Zinc in PDB 1g4k: X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Enzymatic activity of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
All present enzymatic activity of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin:
3.4.24.17;
Protein crystallography data
The structure of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin, PDB code: 1g4k
was solved by
P.Dunten,
U.Kammlott,
R.Crowther,
W.Levin,
L.H.Foley,
P.Wang,
R.Palermo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.800,
103.800,
147.490,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.4 /
28.4
|
Other elements in 1g4k:
The structure of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
(pdb code 1g4k). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin, PDB code: 1g4k:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 1g4k
Go back to
Zinc Binding Sites List in 1g4k
Zinc binding site 1 out
of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:19.2
occ:1.00
|
NE2
|
A:HIS211
|
1.9
|
18.4
|
1.0
|
NE2
|
A:HIS201
|
1.9
|
14.8
|
1.0
|
N3
|
A:HQQ306
|
2.0
|
27.5
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
18.6
|
1.0
|
C4
|
A:HQQ306
|
2.7
|
28.6
|
1.0
|
CE1
|
A:HIS201
|
2.8
|
12.2
|
1.0
|
C2
|
A:HQQ306
|
2.9
|
28.9
|
1.0
|
CE1
|
A:HIS211
|
2.9
|
23.0
|
1.0
|
O4
|
A:HQQ306
|
2.9
|
27.6
|
1.0
|
CD2
|
A:HIS211
|
2.9
|
14.9
|
1.0
|
CE1
|
A:HIS205
|
3.0
|
15.4
|
1.0
|
O2
|
A:HQQ306
|
3.0
|
29.0
|
1.0
|
CD2
|
A:HIS201
|
3.1
|
17.4
|
1.0
|
CD2
|
A:HIS205
|
3.1
|
11.7
|
1.0
|
ND1
|
A:HIS201
|
4.0
|
14.1
|
1.0
|
ND1
|
A:HIS211
|
4.0
|
17.8
|
1.0
|
CG
|
A:HIS211
|
4.1
|
21.7
|
1.0
|
N1
|
A:HQQ306
|
4.1
|
27.8
|
1.0
|
CG
|
A:HIS201
|
4.1
|
18.6
|
1.0
|
C5
|
A:HQQ306
|
4.2
|
27.4
|
1.0
|
ND1
|
A:HIS205
|
4.2
|
13.7
|
1.0
|
CG
|
A:HIS205
|
4.2
|
13.4
|
1.0
|
C8
|
A:HQQ306
|
4.4
|
28.9
|
1.0
|
O
|
A:HOH313
|
4.6
|
18.5
|
1.0
|
OE2
|
A:GLU202
|
4.6
|
24.5
|
1.0
|
C6
|
A:HQQ306
|
4.7
|
27.6
|
1.0
|
C9
|
A:HQQ306
|
4.7
|
27.8
|
1.0
|
C13
|
A:HQQ306
|
4.8
|
28.9
|
1.0
|
CE
|
A:MET219
|
4.9
|
15.6
|
1.0
|
O
|
A:HOH358
