: 4h2e
was solved by
E.A.Stura,
L.Vera,
E.Cassar-Lajeunesse,
E.Nuti,
M.P.Catalani,
V.Dive,
A.Rossello,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.85 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.180,
97.400,
45.690,
90.00,
111.99,
90.00
|
R / Rfree (%)
|
27.7 /
31.1
|
Other elements in 4h2e:
The structure of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
(pdb code 4h2e). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains, PDB code: 4h2e:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4h2e
Go back to
Zinc Binding Sites List in 4h2e
Zinc binding site 1 out
of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:16.4
occ:1.00
|
NE2
|
A:HIS226
|
1.9
|
9.3
|
1.0
|
NE2
|
A:HIS236
|
1.9
|
2.8
|
1.0
|
O23
|
B:0Y3306
|
2.0
|
37.5
|
1.0
|
O25
|
B:0Y3306
|
2.1
|
36.7
|
1.0
|
NE2
|
A:HIS230
|
2.2
|
20.0
|
1.0
|
N22
|
B:0Y3306
|
2.7
|
37.4
|
1.0
|
C21
|
B:0Y3306
|
2.7
|
36.6
|
1.0
|
CD2
|
A:HIS226
|
2.8
|
9.8
|
1.0
|
CE1
|
A:HIS236
|
2.9
|
2.5
|
1.0
|
CE1
|
A:HIS226
|
2.9
|
9.0
|
1.0
|
CD2
|
A:HIS230
|
2.9
|
20.1
|
1.0
|
CD2
|
A:HIS236
|
2.9
|
3.2
|
1.0
|
CE1
|
A:HIS230
|
3.4
|
19.9
|
1.0
|
ND1
|
A:HIS226
|
4.0
|
8.8
|
1.0
|
CG
|
A:HIS226
|
4.0
|
8.8
|
1.0
|
ND1
|
A:HIS236
|
4.0
|
2.9
|
1.0
|
CG
|
A:HIS236
|
4.1
|
3.0
|
1.0
|
CG
|
A:HIS230
|
4.2
|
20.0
|
1.0
|
C20
|
B:0Y3306
|
4.2
|
37.0
|
1.0
|
O36
|
B:0Y3306
|
4.3
|
38.5
|
1.0
|
ND1
|
A:HIS230
|
4.3
|
19.5
|
1.0
|
C29
|
B:0Y3306
|
4.4
|
38.8
|
1.0
|
N28
|
B:0Y3306
|
4.5
|
38.1
|
1.0
|
O17
|
B:0Y3306
|
4.6
|
37.3
|
1.0
|
CE
|
A:MET244
|
4.6
|
6.5
|
1.0
|
N16
|
B:0Y3306
|
4.7
|
37.8
|
1.0
|
OE1
|
A:GLU227
|
4.7
|
18.7
|
1.0
|
C27
|
B:0Y3306
|
4.7
|
37.0
|
1.0
|
OE2
|
A:GLU227
|
4.8
|
17.9
|
1.0
|
O
|
A:HIS226
|
4.9
|
9.4
|
1.0
|
C26
|
B:0Y3306
|
5.0
|
37.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4h2e
Go back to
Zinc Binding Sites List in 4h2e
Zinc binding site 2 out
of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:16.0
occ:1.00
|
ND1
|
A:HIS203
|
2.0
|
8.8
|
1.0
|
OD1
|
A:ASP177
|
2.0
|
5.5
|
1.0
|
NE2
|
A:HIS175
|
2.1
|
21.9
|
1.0
|
NE2
|
A:HIS190
|
2.3
|
14.9
|
1.0
|
CG
|
A:ASP177
|
2.7
|
6.8
|
1.0
|
OD2
|
A:ASP177
|
2.8
|
7.0
|
1.0
|
CE1
|
A:HIS203
|
2.9
|
9.1
|
1.0
|
CD2
|
A:HIS175
|
2.9
|
23.6
|
1.0
|
CE1
|
A:HIS190
|
2.9
|
14.3
|
1.0
|
CG
|
A:HIS203
|
3.0
|
8.9
|
1.0
|
CE1
|
A:HIS175
|
3.2
|
22.8
|
1.0
|
CB
|
A:HIS203
|
3.4
|
9.5
|
1.0
|
CD2
|
A:HIS190
|
3.5
|
14.6
|
1.0
|
NE2
|
A:HIS203
|
4.0
|
9.5
|
1.0
|
CB
|
A:ASP177
|
4.1
|
7.8
|
1.0
|
CD2
|
A:HIS203
|
4.1
|
9.7
|
1.0
|
CG
|
A:HIS175
|
4.1
|
25.4
|
1.0
|
ND1
|
A:HIS190
|
4.2
|
14.9
|
1.0
|
ND1
|
A:HIS175
|
4.2
|
24.2
|
1.0
|
O
|
A:TYR179
|
4.3
|
34.1
|
1.0
|
CG
|
A:HIS190
|
4.5
|
15.3
|
1.0
|
CZ
|
A:PHE192
|
4.6
|
14.8
|
1.0
|
N
|
A:ASP177
|
4.6
|
9.2
|
1.0
|
CE2
|
A:PHE192
|
4.7
|
13.3
|
1.0
|
CE2
|
A:PHE181
|
4.8
|
23.1
