Zinc in PDB 4dpe: 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: 4dpe
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)
|
38.86 /
1.96
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.206,
77.714,
105.615,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
23.1
|
Other elements in 4dpe:
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 4dpe). 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: 4dpe:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4dpe
Go back to
Zinc Binding Sites List in 4dpe
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:23.2
occ:1.00
|
O
|
B:THR255
|
1.9
|
27.1
|
1.0
|
NE2
|
A:HIS201
|
1.9
|
18.9
|
1.0
|
NE2
|
A:HIS211
|
2.1
|
29.9
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
14.3
|
1.0
|
O
|
B:HOH483
|
2.6
|
23.2
|
0.7
|
C
|
B:THR255
|
2.8
|
24.4
|
1.0
|
CD2
|
A:HIS201
|
2.9
|
17.3
|
1.0
|
CE1
|
A:HIS201
|
2.9
|
20.2
|
1.0
|
CE1
|
A:HIS205
|
2.9
|
17.8
|
1.0
|
CD2
|
A:HIS211
|
3.0
|
24.1
|
1.0
|
OXT
|
B:THR255
|
3.1
|
26.1
|
1.0
|
CE1
|
A:HIS211
|
3.1
|
32.5
|
1.0
|
CD2
|
A:HIS205
|
3.2
|
12.0
|
1.0
|
ND1
|
A:HIS201
|
4.0
|
22.1
|
1.0
|
CG
|
A:HIS201
|
4.0
|
15.7
|
1.0
|
ND1
|
A:HIS205
|
4.1
|
14.6
|
1.0
|
CG
|
A:HIS211
|
4.2
|
25.7
|
1.0
|
CA
|
B:THR255
|
4.2
|
23.6
|
1.0
|
ND1
|
A:HIS211
|
4.2
|
22.8
|
1.0
|
CG
|
A:HIS205
|
4.3
|
15.0
|
1.0
|
N
|
B:THR255
|
4.4
|
21.3
|
1.0
|
CG
|
B:GLU254
|
4.5
|
34.7
|
1.0
|
O
|
B:GLU254
|
4.5
|
17.1
|
1.0
|
C
|
B:GLU254
|
4.6
|
22.3
|
1.0
|
OE2
|
A:GLU202
|
4.6
|
18.8
|
1.0
|
CE
|
A:MET219
|
4.7
|
15.8
|
1.0
|
OG1
|
B:THR255
|
4.8
|
23.3
|
1.0
|
O
|
B:HOH482
|
4.9
|
42.5
|
1.0
|
OE1
|
A:GLU202
|
4.9
|
19.6
|
1.0
|
CB
|
B:GLU254
|
4.9
|
24.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4dpe
Go back to
Zinc Binding Sites List in 4dpe
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:HIS151
|
2.0
|
14.7
|
1.0
|
ND1
|
A:HIS179
|
2.0
|
14.1
|
1.0
|
NE2
|
A:HIS166
|
2.0
|
15.6
|
1.0
|
OD2
|
A:ASP153
|
2.1
|
19.4
|
1.0
|
CE1
|
A:HIS166
|
2.9
|
11.1
|
1.0
|
CE1
|
A:HIS179
|
2.9
|
18.3
|
1.0
|
CD2
|
A:HIS151
|
2.9
|
11.8
|
1.0
|
CE1
|
A:HIS151
|
3.0
|
19.2
|
1.0
|
CG
|
A:ASP153
|
3.0
|
22.2
|
1.0
|
CG
|
A:HIS179
|
3.1
|
13.7
|
1.0
|
CD2
|
A:HIS166
|
3.1
|
12.9
|
1.0
|
OD1
|
A:ASP153
|
3.2
|
16.5
|
1.0
|
CB
|
A:HIS179
|
3.5
|
13.1
|
1.0
|
ND1
|
A:HIS166
|
4.0
|
11.8
|
1.0
|
ND1
|
A:HIS151
|
4.1
|
13.9
|
1.0
|
NE2
|
A:HIS179
|
4.1
|
14.0
|
1.0
|
CG
|
A:HIS151
|
4.1
|
13.6
|
1.0
|
CG
|
A:HIS166
|
4.2
|
13.6
|
1.0
|
CD2
|
A:HIS179
|
4.2
|
13.5
|
1.0
|
OH
|
A:TYR168
