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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:

Chlorine (Cl) 8 atoms

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

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