Zinc in PDB 2ow1: Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
Enzymatic activity of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
All present enzymatic activity of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor:
3.4.24.35;
Protein crystallography data
The structure of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor, PDB code: 2ow1
was solved by
A.Tochowicz,
W.Bode,
K.Maskos,
P.Goettig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.79 /
2.20
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.720,
55.720,
260.450,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
26.7
|
Other elements in 2ow1:
The structure of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
(pdb code 2ow1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor, PDB code: 2ow1:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2ow1
Go back to
Zinc Binding Sites List in 2ow1
Zinc binding site 1 out
of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn444
b:17.9
occ:1.00
|
NE2
|
A:HIS411
|
2.1
|
22.1
|
1.0
|
NE2
|
A:HIS401
|
2.1
|
12.3
|
1.0
|
OAA
|
A:7MR501
|
2.1
|
22.1
|
1.0
|
NE2
|
A:HIS405
|
2.2
|
13.0
|
1.0
|
OAB
|
A:7MR501
|
2.2
|
23.5
|
1.0
|
CAE
|
A:7MR501
|
2.8
|
23.1
|
1.0
|
NAD
|
A:7MR501
|
2.9
|
22.5
|
1.0
|
CD2
|
A:HIS411
|
3.0
|
21.8
|
1.0
|
CD2
|
A:HIS401
|
3.0
|
13.5
|
1.0
|
CE1
|
A:HIS401
|
3.1
|
11.4
|
1.0
|
CE1
|
A:HIS411
|
3.1
|
23.6
|
1.0
|
CD2
|
A:HIS405
|
3.1
|
13.9
|
1.0
|
CE1
|
A:HIS405
|
3.2
|
15.2
|
1.0
|
O
|
A:HOH551
|
4.1
|
13.1
|
1.0
|
CG
|
A:HIS411
|
4.1
|
22.4
|
1.0
|
ND1
|
A:HIS411
|
4.2
|
24.0
|
1.0
|
ND1
|
A:HIS401
|
4.2
|
11.8
|
1.0
|
CG
|
A:HIS401
|
4.2
|
11.9
|
1.0
|
ND1
|
A:HIS405
|
4.3
|
15.4
|
1.0
|
CG
|
A:HIS405
|
4.3
|
15.4
|
1.0
|
NE2
|
A:GLN402
|
4.3
|
18.2
|
1.0
|
CAO
|
A:7MR501
|
4.3
|
23.8
|
1.0
|
FBA
|
A:7MR501
|
4.5
|
25.6
|
1.0
|
FAF
|
A:7MR501
|
4.7
|
24.5
|
1.0
|
CAX
|
A:7MR501
|
4.8
|
19.4
|
1.0
|
CAP
|
A:7MR501
|
4.8
|
24.4
|
1.0
|
CAW
|
A:7MR501
|
4.9
|
19.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2ow1
Go back to
Zinc Binding Sites List in 2ow1
Zinc binding site 2 out
of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn445
b:16.8
occ:1.00
|
OD2
|
A:ASP177
|
1.9
|
16.5
|
1.0
|
NE2
|
A:HIS175
|
1.9
|
16.1
|
1.0
|
NE2
|
A:HIS190
|
2.0
|
16.9
|
1.0
|
ND1
|
A:HIS203
|
2.1
|
9.1
|
1.0
|
CD2
|
A:HIS175
|
2.8
|
16.6
|
1.0
|
CE1
|
A:HIS190
|
2.9
|
19.4
|
1.0
|
CG
|
A:ASP177
|
2.9
|
19.2
|
1.0
|
CE1
|
A:HIS175
|
3.0
|
19.0
|
1.0
|
CG
|
A:HIS203
|
3.1
|
11.4
|
1.0
|
CE1
|
A:HIS203
|
3.1
|
10.8
|
1.0
|
CD2
|
A:HIS190
|
3.1
|
19.4
|
1.0
|
OD1
|
A:ASP177
|
3.3
|
18.1
|
1.0
|
CB
|
A:HIS203
|
3.4
|
11.3
|
1.0
|
CG
|
A:HIS175
|
4.0
|
17.1
|
1.0
|
ND1
|
A:HIS190
|
4.0
|
18.3
|
1.0
|
ND1
|
A:HIS175
|
4.0
|
16.7
|
1.0
|
NE2
|
A:HIS203
|
4.2
|
9.7
|
1.0
|
CG
|
A:HIS190
|
4.2
|
16.7
|
1.0
|
CD2
|
A:HIS203
|
4.2
|
9.9
|
1.0
|
CB
|
A:ASP177
|
4.3
|
20.3
|
1.0
|
CE1
|
A:PHE192
|
4.3
|
21.9
|
1.0
|
O
|
A:TYR179
|
4.3
|
21.8
|
