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Iodine in PDB 1sdw: Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen

Enzymatic activity of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen

All present enzymatic activity of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen:
1.14.17.3;

Protein crystallography data

The structure of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen, PDB code: 1sdw was solved by S.T.Prigge, B.A.Eipper, R.E.Mains, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.69 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.478, 68.979, 82.108, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.6

Other elements in 1sdw:

The structure of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen 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 Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen (pdb code 1sdw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen, PDB code: 1sdw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 1sdw

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Iodine binding site 1 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I701

b:55.4
occ:0.29
 I1 A:IYT701 0.0 55.4 0.3
CE1 A:IYT701 2.1 52.3 0.6
CD1 A:IYT701 3.0 49.9 0.6
O3 A:GOL368 3.0 34.9 1.0
O A:ALA135 3.0 39.9 1.0
CZ A:IYT701 3.0 52.6 0.6
OH A:IYT701 3.2 48.7 0.6
C3 A:GOL368 3.4 45.2 1.0
CE1 A:IYT701 3.6 55.8 0.5
CE2 A:PHE112 3.8 36.6 1.0
CD1 A:IYT701 3.8 52.4 0.5
C A:ALA135 3.8 40.1 1.0
N A:ILE137 3.9 28.7 1.0
CD2 A:PHE112 4.0 32.1 1.0
CZ A:IYT701 4.0 55.9 0.5
I1 A:IYT701 4.1 60.1 0.3
CE2 A:TYR318 4.1 30.7 1.0
CB A:ILE137 4.2 31.7 1.0
OH A:TYR318 4.2 36.1 1.0
OGT A:IYT701 4.3 51.9 1.0
CG A:IYT701 4.3 48.4 0.6
CE2 A:IYT701 4.3 53.0 0.6
CG A:IYT701 4.4 49.8 0.5
N A:ASN136 4.5 33.8 1.0
CB A:ALA135 4.5 41.2 1.0
CE2 A:IYT701 4.5 55.6 0.5
OH A:IYT701 4.5 56.7 0.5
CA A:ASN136 4.5 32.5 1.0
C A:ASN136 4.5 32.5 1.0
CA A:ILE137 4.5 29.6 1.0
CG2 A:ILE137 4.6 36.3 1.0
CD2 A:IYT701 4.7 51.7 0.5
CZ A:TYR318 4.7 33.3 1.0
CA A:ALA135 4.7 39.8 1.0
C2 A:GOL368 4.8 49.9 1.0
CD2 A:IYT701 4.8 49.9 0.6
CZ A:PHE112 5.0 35.0 1.0

Iodine binding site 2 out of 8 in 1sdw

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Iodine binding site 2 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I701

b:60.1
occ:0.31
 I1 A:IYT701 0.0 60.1 0.3
CE1 A:IYT701 2.1 55.8 0.5
CD1 A:IYT701 3.1 52.4 0.5
CZ A:IYT701 3.1 55.9 0.5
OH A:IYT701 3.3 56.7 0.5
O A:HOH540 3.3 58.7 1.0
CE1 A:IYT701 3.7 52.3 0.6
CZ A:IYT701 3.8 52.6 0.6
OGT A:IYT701 3.9 51.9 1.0
OG1 A:THR130 4.0 53.0 1.0
OH A:IYT701 4.0 48.7 0.6
I1 A:IYT701 4.1 55.4 0.3
CB A:ALA135 4.1 41.2 1.0
CB A:THR130 4.1 51.7 1.0
CD1 A:IYT701 4.2 49.9 0.6
CBT A:IYT701 4.3 40.5 1.0
CE2 A:PHE112 4.3 36.6 1.0
CE2 A:IYT701 4.3 53.0 0.6
CG A:IYT701 4.4 49.8 0.5
O A:HOH531 4.4 57.5 1.0
CE2 A:IYT701 4.4 55.6 0.5
O A:IYT701 4.6 42.1 1.0
CZ A:PHE112 4.6 35.0 1.0
CG2 A:THR130 4.7 53.0 1.0
CD2 A:PHE112 4.8 32.1 1.0
CG A:IYT701 4.8 48.4 0.6
CD2 A:IYT701 4.8 49.9 0.6
CD2 A:IYT701 4.9 51.7 0.5
CGT A:IYT701 5.0 43.6 1.0

