Iron in PDB 1pxx: Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
Enzymatic activity of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
All present enzymatic activity of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2:
1.14.99.1;
Protein crystallography data
The structure of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2, PDB code: 1pxx
was solved by
J.R.Kiefer,
S.W.Rowlinson,
J.J.Prusakiewicz,
J.L.Pawlitz,
K.R.Kozak,
A.S.Kalgutkar,
W.C.Stallings,
L.J.Marnett,
R.G.Kurumbail,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.90
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.145,
135.090,
124.165,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.4 /
30.2
|
Other elements in 1pxx:
The structure of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
(pdb code 1pxx). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2, PDB code: 1pxx:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1pxx
Go back to
Iron Binding Sites List in 1pxx
Iron binding site 1 out
of 4 in the Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe704
b:18.8
occ:1.00
|
FE
|
A:HEM704
|
0.0
|
18.8
|
1.0
|
ND
|
A:HEM704
|
1.9
|
15.6
|
1.0
|
NA
|
A:HEM704
|
2.0
|
18.3
|
1.0
|
NC
|
A:HEM704
|
2.0
|
11.1
|
1.0
|
NB
|
A:HEM704
|
2.0
|
14.0
|
1.0
|
NE2
|
A:HIS388
|
2.2
|
17.7
|
1.0
|
C1D
|
A:HEM704
|
3.0
|
15.4
|
1.0
|
C4D
|
A:HEM704
|
3.0
|
16.7
|
1.0
|
C4C
|
A:HEM704
|
3.0
|
9.9
|
1.0
|
C1A
|
A:HEM704
|
3.0
|
22.0
|
1.0
|
C4A
|
A:HEM704
|
3.0
|
16.4
|
1.0
|
C1C
|
A:HEM704
|
3.0
|
9.1
|
1.0
|
C1B
|
A:HEM704
|
3.0
|
13.6
|
1.0
|
C4B
|
A:HEM704
|
3.0
|
12.4
|
1.0
|
CD2
|
A:HIS388
|
3.2
|
19.4
|
1.0
|
CE1
|
A:HIS388
|
3.2
|
17.9
|
1.0
|
CHD
|
A:HEM704
|
3.4
|
13.8
|
1.0
|
CHA
|
A:HEM704
|
3.4
|
17.9
|
1.0
|
CHB
|
A:HEM704
|
3.4
|
13.9
|
1.0
|
CHC
|
A:HEM704
|
3.4
|
9.9
|
1.0
|
C2D
|
A:HEM704
|
4.2
|
16.2
|
1.0
|
C3D
|
A:HEM704
|
4.2
|
17.6
|
1.0
|
C3A
|
A:HEM704
|
4.2
|
20.4
|
1.0
|
C2A
|
A:HEM704
|
4.2
|
24.6
|
1.0
|
C3C
|
A:HEM704
|
4.3
|
7.0
|
1.0
|
C2C
|
A:HEM704
|
4.3
|
8.1
|
1.0
|
CG
|
A:HIS388
|
4.3
|
20.2
|
1.0
|
C2B
|
A:HEM704
|
4.3
|
10.3
|
1.0
|
C3B
|
A:HEM704
|
4.3
|
11.4
|
1.0
|
ND1
|
A:HIS388
|
4.3
|
20.2
|
1.0
|
NE2
|
A:HIS207
|
4.5
|
28.1
|
1.0
|
OE1
|
A:GLN203
|
4.5
|
14.4
|
1.0
|
CE1
|
A:HIS207
|
4.7
|
27.2
|
1.0
|
CG1
|
A:VAL447
|
4.9
|
19.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 1pxx
Go back to
Iron Binding Sites List in 1pxx