|
5.0
|
36.5
|
1.0
|
|
Zinc binding site 2 out
of 6 in 1g4k
Go back to
Zinc Binding Sites List in 1g4k
Zinc binding site 2 out
of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:18.4
occ:1.00
|
OD2
|
A:ASP153
|
1.9
|
16.6
|
1.0
|
NE2
|
A:HIS166
|
2.0
|
25.5
|
1.0
|
NE2
|
A:HIS151
|
2.0
|
20.8
|
1.0
|
ND1
|
A:HIS179
|
2.1
|
12.4
|
1.0
|
CE1
|
A:HIS179
|
2.9
|
14.4
|
1.0
|
CG
|
A:ASP153
|
2.9
|
25.4
|
1.0
|
CE1
|
A:HIS166
|
2.9
|
25.6
|
1.0
|
CD2
|
A:HIS151
|
2.9
|
19.9
|
1.0
|
CD2
|
A:HIS166
|
3.0
|
16.6
|
1.0
|
CE1
|
A:HIS151
|
3.1
|
18.4
|
1.0
|
CG
|
A:HIS179
|
3.2
|
12.1
|
1.0
|
OD1
|
A:ASP153
|
3.2
|
19.1
|
1.0
|
CB
|
A:HIS179
|
3.6
|
11.4
|
1.0
|
NE2
|
A:HIS179
|
4.1
|
20.4
|
1.0
|
ND1
|
A:HIS166
|
4.1
|
23.2
|
1.0
|
CG
|
A:HIS151
|
4.1
|
22.4
|
1.0
|
CG
|
A:HIS166
|
4.2
|
20.0
|
1.0
|
ND1
|
A:HIS151
|
4.2
|
21.1
|
1.0
|
OH
|
A:TYR168
|
4.2
|
28.3
|
1.0
|
O
|
A:TYR155
|
4.2
|
21.5
|
1.0
|
CB
|
A:ASP153
|
4.3
|
21.4
|
1.0
|
CD2
|
A:HIS179
|
4.3
|
16.0
|
1.0
|
CE1
|
A:TYR168
|
4.5
|
24.3
|
1.0
|
CZ
|
A:PHE157
|
4.5
|
15.1
|
1.0
|
CE2
|
A:PHE157
|
4.7
|
24.3
|
1.0
|
CZ
|
A:TYR168
|
4.9
|
26.8
|
1.0
|
|
Zinc binding site 3 out
of 6 in 1g4k
Go back to
Zinc Binding Sites List in 1g4k
Zinc binding site 3 out
of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:13.8
occ:1.00
|
NE2
|
B:HIS205
|
2.0
|
14.1
|
1.0
|
NE2
|
B:HIS211
|
2.1
|
17.6
|
1.0
|
NE2
|
B:HIS201
|
2.1
|
14.9
|
1.0
|
N3
|
B:HQQ306
|
2.1
|
14.2
|
1.0
|
CE1
|
B:HIS205
|
2.9
|
9.7
|
1.0
|
C2
|
B:HQQ306
|
2.9
|
13.8
|
1.0
|
CD2
|
B:HIS211
|
3.0
|
13.9
|
1.0
|
C4
|
B:HQQ306
|
3.0
|
14.0
|
1.0
|
O2
|
B:HQQ306
|
3.0
|
15.7
|
1.0
|
CD2
|
B:HIS201
|
3.0
|
13.2
|
1.0
|
CE1
|
B:HIS211
|
3.0
|
11.1
|
1.0
|
CD2
|
B:HIS205
|
3.1
|
11.1
|
1.0
|
O4
|
B:HQQ306
|
3.1
|
13.8
|
1.0
|
CE1
|
B:HIS201
|
3.1
|
13.8
|
1.0
|
ND1
|
B:HIS205
|
4.1
|
10.2
|
1.0
|
CG
|
B:HIS211
|
4.2
|
12.0
|
1.0
|
CG
|
B:HIS201
|
4.2
|
12.4
|
1.0
|
ND1
|
B:HIS211
|
4.2
|
9.4
|
1.0
|
CG
|
B:HIS205
|
4.2
|
10.7
|
1.0
|
N1
|
B:HQQ306
|
4.2
|
13.8
|
1.0
|
ND1
|
B:HIS201
|
4.2