|
4.2
|
18.9
|
1.0
|
O
|
A:TYR155
|
4.3
|
20.1
|
1.0
|
CB
|
A:ASP153
|
4.4
|
20.1
|
1.0
|
CE1
|
A:TYR168
|
4.5
|
16.8
|
1.0
|
CZ
|
A:PHE157
|
4.6
|
13.9
|
1.0
|
CE2
|
A:PHE157
|
4.7
|
15.7
|
1.0
|
CZ
|
A:TYR168
|
4.9
|
19.1
|
1.0
|
CA
|
A:HIS179
|
5.0
|
12.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4dpe
Go back to
Zinc Binding Sites List in 4dpe
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:28.2
occ:1.00
|
NE2
|
B:HIS211
|
2.1
|
32.1
|
1.0
|
NE2
|
B:HIS205
|
2.1
|
20.6
|
1.0
|
NE2
|
B:HIS201
|
2.1
|
29.3
|
1.0
|
O5
|
B:NGH313
|
2.2
|
40.3
|
1.0
|
O4
|
B:NGH313
|
2.3
|
38.9
|
1.0
|
C11
|
B:NGH313
|
3.0
|
42.9
|
1.0
|
CD2
|
B:HIS201
|
3.0
|
29.9
|
1.0
|
CD2
|
B:HIS205
|
3.0
|
20.1
|
1.0
|
N1
|
B:NGH313
|
3.0
|
41.7
|
1.0
|
CD2
|
B:HIS211
|
3.0
|
31.9
|
1.0
|
CE1
|
B:HIS211
|
3.1
|
31.3
|
1.0
|
CE1
|
B:HIS205
|
3.1
|
23.1
|
1.0
|
CE1
|
B:HIS201
|
3.1
|
28.8
|
1.0
|
O
|
B:HOH426
|
4.1
|
27.8
|
1.0
|
ND1
|
B:HIS211
|
4.2
|
34.0
|
1.0
|
CG
|
B:HIS201
|
4.2
|
24.3
|
1.0
|
CG
|
B:HIS211
|
4.2
|
31.4
|
1.0
|
CG
|
B:HIS205
|
4.2
|
21.5
|
1.0
|
ND1
|
B:HIS205
|
4.2
|
22.6
|
1.0
|
OE2
|
B:GLU202
|
4.2
|
26.8
|
1.0
|
ND1
|
B:HIS201
|
4.2
|
23.2
|
1.0
|
C10
|
B:NGH313
|
4.4
|
41.3
|
1.0
|
C1
|
B:NGH313
|
4.7
|
38.0
|
1.0
|
CB
|
B:PRO221
|
4.8
|
36.4
|
1.0
|
C2
|
B:NGH313
|
4.9
|
35.6
|
1.0
|
CE
|
B:MET219
|
5.0
|
25.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4dpe
Go back to
Zinc Binding Sites List in 4dpe
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:21.5
occ:1.00
|
OD2
|
B:ASP153
|
1.8
|
25.8
|
1.0
|
NE2
|
B:HIS166
|
1.9
|
20.2
|
1.0
|
NE2
|
B:HIS151
|
2.1
|
24.7
|
1.0
|
ND1
|
B:HIS179
|
2.1
|
20.7
|
1.0
|
CG
|
B:ASP153
|
2.8
|
26.4
|
1.0
|
CE1
|
B:HIS166
|
2.8
|
26.2
|
1.0
|
CD2
|
B:HIS166
|
3.0
|
22.9
|
1.0
|
CD2
|
B:HIS151
|
3.0
|
19.9
|
1.0
|
CE1
|
B:HIS179
|
3.0
|
20.2
|
1.0
|
CE1
|
B:HIS151
|
3.1
|
20.9
|
1.0
|
OD1
|
B:ASP153
|
3.1
|
19.3
|
1.0
|
CG
|
B:HIS179
|
3.2
|
17.2
|
1.0
|
CB
|
B:HIS179
|
3.5
|
16.1
|
1.0
|
ND1
|
B:HIS166
|
4.0
|
23.6
|
1.0
|
OH
|
B:TYR168
|
4.0
|
26.6
|
1.0
|
CG
|
B:HIS166
|
4.1
|
21.9
|
1.0
|
CB
|
B:ASP153
|
4.1
|
23.5
|
1.0
|
ND1
|
B:HIS151
|
4.2
|
19.8
|
1.0
|
CG
|
B:HIS151
|
4.2
|
22.1
|
1.0
|
NE2
|
B:HIS179
|
4.2
|
19.0
|
1.0
|
O
|
B:TYR155
|
4.3
|
26.6
|
1.0
|
CD2
|
B:HIS179
|
4.3
|
18.0
|
1.0
|
CE1
|
B:TYR168
|
4.5
|
24.3
|
1.0
|
CE2
|
B:PHE157
|
4.7
|
20.3
|
1.0
|
CZ
|
B:PHE157
|
4.7
|
23.8
|
1.0
|
CZ
|
B:TYR168
|
4.8
|
31.9
|
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: Sat Oct 26 21:32:55 2024
|