Iron binding site 2 out
of 4 in the Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1601
b:22.9
occ:1.00
|
FE
|
B:HEM1601
|
0.0
|
22.9
|
1.0
|
NA
|
B:HEM1601
|
1.9
|
22.7
|
1.0
|
ND
|
B:HEM1601
|
2.0
|
23.5
|
1.0
|
NB
|
B:HEM1601
|
2.0
|
22.9
|
1.0
|
NC
|
B:HEM1601
|
2.0
|
18.0
|
1.0
|
NE2
|
B:HIS1388
|
2.2
|
18.3
|
1.0
|
C1A
|
B:HEM1601
|
3.0
|
27.3
|
1.0
|
C4D
|
B:HEM1601
|
3.0
|
23.7
|
1.0
|
C4A
|
B:HEM1601
|
3.0
|
25.6
|
1.0
|
C1B
|
B:HEM1601
|
3.0
|
22.1
|
1.0
|
C1D
|
B:HEM1601
|
3.0
|
23.4
|
1.0
|
C1C
|
B:HEM1601
|
3.0
|
17.8
|
1.0
|
C4B
|
B:HEM1601
|
3.0
|
18.8
|
1.0
|
C4C
|
B:HEM1601
|
3.0
|
15.9
|
1.0
|
CD2
|
B:HIS1388
|
3.2
|
17.6
|
1.0
|
CE1
|
B:HIS1388
|
3.2
|
17.3
|
1.0
|
O
|
B:HOH5098
|
3.3
|
30.0
|
1.0
|
CHA
|
B:HEM1601
|
3.4
|
27.2
|
1.0
|
CHB
|
B:HEM1601
|
3.4
|
23.3
|
1.0
|
CHC
|
B:HEM1601
|
3.4
|
16.0
|
1.0
|
CHD
|
B:HEM1601
|
3.4
|
18.2
|
1.0
|
C3D
|
B:HEM1601
|
4.2
|
22.1
|
1.0
|
C3A
|
B:HEM1601
|
4.2
|
27.7
|
1.0
|
C2A
|
B:HEM1601
|
4.2
|
31.5
|
1.0
|
C2D
|
B:HEM1601
|
4.3
|
22.2
|
1.0
|
C2B
|
B:HEM1601
|
4.3
|
19.8
|
1.0
|
C3B
|
B:HEM1601
|
4.3
|
19.5
|
1.0
|
C2C
|
B:HEM1601
|
4.3
|
15.2
|
1.0
|
C3C
|
B:HEM1601
|
4.3
|
14.1
|
1.0
|
CG
|
B:HIS1388
|
4.3
|
19.4
|
1.0
|
ND1
|
B:HIS1388
|
4.3
|
18.7
|
1.0
|
NE2
|
B:HIS1207
|
4.4
|
28.3
|
1.0
|
OE1
|
B:GLN1203
|
4.5
|
17.5
|
1.0
|
CE1
|
B:HIS1207
|
4.6
|
27.6
|
1.0
|
CG1
|
B:VAL1447
|
5.0
|
18.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 1pxx
Go back to
Iron Binding Sites List in 1pxx
Iron binding site 3 out
of 4 in the Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe2601
b:19.4
occ:1.00
|
FE
|
C:HEM2601
|
0.0
|
19.4
|
1.0
|
ND
|
C:HEM2601
|
2.0
|
20.4
|
1.0
|
NA
|
C:HEM2601
|
2.0
|
19.6
|
1.0
|
NC
|
C:HEM2601
|
2.0
|
16.0
|
1.0
|
NB
|
C:HEM2601
|
2.0
|
19.9
|
1.0
|
NE2
|
C:HIS2388
|
2.2
|
19.1
|
1.0
|
C4D
|
C:HEM2601
|
3.0
|
22.1
|
1.0
|
C1A
|
C:HEM2601
|
3.0
|
20.8
|
1.0
|
C1D
|
C:HEM2601
|
3.0
|
20.6
|
1.0
|
C4C
|
C:HEM2601
|
3.0
|
15.4
|
1.0
|
C4A
|
C:HEM2601
|
3.0
|
19.8
|
1.0
|
C1C
|
C:HEM2601
|
3.0
|
16.3
|
1.0
|
C4B
|
C:HEM2601
|
3.0
|
17.1
|
1.0
|
C1B
|
C:HEM2601
|
3.0
|
19.6
|
1.0
|
CE1
|
C:HIS2388
|
3.1
|
19.2
|
1.0
|
CD2
|
C:HIS2388
|
3.2
|
18.2
|
1.0
|
CHA
|
C:HEM2601
|
3.4
|
21.6
|
1.0
|
CHD
|
C:HEM2601
|
3.4
|
18.0
|
1.0
|
CHC
|
C:HEM2601
|
3.4
|
17.0
|
1.0
|
CHB
|
C:HEM2601
|
3.4
|
18.4
|
1.0
|
C3D
|
C:HEM2601
|
4.2
|
23.4
|
1.0
|
C2D
|
C:HEM2601