|
12.7
|
1.0
|
C5
|
B:HQQ306
|
4.4
|
13.4
|
1.0
|
O
|
B:HOH311
|
4.5
|
13.8
|
1.0
|
C8
|
B:HQQ306
|
4.6
|
13.0
|
1.0
|
C9
|
B:HQQ306
|
4.7
|
13.3
|
1.0
|
CE
|
B:MET219
|
4.7
|
14.8
|
1.0
|
OE2
|
B:GLU202
|
4.7
|
17.5
|
1.0
|
C6
|
B:HQQ306
|
4.8
|
13.5
|
1.0
|
O
|
A:HOH370
|
4.9
|
33.5
|
1.0
|
|
Zinc binding site 4 out
of 6 in 1g4k
Go back to
Zinc Binding Sites List in 1g4k
Zinc binding site 4 out
of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:16.7
occ:1.00
|
OD2
|
B:ASP153
|
1.9
|
16.1
|
1.0
|
NE2
|
B:HIS166
|
2.0
|
16.2
|
1.0
|
ND1
|
B:HIS179
|
2.0
|
12.5
|
1.0
|
NE2
|
B:HIS151
|
2.1
|
18.5
|
1.0
|
CE1
|
B:HIS179
|
2.9
|
16.9
|
1.0
|
CG
|
B:ASP153
|
2.9
|
19.2
|
1.0
|
CD2
|
B:HIS166
|
2.9
|
19.8
|
1.0
|
CD2
|
B:HIS151
|
3.0
|
16.7
|
1.0
|
CE1
|
B:HIS166
|
3.0
|
12.4
|
1.0
|
CG
|
B:HIS179
|
3.1
|
13.5
|
1.0
|
CE1
|
B:HIS151
|
3.2
|
17.5
|
1.0
|
OD1
|
B:ASP153
|
3.2
|
17.0
|
1.0
|
CB
|
B:HIS179
|
3.5
|
10.4
|
1.0
|
NE2
|
B:HIS179
|
4.0
|
14.9
|
1.0
|
ND1
|
B:HIS166
|
4.1
|
17.9
|
1.0
|
CG
|
B:HIS166
|
4.1
|
15.7
|
1.0
|
CG
|
B:HIS151
|
4.2
|
18.3
|
1.0
|
CD2
|
B:HIS179
|
4.2
|
11.6
|
1.0
|
OH
|
B:TYR168
|
4.2
|
25.4
|
1.0
|
ND1
|
B:HIS151
|
4.2
|
15.8
|
1.0
|
CB
|
B:ASP153
|
4.2
|
19.6
|
1.0
|
O
|
B:TYR155
|
4.4
|
16.6
|
1.0
|
CE1
|
B:TYR168
|
4.5
|
19.3
|
1.0
|
CZ
|
B:PHE157
|
4.5
|
9.9
|
1.0
|
CE2
|
B:PHE157
|
4.7
|
12.6
|
1.0
|
CZ
|
B:TYR168
|
4.8
|
26.3
|
1.0
|
CA
|
B:HIS179
|
5.0
|
12.1
|
1.0
|
O
|
B:HOH316
|
5.0
|
15.1
|
1.0
|
|
Zinc binding site 5 out
of 6 in 1g4k
Go back to
Zinc Binding Sites List in 1g4k
Zinc binding site 5 out
of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:34.8
occ:1.00
|
NE2
|
C:HIS201
|
2.0
|
34.6
|
1.0
|
NE2
|
C:HIS211
|
2.0
|
40.1
|
1.0
|
N3
|
C:HQQ306
|
2.1
|
44.1
|
1.0
|
NE2
|
C:HIS205
|
2.2
|
36.4
|
1.0
|
CD2
|
C:HIS201
|
2.9
|
25.8
|
1.0
|
CD2
|
C:HIS211
|
2.9
|
31.1
|
1.0
|
C2
|
C:HQQ306
|
3.0
|
43.2
|
1.0
|
C4
|
C:HQQ306
|
3.0
|
43.4
|
1.0
|
O4
|
C:HQQ306
|
3.0
|
42.9
|
1.0
|
CD2
|
C:HIS205
|
3.1
|
38.8
|
1.0
|
CE1
|
C:HIS211
|
3.1
|
48.8
|
1.0