Iodine binding site 3 out of 8 in 1sdw

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Iodine binding site 3 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I701

b:59.0
occ:0.16
 I2 A:IYT701 0.0 59.0 0.2
I2 A:IYT701 1.3 59.0 0.2
CE2 A:IYT701 1.8 55.6 0.5
CE2 A:IYT701 2.1 53.0 0.6
CZ A:IYT701 2.5 55.9 0.5
OH A:IYT701 2.6 56.7 0.5
CD2 A:IYT701 2.8 51.7 0.5
CD2 A:IYT701 3.0 49.9 0.6
CZ A:IYT701 3.0 52.6 0.6
OH A:IYT701 3.2 48.7 0.6
CE1 A:IYT701 3.8 55.8 0.5
CG A:IYT701 4.0 49.8 0.5
CG A:LYS134 4.1 55.9 1.0
CD1 A:IYT701 4.3 52.4 0.5
CG A:IYT701 4.3 48.4 0.6
CE1 A:IYT701 4.3 52.3 0.6
CB A:LYS134 4.7 49.5 1.0
O A:HOH540 4.8 58.7 1.0
CD1 A:IYT701 4.8 49.9 0.6
O A:HOH479 4.9 49.8 1.0
CA A:LYS134 4.9 44.0 1.0

Iodine binding site 4 out of 8 in 1sdw

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Iodine binding site 4 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I701

b:59.0
occ:0.19
 I2 A:IYT701 0.0 59.0 0.2
I2 A:IYT701 1.3 59.0 0.2
CE2 A:IYT701 2.1 55.6 0.5
CE2 A:IYT701 2.3 53.0 0.6
CD2 A:IYT701 3.0 51.7 0.5
CZ A:IYT701 3.0 52.6 0.6
CZ A:IYT701 3.1 55.9 0.5
OH A:IYT701 3.1 48.7 0.6
OH A:IYT701 3.3 56.7 0.5
CD2 A:IYT701 3.3 49.9 0.6
CG A:LYS134 3.7 55.9 1.0
CB A:LYS134 4.2 49.5 1.0
CE1 A:IYT701 4.3 52.3 0.6
CG A:IYT701 4.3 49.8 0.5
CE1 A:IYT701 4.4 55.8 0.5
CG A:IYT701 4.5 48.4 0.6
CA A:LYS134 4.8 44.0 1.0
CD1 A:IYT701 4.9 52.4 0.5
CD1 A:IYT701 4.9 49.9 0.6
SD A:MET208 5.0 44.4 1.0

Iodine binding site 5 out of 8 in 1sdw

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Iodine binding site 5 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I702

b:47.9
occ:0.95
 I1 A:IYT702 0.0 47.9 0.9
CE1 A:IYT702 2.1 58.0 0.9
CD1 A:IYT702 3.0 60.4 0.9
CZ A:IYT702 3.1 58.4 0.9
OH A:IYT702 3.3 60.7 0.9
O A:SER190 3.5 36.7 1.0
OG A:SER190 3.6 36.7 0.4
CG A:LYS98 3.6 48.0 1.0
CD A:LYS98 3.7 55.0 1.0
N A:HIS192 3.7 27.3 1.0
C A:SER190 3.8 35.8 1.0
C A:VAL191 3.9 31.0 1.0
CE A:LYS98 3.9 59.5 1.0
CB A:HIS192 3.9 31.1 1.0
CB A:SER190 4.0 36.8 0.6
CB A:SER190 4.0 36.6 0.4
CB A:LYS98 4.1 40.8 1.0
N A:LYS98 4.1 33.2 1.0
CA A:VAL191 4.1 30.7 1.0
N A:VAL191 4.1 32.0 1.0
CA A:HIS192 4.2 26.3 1.0
O A:ASP96 4.4 27.2 1.0
CG A:IYT702 4.4 64.8 0.9
O A:VAL191 4.4 27.8 1.0
CE2 A:IYT702 4.4 59.6 0.9
C A:PHE97 4.4 34.9 1.0
C A:ASP96 4.5 28.9 1.0
CA A:PHE97 4.5 29.9 1.0
CA A:SER190 4.6 34.6 0.6
CA A:SER190 4.6 34.7 0.4
N A:PHE97 4.6 30.0 1.0
CB A:ASP96 4.7 32.2 1.0
CA A:LYS98 4.7 34.2 1.0
O A:HOH492 4.8 51.4 1.0
CB A:ALA63 4.8 32.3 1.0
CD2 A:IYT702 4.9 60.7 0.9
NZ A:LYS98 4.9 60.4 1.0
OD2 A:ASP96 4.9 40.0 1.0
CG A:ASP96 5.0 38.3 1.0
CG A:HIS192 5.0 32.8 1.0

