Zinc in PDB 4ja1: Structure of MMP3 Complexed with A Platinum-Based Inhibitor
Enzymatic activity of Structure of MMP3 Complexed with A Platinum-Based Inhibitor
All present enzymatic activity of Structure of MMP3 Complexed with A Platinum-Based Inhibitor:
3.4.24.17;
Protein crystallography data
The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor, PDB code: 4ja1
was solved by
B.D.Belviso,
F.Arnesano,
V.Calderone,
R.Caliandro,
G.Natile,
D.Siliqi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.22 /
1.96
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.119,
77.615,
106.048,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
24.4
|
Other elements in 4ja1:
The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor
(pdb code 4ja1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of MMP3 Complexed with A Platinum-Based Inhibitor, PDB code: 4ja1:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4ja1
Go back to
Zinc Binding Sites List in 4ja1
Zinc binding site 1 out
of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:22.7
occ:1.00
|
NE2
|
A:HIS201
|
1.9
|
17.2
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
11.4
|
1.0
|
NE2
|
A:HIS211
|
2.1
|
28.7
|
1.0
|
CE1
|
A:HIS201
|
2.8
|
19.3
|
1.0
|
CE1
|
A:HIS205
|
2.9
|
14.8
|
1.0
|
CD2
|
A:HIS211
|
3.0
|
26.1
|
1.0
|
CD2
|
A:HIS201
|
3.0
|
18.7
|
1.0
|
CE1
|
A:HIS211
|
3.1
|
29.7
|
1.0
|
CD2
|
A:HIS205
|
3.2
|
12.1
|
1.0
|
ND1
|
A:HIS201
|
3.9
|
18.7
|
1.0
|
CG
|
A:HIS201
|
4.1
|
15.8
|
1.0
|
ND1
|
A:HIS205
|
4.1
|
14.5
|
1.0
|
CG
|
A:HIS211
|
4.1
|
26.3
|
1.0
|
ND1
|
A:HIS211
|
4.1
|
24.8
|
1.0
|
CG
|
A:HIS205
|
4.2
|
13.6
|
1.0
|
CE
|
A:MET219
|
4.7
|
16.0
|
1.0
|
OE2
|
A:GLU202
|
4.7
|
17.0
|
1.0
|
CA
|
A:PRO221
|
4.8
|
39.5
|
1.0
|
OE1
|
A:GLU202
|
4.9
|
20.4
|
1.0
|
O
|
A:PRO221
|
5.0
|
44.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4ja1
Go back to
Zinc Binding Sites List in 4ja1
Zinc binding site 2 out
of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:15.8
occ:1.00
|
NE2
|
A:HIS166
|
2.0
|
14.4
|
1.0
|
NE2
|
A:HIS151
|
2.0
|
14.5
|
1.0
|
ND1
|
A:HIS179
|
2.0
|
14.0
|
1.0
|
OD2
|
A:ASP153
|
2.3
|
25.6
|
1.0
|
CE1
|
A:HIS166
|
2.9
|
13.3
|
1.0
|
CE1
|
A:HIS179
|
3.0
|
14.9
|
1.0
|
CE1
|
A:HIS151
|
3.0
|
18.5
|
1.0
|
CD2
|
A:HIS151
|
3.0
|
17.1
|
1.0
|
CD2
|
A:HIS166
|
3.0
|
12.9
|
1.0
|
CG
|
A:HIS179
|
3.1
|
10.8
|
1.0
|
CG
|
A:ASP153
|
3.2
|
22.4
|
1.0
|
OD1
|
A:ASP153
|
3.4
|
20.4
|
1.0
|
CB
|
A:HIS179
|
3.5
|
11.6
|
1.0
|
ND1
|
A:HIS166
|
4.0
|
13.0
|
1.0
|
ND1
|
A:HIS151
|
4.1
|
17.9
|
1.0
|
NE2
|
A:HIS179
|
4.1
|
14.1
|
1.0
|
CG
|
A:HIS166
|
4.1
|
13.2
|
1.0
|
CG
|
A:HIS151
|
4.2
|
18.6
|
1.0
|
CD2
|
A:HIS179
|
4.2
|
12.0
|
1.0
|
O
|
A:TYR155
|
4.3
|
20.0
|
1.0
|
OH
|
A:TYR168
|
4.3
|
19.1
|
1.0
|
CB
|
A:ASP153
|
4.5
|
22.3
|
1.0