|
O2
|
C:HQQ306
|
3.1
|
42.6
|
1.0
|
CE1
|
C:HIS201
|
3.2
|
31.2
|
1.0
|
CE1
|
C:HIS205
|
3.2
|
39.6
|
1.0
|
CG
|
C:HIS211
|
4.1
|
36.5
|
1.0
|
CG
|
C:HIS201
|
4.1
|
32.4
|
1.0
|
ND1
|
C:HIS211
|
4.2
|
39.5
|
1.0
|
ND1
|
C:HIS201
|
4.2
|
32.8
|
1.0
|
N1
|
C:HQQ306
|
4.3
|
43.6
|
1.0
|
CG
|
C:HIS205
|
4.3
|
37.4
|
1.0
|
ND1
|
C:HIS205
|
4.3
|
36.9
|
1.0
|
C5
|
C:HQQ306
|
4.4
|
43.8
|
1.0
|
C8
|
C:HQQ306
|
4.5
|
45.1
|
1.0
|
C9
|
C:HQQ306
|
4.7
|
45.1
|
1.0
|
OE2
|
C:GLU202
|
4.7
|
37.3
|
1.0
|
CE
|
C:MET219
|
4.8
|
20.4
|
1.0
|
C6
|
C:HQQ306
|
4.8
|
44.0
|
1.0
|
|
Zinc binding site 6 out
of 6 in 1g4k
Go back to
Zinc Binding Sites List in 1g4k
Zinc binding site 6 out
of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn302
b:45.5
occ:1.00
|
NE2
|
C:HIS151
|
1.6
|
74.8
|
1.0
|
OD2
|
C:ASP153
|
1.8
|
39.9
|
1.0
|
NE2
|
C:HIS166
|
1.9
|
50.7
|
1.0
|
ND1
|
C:HIS179
|
2.2
|
36.8
|
1.0
|
CD2
|
C:HIS151
|
2.4
|
75.5
|
1.0
|
CE1
|
C:HIS166
|
2.5
|
56.2
|
1.0
|
CE1
|
C:HIS151
|
2.8
|
75.3
|
1.0
|
CG
|
C:ASP153
|
2.8
|
49.5
|
1.0
|
CG
|
C:HIS179
|
3.1
|
31.7
|
1.0
|
CD2
|
C:HIS166
|
3.1
|
57.8
|
1.0
|
OD1
|
C:ASP153
|
3.2
|
47.1
|
1.0
|
CE1
|
C:HIS179
|
3.2
|
37.5
|
1.0
|
CB
|
C:HIS179
|
3.4
|
32.1
|
1.0
|
CG
|
C:HIS151
|
3.6
|
75.7
|
1.0
|
ND1
|
C:HIS151
|
3.7
|
75.2
|
1.0
|
ND1
|
C:HIS166
|
3.7
|
54.5
|
1.0
|
CG
|
C:HIS166
|
4.0
|
54.4
|
1.0
|
OH
|
C:TYR168
|
4.1
|
48.5
|
1.0
|
O
|
C:TYR155
|
4.1
|
70.5
|
1.0
|
CB
|
C:ASP153
|
4.2
|
54.6
|
1.0
|
CD2
|
C:HIS179
|
4.2
|
37.5
|
1.0
|
NE2
|
C:HIS179
|
4.3
|
33.6
|
1.0
|
CE1
|
C:TYR168
|
4.7
|
43.4
|
1.0
|
CZ
|
C:PHE157
|
4.8
|
41.5
|
1.0
|
CA
|
C:HIS179
|
4.9
|
37.6
|
1.0
|
CZ
|
C:TYR168
|
4.9
|
45.4
|
1.0
|
CB
|
C:HIS151
|
4.9
|
75.3
|
1.0
|
CE2
|
C:PHE157
|
5.0
|
44.2
|
1.0
|
|
Reference:
P.Dunten,
U.Kammlott,
R.Crowther,
W.Levin,
L.H.Foley,
P.Wang,
R.Palermo.
X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin. Protein Sci. V. 10 923 2001.
ISSN: ISSN 0961-8368
PubMed: 11316871
DOI: 10.1110/PS.48401
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