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Iodine in PDB 1pgf: Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model

Enzymatic activity of Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model

All present enzymatic activity of Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model:
1.14.99.1;

Protein crystallography data

The structure of Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model, PDB code: 1pgf was solved by P.J.Loll, D.Picot, R.M.Garavito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 4.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 99.220, 208.990, 232.430, 90.00, 90.00, 90.00
R / Rfree (%) 25.4 / 26.7

Other elements in 1pgf:

The structure of Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model (pdb code 1pgf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model, PDB code: 1pgf:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 1pgf

Go back to Iodine Binding Sites List in 1pgf
Iodine binding site 1 out of 2 in the Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I800

b:15.0
occ:1.00
 I1 A:IMM800 0.0 15.0 1.0
C14 A:IMM800 2.1 15.0 1.0
C15 A:IMM800 3.1 15.0 1.0
C13 A:IMM800 3.1 15.0 1.0
NE1 A:TRP387 3.4 7.1 1.0
CZ2 A:TRP387 3.4 4.4 1.0
CE2 A:TRP387 3.6 5.9 1.0
CG A:LEU384 3.7 2.0 1.0
O A:LEU384 3.7 14.5 1.0
CA A:TYR385 3.9 12.1 1.0
C A:LEU384 3.9 4.7 1.0
CD2 A:LEU384 3.9 2.0 1.0
CD1 A:TYR385 4.0 19.1 1.0
N A:TYR385 4.0 15.4 1.0
CE A:MET522 4.1 5.2 1.0
SD A:MET522 4.1 19.1 1.0
CG A:TYR385 4.1 18.5 1.0
CG A:MET522 4.2 10.6 1.0
CA A:GLY526 4.3 3.7 1.0
CE1 A:TYR385 4.3 12.7 1.0
C16 A:IMM800 4.4 15.0 1.0
C12 A:IMM800 4.4 15.0 1.0
O A:MET522 4.5 25.8 1.0
CD1 A:TRP387 4.5 11.1 1.0
CD2 A:TYR385 4.5 11.7 1.0
CB A:TYR385 4.5 15.9 1.0
CB A:LEU384 4.5 2.0 1.0
CH2 A:TRP387 4.5 14.6 1.0
O A:GLY526 4.5 17.6 1.0
CZ A:TYR385 4.6 17.0 1.0
CE1 A:PHE381 4.6 12.3 1.0
CD1 A:LEU384 4.7 2.0 1.0
CE2 A:TYR385 4.7 21.4 1.0
CE2 A:PHE518 4.8 12.0 1.0
CA A:LEU384 4.8 3.6 1.0
CD2 A:TRP387 4.8 11.8 1.0
C A:GLY526 4.9 7.4 1.0
C11 A:IMM800 4.9 15.0 1.0
C A:TYR385 4.9 18.4 1.0

Iodine binding site 2 out of 2 in 1pgf

Go back to Iodine Binding Sites List in 1pgf
Iodine binding site 2 out of 2 in the Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Prostaglandin H2 Synthase-1 Complexed with 1-(4-Iodobenzoyl)-5- Methoxy-2-Methylindole-3-Acetic Acid (Iodoindomethacin), Cis Model within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I800

b:15.0
occ:1.00
 I1 B:IMM800 0.0 15.0 1.0
C14 B:IMM800 2.1 15.0 1.0
C15 B:IMM800 3.1 15.0 1.0
C13 B:IMM800 3.1 15.0 1.0
NE1 B:TRP387 3.4 7.1 1.0
CZ2 B:TRP387 3.4 4.4 1.0
CE2 B:TRP387 3.6 5.9 1.0
CG B:LEU384 3.7 2.0 1.0
O B:LEU384 3.7 14.5 1.0
CA B:TYR385 3.9 12.1 1.0
C B:LEU384 3.9 4.7 1.0
CD2 B:LEU384 3.9 2.0 1.0
CD1 B:TYR385 4.0 19.1 1.0
N B:TYR385 4.0 15.4 1.0
CE B:MET522 4.1 5.2 1.0
SD B:MET522 4.1 19.1 1.0
CG B:TYR385 4.1 18.5 1.0
CG B:MET522 4.2 10.6 1.0
CA B:GLY526 4.3 3.7 1.0
CE1 B:TYR385 4.3 12.7 1.0
C16 B:IMM800 4.4 15.0 1.0
C12 B:IMM800 4.4 15.0 1.0
O B:MET522 4.5 25.8 1.0
CD1 B:TRP387 4.5 11.1 1.0
CD2 B:TYR385 4.5 11.7 1.0
CB B:TYR385 4.5 15.9 1.0
CB B:LEU384 4.5 2.0 1.0
CH2 B:TRP387 4.5 14.6 1.0
O B:GLY526 4.5 17.6 1.0
CZ B:TYR385 4.6 17.0 1.0
CE1 B:PHE381 4.6 12.3 1.0
CD1 B:LEU384 4.7 2.0 1.0
CE2 B:TYR385 4.7 21.4 1.0
CE2 B:PHE518 4.8 12.0 1.0
CA B:LEU384 4.8 3.6 1.0
CD2 B:TRP387 4.8 11.8 1.0
C B:GLY526 4.9 7.4 1.0
C11 B:IMM800 4.9 15.0 1.0
C B:TYR385 4.9 18.4 1.0

Reference:

P.J.Loll, D.Picot, O.Ekabo, R.M.Garavito. Synthesis and Use of Iodinated Nonsteroidal Antiinflammatory Drug Analogs As Crystallographic Probes of the Prostaglandin H2 Synthase Cyclooxygenase Active Site. Biochemistry V. 35 7330 1996.
ISSN: ISSN 0006-2960
PubMed: 8652509
DOI: 10.1021/BI952776W
Page generated: Sun Aug 11 12:36:19 2024

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