|
CE1
|
A:TYR168
|
4.5
|
16.3
|
1.0
|
CZ
|
A:PHE157
|
4.7
|
12.4
|
1.0
|
CE2
|
A:PHE157
|
4.7
|
9.7
|
1.0
|
CZ
|
A:TYR168
|
4.9
|
17.9
|
1.0
|
CA
|
A:HIS179
|
5.0
|
11.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4ja1
Go back to
Zinc Binding Sites List in 4ja1
Zinc binding site 3 out
of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:27.0
occ:1.00
|
NE2
|
B:HIS205
|
2.1
|
20.9
|
1.0
|
NE2
|
B:HIS201
|
2.1
|
20.7
|
1.0
|
O5
|
B:NGH306
|
2.2
|
38.1
|
1.0
|
NE2
|
B:HIS211
|
2.3
|
29.0
|
1.0
|
O4
|
B:NGH306
|
2.3
|
34.1
|
1.0
|
C11
|
B:NGH306
|
2.9
|
38.7
|
1.0
|
N1
|
B:NGH306
|
3.0
|
37.8
|
1.0
|
CD2
|
B:HIS201
|
3.0
|
20.4
|
1.0
|
CD2
|
B:HIS205
|
3.0
|
20.7
|
1.0
|
CD2
|
B:HIS211
|
3.1
|
28.3
|
1.0
|
CE1
|
B:HIS205
|
3.1
|
20.0
|
1.0
|
CE1
|
B:HIS201
|
3.2
|
21.5
|
1.0
|
CE1
|
B:HIS211
|
3.4
|
31.6
|
1.0
|
O
|
B:HOH437
|
4.0
|
27.4
|
1.0
|
ND1
|
B:HIS205
|
4.2
|
21.9
|
1.0
|
CG
|
B:HIS205
|
4.2
|
20.2
|
1.0
|
CG
|
B:HIS201
|
4.2
|
20.4
|
1.0
|
ND1
|
B:HIS201
|
4.3
|
19.6
|
1.0
|
CG
|
B:HIS211
|
4.3
|
29.6
|
1.0
|
OE2
|
B:GLU202
|
4.3
|
23.8
|
1.0
|
C10
|
B:NGH306
|
4.4
|
40.2
|
1.0
|
ND1
|
B:HIS211
|
4.4
|
32.2
|
1.0
|
C5
|
B:NGH306
|
4.7
|
34.6
|
1.0
|
C4
|
B:NGH306
|
4.8
|
32.5
|
1.0
|
CB
|
B:PRO221
|
4.9
|
34.2
|
1.0
|
N
|
B:NGH306
|
4.9
|
40.6
|
1.0
|
CD
|
B:GLU202
|
5.0
|
21.9
|
1.0
|
OE1
|
B:GLU202
|
5.0
|
24.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4ja1
Go back to
Zinc Binding Sites List in 4ja1
Zinc binding site 4 out
of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:20.8
occ:0.99
|
NE2
|
B:HIS166
|
1.9
|
19.5
|
1.0
|
OD2
|
B:ASP153
|
2.0
|
24.8
|
1.0
|
NE2
|
B:HIS151
|
2.1
|
19.3
|
1.0
|
ND1
|
B:HIS179
|
2.1
|
19.0
|
1.0
|
CE1
|
B:HIS166
|
2.8
|
20.4
|
1.0
|
CG
|
B:ASP153
|
2.9
|
23.1
|
1.0
|
CD2
|
B:HIS166
|
3.0
|
21.6
|
1.0
|
CE1
|
B:HIS151
|
3.1
|
18.9
|
1.0
|
CE1
|
B:HIS179
|
3.1
|
18.7
|
1.0
|
CG
|
B:HIS179
|
3.1
|
18.6
|
1.0
|
CD2
|
B:HIS151
|
3.2
|
19.8
|
1.0
|
OD1
|
B:ASP153
|
3.2
|
19.8
|
1.0
|
CB
|
B:HIS179
|
3.5
|
16.4
|
1.0
|
ND1
|
B:HIS166
|
4.0
|
19.1
|
1.0
|
OH
|
B:TYR168
|
4.0
|
25.6
|
1.0
|
CG
|
B:HIS166
|
4.1
|
19.2
|
1.0
|
CB
|
B:ASP153
|
4.2
|
23.1
|
1.0
|
ND1
|
B:HIS151
|
4.2
|
19.3
|
1.0
|
NE2
|
B:HIS179
|
4.2
|
16.3
|
1.0
|
O
|
B:TYR155
|
4.2
|
26.2
|
1.0
|
CG
|
B:HIS151
|
4.3
|
22.3
|
1.0
|
CD2
|
B:HIS179
|
4.3
|
17.8
|
1.0
|
CE1
|
B:TYR168
|
4.5
|
25.2
|
1.0
|
CE2
|
B:PHE157
|
4.6
|
20.0
|
1.0
|
CZ
|
B:PHE157
|
4.7
|
21.8
|
1.0
|
CZ
|
B:TYR168
|
4.7
|
27.3
|
1.0
|
|
Reference:
B.D.Belviso,
R.Caliandro,
D.Siliqi,
V.Calderone,
F.Arnesano,
G.Natile.
Structure of Matrix Metalloproteinase-3 with A Platinum-Based Inhibitor. Chem.Commun.(Camb.) V. 49 5492 2013.
ISSN: ISSN 1359-7345
PubMed: 23660647
DOI: 10.1039/C3CC41278D
Page generated: Sun Oct 27 01:06:25 2024
|