|
4.2
|
23.0
|
1.0
|
C2A
|
C:HEM2601
|
4.2
|
22.5
|
1.0
|
C3A
|
C:HEM2601
|
4.2
|
18.7
|
1.0
|
C3C
|
C:HEM2601
|
4.3
|
12.7
|
1.0
|
C2C
|
C:HEM2601
|
4.3
|
12.3
|
1.0
|
C2B
|
C:HEM2601
|
4.3
|
20.3
|
1.0
|
C3B
|
C:HEM2601
|
4.3
|
18.8
|
1.0
|
CG
|
C:HIS2388
|
4.3
|
19.0
|
1.0
|
ND1
|
C:HIS2388
|
4.3
|
19.8
|
1.0
|
NE2
|
C:HIS2207
|
4.4
|
28.9
|
1.0
|
OE1
|
C:GLN2203
|
4.5
|
15.9
|
1.0
|
CE1
|
C:HIS2207
|
4.7
|
27.2
|
1.0
|
CG1
|
C:VAL2447
|
4.9
|
18.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1pxx
Go back to
Iron Binding Sites List in 1pxx
Iron binding site 4 out
of 4 in the Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Diclofenac Bound to the Cyclooxygenase Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe3601
b:21.0
occ:1.00
|
FE
|
D:HEM3601
|
0.0
|
21.0
|
1.0
|
NA
|
D:HEM3601
|
1.9
|
21.5
|
1.0
|
ND
|
D:HEM3601
|
2.0
|
22.7
|
1.0
|
NC
|
D:HEM3601
|
2.0
|
16.4
|
1.0
|
NB
|
D:HEM3601
|
2.0
|
20.7
|
1.0
|
NE2
|
D:HIS3388
|
2.2
|
16.5
|
1.0
|
C1A
|
D:HEM3601
|
3.0
|
26.1
|
1.0
|
C4A
|
D:HEM3601
|
3.0
|
23.5
|
1.0
|
C4D
|
D:HEM3601
|
3.0
|
23.5
|
1.0
|
C1D
|
D:HEM3601
|
3.0
|
20.4
|
1.0
|
C1C
|
D:HEM3601
|
3.0
|
14.7
|
1.0
|
C1B
|
D:HEM3601
|
3.0
|
21.9
|
1.0
|
C4C
|
D:HEM3601
|
3.0
|
13.7
|
1.0
|
C4B
|
D:HEM3601
|
3.0
|
19.2
|
1.0
|
CD2
|
D:HIS3388
|
3.1
|
18.3
|
1.0
|
CE1
|
D:HIS3388
|
3.1
|
18.6
|
1.0
|
CHA
|
D:HEM3601
|
3.4
|
23.8
|
1.0
|
CHB
|
D:HEM3601
|
3.4
|
21.3
|
1.0
|
CHD
|
D:HEM3601
|
3.4
|
14.8
|
1.0
|
CHC
|
D:HEM3601
|
3.4
|
13.3
|
1.0
|
C2A
|
D:HEM3601
|
4.2
|
29.9
|
1.0
|
C3A
|
D:HEM3601
|
4.2
|
27.0
|
1.0
|
CG
|
D:HIS3388
|
4.2
|
19.7
|
1.0
|
C3D
|
D:HEM3601
|
4.2
|
21.2
|
1.0
|
C2C
|
D:HEM3601
|
4.2
|
13.3
|
1.0
|
C2D
|
D:HEM3601
|
4.3
|
19.6
|
1.0
|
C3C
|
D:HEM3601
|
4.3
|
13.1
|
1.0
|
C2B
|
D:HEM3601
|
4.3
|
17.7
|
1.0
|
ND1
|
D:HIS3388
|
4.3
|
18.9
|
1.0
|
C3B
|
D:HEM3601
|
4.3
|
19.5
|
1.0
|
NE2
|
D:HIS3207
|
4.5
|
27.2
|
1.0
|
OE1
|
D:GLN3203
|
4.6
|
16.8
|
1.0
|
CE1
|
D:HIS3207
|
4.7
|
27.3
|
1.0
|
CG1
|
D:VAL3447
|
4.9
|
19.5
|
1.0
|
|
Reference:
S.W.Rowlinson,
J.R.Kiefer,
J.J.Prusakiewicz,
J.L.Pawlitz,
K.R.Kozak,
A.S.Kalgutkar,
W.C.Stallings,
R.G.Kurumbail,
L.J.Marnett.
A Novel Mechanism of Cyclooxygenase-2 Inhibition Involving Interactions with Ser-530 and Tyr-385. J.Biol.Chem. V. 278 45763 2003.
ISSN: ISSN 0021-9258
PubMed: 12925531
DOI: 10.1074/JBC.M305481200
Page generated: Sat Aug 3 13:14:16 2024
|