1.0
|
CZ
|
A:PHE192
|
4.6
|
22.0
|
1.0
|
CZ
|
A:PHE181
|
4.6
|
20.0
|
1.0
|
CE2
|
A:PHE181
|
4.8
|
19.8
|
1.0
|
CA
|
A:HIS203
|
4.9
|
11.6
|
1.0
|
O
|
A:HOH535
|
4.9
|
26.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2ow1
Go back to
Zinc Binding Sites List in 2ow1
Zinc binding site 3 out
of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn444
b:22.6
occ:1.00
|
NE2
|
B:HIS401
|
2.0
|
17.6
|
1.0
|
NE2
|
B:HIS411
|
2.0
|
29.6
|
1.0
|
OAA
|
B:7MR502
|
2.1
|
30.3
|
1.0
|
NE2
|
B:HIS405
|
2.2
|
22.6
|
1.0
|
OAB
|
B:7MR502
|
2.3
|
33.3
|
1.0
|
CD2
|
B:HIS401
|
2.9
|
17.3
|
1.0
|
NAD
|
B:7MR502
|
2.9
|
32.6
|
1.0
|
CAE
|
B:7MR502
|
2.9
|
33.7
|
1.0
|
CD2
|
B:HIS411
|
3.0
|
27.6
|
1.0
|
CE1
|
B:HIS411
|
3.0
|
28.8
|
1.0
|
CE1
|
B:HIS401
|
3.1
|
18.0
|
1.0
|
CD2
|
B:HIS405
|
3.1
|
20.1
|
1.0
|
CE1
|
B:HIS405
|
3.3
|
22.4
|
1.0
|
CG
|
B:HIS401
|
4.1
|
17.5
|
1.0
|
ND1
|
B:HIS411
|
4.1
|
29.7
|
1.0
|
CG
|
B:HIS411
|
4.1
|
28.8
|
1.0
|
ND1
|
B:HIS401
|
4.1
|
16.5
|
1.0
|
NE2
|
B:GLN402
|
4.2
|
23.9
|
1.0
|
O
|
B:HOH532
|
4.3
|
15.3
|
1.0
|
CG
|
B:HIS405
|
4.3
|
20.4
|
1.0
|
ND1
|
B:HIS405
|
4.4
|
21.2
|
1.0
|
CAO
|
B:7MR502
|
4.4
|
33.8
|
1.0
|
FAF
|
B:7MR502
|
4.6
|
36.1
|
1.0
|
FBA
|
B:7MR502
|
4.8
|
36.3
|
1.0
|
CAK
|
B:7MR502
|
4.8
|
26.7
|
1.0
|
CE
|
B:MET419
|
4.9
|
12.9
|
1.0
|
CAP
|
B:7MR502
|
4.9
|
36.1
|
1.0
|
CAJ
|
B:7MR502
|
4.9
|
25.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2ow1
Go back to
Zinc Binding Sites List in 2ow1
Zinc binding site 4 out
of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn445
b:17.6
occ:1.00
|
NE2
|
B:HIS190
|
2.0
|
14.2
|
1.0
|
OD2
|
B:ASP177
|
2.0
|
17.1
|
1.0
|
ND1
|
B:HIS203
|
2.1
|
11.7
|
1.0
|
CE1
|
B:HIS175
|
2.1
|
19.6
|
1.0
|
CE1
|
B:HIS190
|
2.8
|
15.9
|
1.0
|
ND1
|
B:HIS175
|
2.9
|
21.7
|
1.0
|
CG
|
B:ASP177
|
3.0
|
21.7
|
1.0
|
CE1
|
B:HIS203
|
3.0
|
14.3
|
1.0
|
CG
|
B:HIS203
|
3.1
|
13.3
|
1.0
|
NE2
|
B:HIS175
|
3.1
|
22.0
|
1.0
|
CD2
|
B:HIS190
|
3.2
|
16.1
|
1.0
|
OD1
|
B:ASP177
|
3.3
|
21.2
|
1.0
|
CB
|
B:HIS203
|
3.4
|
11.9
|
1.0
|
ND1
|
B:HIS190
|
4.0
|
15.2
|
1.0
|
O
|
B:TYR179
|
4.1
|
20.0
|
1.0
|
CG
|
B:HIS175
|
4.1
|
20.3
|
1.0
|
NE2
|
B:HIS203
|
4.1
|
15.5
|
1.0
|
CD2
|
B:HIS203
|
4.2
|
14.3
|
1.0
|
CG
|
B:HIS190
|
4.2
|
16.6
|
1.0
|
CB
|
B:ASP177
|
4.2
|
23.7
|
1.0
|
CD2
|
B:HIS175
|
4.2
|
17.6
|
1.0
|
CZ
|
B:PHE181
|
4.5
|
18.7
|
1.0
|
CE1
|
B:PHE192
|
4.6
|
24.6
|
1.0
|
CZ
|
B:PHE192
|
4.7
|
25.8
|
1.0
|
CE2
|
B:PHE181
|
4.8
|
16.1
|
1.0
|
CB
|
B:TYR179
|
4.8
|
23.8
|
1.0
|
CA
|
B:HIS203
|
4.9
|
14.4
|
1.0
|
O
|
B:HOH601
|
5.0
|
31.0
|
1.0
|
|
Reference:
A.Tochowicz,
K.Maskos,
R.Huber,
R.Oltenfreiter,
V.Dive,
A.Yiotakis,
M.Zanda,
W.Bode,
P.Goettig.
Crystal Structures of Mmp-9 Complexes with Five Inhibitors: Contribution of the Flexible ARG424 Side-Chain to Selectivity. J.Mol.Biol. V. 371 989 2007.
ISSN: ISSN 0022-2836
PubMed: 17599356
DOI: 10.1016/J.JMB.2007.05.068
Page generated: Thu Oct 17 02:48:54 2024
|