Iodine binding site 6 out of 8 in 1sdw

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Iodine binding site 6 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I702

b:57.9
occ:0.16
 I2 A:IYT702 0.0 57.9 0.2
CE2 A:IYT702 2.1 59.6 0.9
CD2 A:IYT702 3.0 60.7 0.9
CZ A:IYT702 3.0 58.4 0.9
OH A:IYT702 3.2 60.7 0.9
CG A:IYT702 4.3 64.8 0.9
CB A:ALA63 4.3 32.3 1.0
CE1 A:IYT702 4.4 58.0 0.9
CG2 A:THR55 4.5 44.9 1.0
OG1 A:THR55 4.5 44.2 1.0
CB A:THR55 4.6 42.2 1.0
CD1 A:IYT702 4.8 60.4 0.9
NH2 A:ARG100 4.9 67.3 1.0
CD2 A:LEU57 5.0 55.3 1.0

Iodine binding site 7 out of 8 in 1sdw

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Iodine binding site 7 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I703

b:57.9
occ:0.40
 I1 A:IYT703 0.0 57.9 0.4
CE1 A:IYT703 2.1 61.2 0.6
CD1 A:IYT703 3.0 62.2 0.6
CZ A:IYT703 3.0 61.9 0.6
OH A:IYT703 3.2 64.4 0.6
CG A:ARG195 3.2 59.6 1.0
OE1 A:GLU90 3.4 68.0 1.0
CB A:ARG195 3.6 47.6 1.0
O A:GLU91 3.6 34.6 1.0
CG A:GLU90 3.7 57.6 1.0
CD A:GLU90 3.8 64.5 1.0
CA A:ARG195 3.9 40.0 1.0
CB A:ALA92 4.0 28.6 1.0
CD A:ARG195 4.2 68.0 1.0
CG2 A:VAL88 4.2 47.5 1.0
CG A:IYT703 4.3 63.9 0.6
CE2 A:IYT703 4.3 62.8 0.6
N A:ARG195 4.4 36.4 1.0
CG1 A:VAL88 4.4 49.8 1.0
CB A:VAL88 4.4 46.0 1.0
O A:HOH516 4.4 55.1 1.0
C A:GLU91 4.5 35.6 1.0
CA A:ALA92 4.5 30.1 1.0
O A:GLU90 4.6 40.0 1.0
NE A:ARG195 4.7 75.5 1.0
CD2 A:IYT703 4.8 63.4 0.6
C A:THR194 4.8 35.0 1.0
OE2 A:GLU90 4.8 66.0 1.0
O A:THR194 4.9 31.8 1.0
N A:ALA92 4.9 34.1 1.0
N A:IYT703 5.0 69.6 0.6
C A:GLU90 5.0 43.7 1.0

Iodine binding site 8 out of 8 in 1sdw

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Iodine binding site 8 out of 8 in the Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase with Bound Peptide and Dioxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I703

b:64.5
occ:0.13
 I2 A:IYT703 0.0 64.5 0.1
CE2 A:IYT703 2.0 62.8 0.6
CD2 A:IYT703 3.0 63.4 0.6
CZ A:IYT703 3.0 61.9 0.6
N A:ASP61 3.1 49.9 1.0
OH A:IYT703 3.2 64.4 0.6
C A:SER60 3.2 56.1 1.0
O A:ALA59 3.4 61.8 1.0
CA A:SER60 3.4 59.6 1.0
O A:ASP61 3.6 42.4 1.0
C A:ASP61 3.7 42.0 1.0
O A:SER60 3.7 56.9 1.0
O A:ASP58 3.8 65.0 1.0
CA A:ASP61 3.8 44.7 1.0
CD2 A:PHE62 3.8 37.7 1.0
C A:ALA59 3.9 62.8 1.0
N A:SER60 3.9 60.7 1.0
CG A:IYT703 4.3 63.9 0.6
CE1 A:IYT703 4.3 61.2 0.6
N A:PHE62 4.4 35.9 1.0
CB A:PHE62 4.5 34.1 1.0
CG A:PHE62 4.7 34.5 1.0
CE2 A:PHE62 4.7 38.9 1.0
CB A:SER60 4.8 61.4 1.0
CD1 A:IYT703 4.8 62.2 0.6
C A:ASP58 4.9 64.1 1.0

Reference:

S.T.Prigge, B.A.Eipper, R.E.Mains, L.M.Amzel. Dioxygen Binds End-on to Mononuclear Copper in A Precatalytic Enzyme Complex. Science V. 304 864 2004.
ISSN: ISSN 0036-8075
PubMed: 15131304
DOI: 10.1126/SCIENCE.1094583
Page generated: Sun Dec 13 19:21:15 2020

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