|
1.0
|
CZ
|
A:PHE181
|
4.8
|
21.4
|
1.0
|
CA
|
A:HIS203
|
4.9
|
8.9
|
1.0
|
CA
|
A:ASP177
|
4.9
|
7.8
|
1.0
|
NE2
|
A:GLN169
|
4.9
|
20.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4h2e
Go back to
Zinc Binding Sites List in 4h2e
Zinc binding site 3 out
of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:17.9
occ:1.00
|
NE2
|
B:HIS236
|
2.0
|
4.2
|
1.0
|
O78
|
B:0Y3306
|
2.0
|
39.7
|
1.0
|
O77
|
B:0Y3306
|
2.0
|
41.1
|
1.0
|
NE2
|
B:HIS226
|
2.1
|
14.8
|
1.0
|
NE2
|
B:HIS230
|
2.3
|
13.1
|
1.0
|
C75
|
B:0Y3306
|
2.7
|
39.8
|
1.0
|
N76
|
B:0Y3306
|
2.7
|
40.8
|
1.0
|
CD2
|
B:HIS226
|
2.9
|
14.9
|
1.0
|
CD2
|
B:HIS236
|
2.9
|
4.4
|
1.0
|
CE1
|
B:HIS236
|
3.0
|
3.9
|
1.0
|
CD2
|
B:HIS230
|
3.0
|
12.8
|
1.0
|
CE1
|
B:HIS226
|
3.2
|
14.4
|
1.0
|
CE1
|
B:HIS230
|
3.5
|
12.7
|
1.0
|
ND1
|
B:HIS236
|
4.1
|
4.0
|
1.0
|
CG
|
B:HIS236
|
4.1
|
4.2
|
1.0
|
CG
|
B:HIS226
|
4.1
|
14.2
|
1.0
|
C54
|
B:0Y3306
|
4.1
|
40.3
|
1.0
|
ND1
|
B:HIS226
|
4.2
|
14.2
|
1.0
|
CG
|
B:HIS230
|
4.2
|
12.8
|
1.0
|
ND1
|
B:HIS230
|
4.4
|
12.5
|
1.0
|
OE1
|
B:GLU227
|
4.4
|
9.3
|
1.0
|
OE2
|
B:GLU227
|
4.4
|
8.6
|
1.0
|
O53
|
B:0Y3306
|
4.5
|
40.8
|
1.0
|
C50
|
B:0Y3306
|
4.6
|
42.3
|
1.0
|
CE
|
B:MET244
|
4.6
|
10.7
|
1.0
|
N49
|
B:0Y3306
|
4.7
|
44.0
|
1.0
|
N55
|
B:0Y3306
|
4.8
|
41.5
|
1.0
|
C48
|
B:0Y3306
|
4.8
|
41.8
|
1.0
|
CD
|
B:GLU227
|
4.9
|
8.9
|
1.0
|
C57
|
B:0Y3306
|
4.9
|
40.3
|
1.0
|
C51
|
B:0Y3306
|
4.9
|
40.7
|
1.0
|
C58
|
B:0Y3306
|
5.0
|
41.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4h2e
Go back to
Zinc Binding Sites List in 4h2e
Zinc binding site 4 out
of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains
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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:13.6
occ:1.00
|
OD1
|
B:ASP177
|
2.0
|
18.4
|
1.0
|
ND1
|
B:HIS203
|
2.2
|
12.4
|
1.0
|
NE2
|
B:HIS190
|
2.4
|
9.3
|
1.0
|
NE2
|
B:HIS175
|
2.5
|
20.5
|
1.0
|
CG
|
B:ASP177
|
2.8
|
19.8
|
1.0
|
OD2
|
B:ASP177
|
3.0
|
19.9
|
1.0
|
CG
|
B:HIS203
|
3.0
|
12.3
|
1.0
|
CE1
|
B:HIS203
|
3.1
|
12.7
|
1.0
|
CE1
|
B:HIS190
|
3.2
|
8.7
|
1.0
|
CB
|
B:HIS203
|
3.3
|
12.9
|
1.0
|
CD2
|
B:HIS190
|
3.4
|
9.3
|
1.0
|
CD2
|
B:HIS175
|
3.4
|
22.1
|
1.0
|
CE1
|
B:HIS175
|
3.4
|
22.0
|
1.0
|
CD2
|
B:HIS203
|
4.0
|
13.2
|
1.0
|
NE2
|
B:HIS203
|
4.1
|
12.9
|
1.0
|
CB
|
B:ASP177
|
4.2
|
20.5
|
1.0
|
CE2
|
B:PHE192
|
4.4
|
18.2
|
1.0
|
ND1
|
B:HIS190
|
4.4
|
9.2
|
1.0
|
CG
|
B:HIS190
|
4.5
|
9.8
|
1.0
|
ND1
|
B:HIS175
|
4.5
|
23.4
|
1.0
|
O
|
B:TYR179
|
4.5
|
20.8
|
1.0
|
CG
|
B:HIS175
|
4.6
|
23.4
|
1.0
|
N
|
B:ASP177
|
4.6
|
22.1
|
1.0
|
CE2
|
B:PHE181
|
4.6
|
20.9
|
1.0
|
CZ
|
B:PHE181
|
4.6
|
19.0
|
1.0
|
CA
|
B:HIS203
|
4.8
|
12.4
|
1.0
|
CZ
|
B:PHE192
|
4.9
|
19.1
|
1.0
|
NE2
|
B:GLN169
|
5.0
|
22.6
|
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 23:49:12 2024
|