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Iodine in PDB 1opm: Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate

Enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate

All present enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate:
1.14.17.3;

Protein crystallography data

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate, PDB code: 1opm was solved by S.T.Prigge, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.399, 68.840, 81.047, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.9

Other elements in 1opm:

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Copper (Cu) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate (pdb code 1opm). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate, PDB code: 1opm:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 1opm

Go back to Iodine Binding Sites List in 1opm
Iodine binding site 1 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I801

b:46.6
occ:0.39
 I1 A:IYG801 0.0 46.6 0.4
CE1 A:IYG801 2.1 52.2 1.0
O A:ALA135 2.9 41.8 1.0
CD1 A:IYG801 3.0 47.3 1.0
CZ A:IYG801 3.0 50.3 1.0
OH A:IYG801 3.2 42.4 1.0
C A:ALA135 3.6 36.1 1.0
O A:HOH378 3.7 23.4 1.0
CE2 A:PHE112 3.7 30.3 1.0
CD2 A:PHE112 3.8 28.1 1.0
N A:ILE137 3.9 30.4 1.0
CB A:ALA135 4.2 33.2 1.0
CB A:ILE137 4.2 31.6 1.0
OH A:TYR318 4.3 29.0 1.0
CE2 A:TYR318 4.3 30.1 1.0
CG A:IYG801 4.3 48.5 1.0
N A:ASN136 4.3 34.0 1.0
CE2 A:IYG801 4.3 52.0 1.0
C A:ASN136 4.4 31.4 1.0
CA A:ALA135 4.4 34.8 1.0
CA A:ASN136 4.4 32.4 1.0
CA A:ILE137 4.6 29.1 1.0
CG2 A:ILE137 4.8 29.5 1.0
CZ A:TYR318 4.8 27.8 1.0
CD2 A:IYG801 4.9 49.1 1.0
N A:ALA135 4.9 35.6 1.0
CZ A:PHE112 5.0 32.1 1.0

Iodine binding site 2 out of 4 in 1opm

Go back to Iodine Binding Sites List in 1opm
Iodine binding site 2 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I801

b:49.0
occ:0.34
 I2 A:IYG801 0.0 49.0 0.3
CE2 A:IYG801 2.1 52.0 1.0
CZ A:IYG801 3.0 50.3 1.0
CD2 A:IYG801 3.0 49.1 1.0
OH A:IYG801 3.1 42.4 1.0
CG A:LYS134 3.4 59.5 1.0
CB A:LYS134 4.3 51.6 1.0
CE1 A:IYG801 4.3 52.2 1.0
CG A:IYG801 4.3 48.5 1.0
CE A:LYS134 4.5 69.7 1.0
CD A:LYS134 4.5 66.7 1.0
SD A:MET208 4.7 44.5 1.0
CD2 A:LEU206 4.8 24.4 1.0
CD1 A:IYG801 4.8 47.3 1.0
CA A:LYS134 5.0 45.5 1.0

Iodine binding site 3 out of 4 in 1opm

Go back to Iodine Binding Sites List in 1opm
Iodine binding site 3 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I802

b:57.3
occ:0.31
 I1 A:IYG802 0.0 57.3 0.3
CE1 A:IYG802 2.1 55.7 1.0
CD1 A:IYG802 3.0 61.2 1.0
CZ A:IYG802 3.1 52.9 1.0
OH A:IYG802 3.2 49.6 1.0
CB A:ALA63 4.3 23.2 1.0
CG2 A:THR55 4.3 36.3 1.0
CG A:IYG802 4.3 66.2 1.0
CE2 A:IYG802 4.4 53.2 1.0
CD2 A:LEU57 4.5 43.4 1.0
CB A:THR55 4.6 35.0 1.0
OG1 A:THR55 4.6 38.6 1.0
CD2 A:IYG802 4.9 57.5 1.0

Iodine binding site 4 out of 4 in 1opm

Go back to Iodine Binding Sites List in 1opm
Iodine binding site 4 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I802

b:44.7
occ:1.00
 I2 A:IYG802 0.0 44.7 1.0
CE2 A:IYG802 2.1 53.2 1.0
CD2 A:IYG802 3.0 57.5 1.0
CZ A:IYG802 3.1 52.9 1.0
OH A:IYG802 3.3 49.6 1.0
O A:SER190 3.4 33.5 1.0
CG A:LYS98 3.6 41.9 1.0
N A:HIS192 3.8 25.9 1.0
C A:SER190 3.8 35.2 1.0
C A:VAL191 3.9 29.1 1.0
CB A:HIS192 3.9 24.5 1.0
OG A:SER190 4.0 44.9 1.0
CB A:SER190 4.0 36.4 1.0
CB A:LYS98 4.1 37.4 1.0
N A:VAL191 4.1 32.5 1.0
N A:LYS98 4.1 28.8 1.0
CA A:VAL191 4.2 30.5 1.0
CA A:HIS192 4.2 25.7 1.0
CG A:IYG802 4.3 66.2 1.0
O A:HOH448 4.4 40.4 1.0
O A:VAL191 4.4 28.6 1.0
CE1 A:IYG802 4.4 55.7 1.0
C A:PHE97 4.5 25.4 1.0
O A:ASP96 4.5 24.4 1.0
CA A:SER190 4.6 30.7 1.0
CA A:PHE97 4.6 24.9 1.0
C A:ASP96 4.6 24.7 1.0
N A:PHE97 4.7 25.6 1.0
CB A:ASP96 4.7 26.2 1.0
OD2 A:ASP96 4.8 33.1 1.0
CB A:ALA63 4.8 23.2 1.0
CA A:LYS98 4.8 29.8 1.0
CG A:ASP96 4.8 34.3 1.0
CD1 A:IYG802 4.9 61.2 1.0
CD A:LYS98 4.9 54.0 1.0
CG A:HIS192 4.9 29.8 1.0

Reference:

S.T.Prigge, A.S.Kolhekar, B.A.Eipper, R.E.Mains, L.M.Amzel. Substrate-Mediated Electron Transfer in Peptidylglycine Alpha-Hydroxylating Monooxygenase. Nat.Struct.Biol. V. 6 976 1999.
ISSN: ISSN 1072-8368
PubMed: 10504734
DOI: 10.1038/13351
Page generated: Sun Aug 11 12:33:25 2024

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