Atomistry » Iodine » PDB 1lkr-1pvh » 1opm
Atomistry »
  Iodine »
    PDB 1lkr-1pvh »
      1opm »

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 Dec 13 19:20:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy