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Iodine in PDB 5ko8: Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)

Protein crystallography data

The structure of Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr), PDB code: 5ko8 was solved by N.Ingavat, J.M.Kavran, Z.Sun, S.E.Rokita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.18 / 2.15
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 152.718, 152.718, 87.286, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23.2

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) (pdb code 5ko8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr), PDB code: 5ko8:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 5ko8

Go back to Iodine Binding Sites List in 5ko8
Iodine binding site 1 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:52.1
occ:0.70
IE A:IYR302 0.0 52.1 0.7
HG A:IYR302 1.0 72.1 0.3
CG A:IYR302 2.0 60.1 0.3
CE A:IYR302 2.0 60.6 0.7
HF A:IYR302 2.3 55.4 0.3
HF A:IYR302 2.9 51.6 0.7
CF A:IYR302 2.9 55.6 0.3
CD A:IYR302 3.0 61.9 0.7
CH A:IYR302 3.0 62.1 0.3
OF A:IYR302 3.0 46.1 0.3
HD A:IYR302 3.0 74.2 0.7
CF A:IYR302 3.0 55.7 0.7
HH A:IYR302 3.1 74.5 0.3
OF A:IYR302 3.4 43.0 0.7
N5 A:FMN301 4.0 45.2 1.0
HE1 A:TRP103 4.1 0.9 1.0
HG23 A:THR173 4.2 71.9 0.9
C5A A:FMN301 4.2 42.2 1.0
CE A:IYR302 4.2 57.1 0.3
CC A:IYR302 4.2 60.9 0.3
HG21 A:THR173 4.3 71.9 0.9
CC A:IYR302 4.3 60.8 0.7
H6 A:FMN301 4.3 58.9 1.0
CG A:IYR302 4.3 57.1 0.7
C6 A:FMN301 4.4 49.0 1.0
HG1 A:THR173 4.4 70.2 0.1
HZ2 A:TRP103 4.5 0.6 1.0
C4A A:FMN301 4.5 45.1 1.0
HG22 A:THR173 4.5 71.9 0.9
CG2 A:THR173 4.6 59.9 0.9
HD21 A:LEU107 4.7 78.3 1.0
CD A:IYR302 4.7 58.6 0.3
OG1 A:THR173 4.7 58.5 0.1
CH A:IYR302 4.8 58.5 0.7
C9A A:FMN301 4.9 45.5 1.0
O4 A:FMN301 4.9 48.0 1.0
NE1 A:TRP103 4.9 85.8 1.0
C4 A:FMN301 4.9 52.5 1.0

Iodine binding site 2 out of 4 in 5ko8

Go back to Iodine Binding Sites List in 5ko8
Iodine binding site 2 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:80.1
occ:0.30
IE A:IYR302 0.0 80.1 0.3
HG A:IYR302 0.9 68.5 0.7
CG A:IYR302 1.9 57.1 0.7
CE A:IYR302 2.0 57.1 0.3
HH21 A:ARG38 2.8 50.6 1.0
CF A:IYR302 2.9 55.7 0.7
CH A:IYR302 2.9 58.5 0.7
CD A:IYR302 2.9 58.6 0.3
OF A:IYR302 3.0 43.0 0.7
HD A:IYR302 3.0 70.3 0.3
HH A:IYR302 3.0 70.2 0.7
CF A:IYR302 3.0 55.6 0.3
O2' A:FMN301 3.2 39.5 1.0
NH2 A:ARG38 3.3 42.2 1.0
HO2' A:FMN301 3.3 47.5 1.0
CD2 A:PHE110 3.3 53.3 1.0
OF A:IYR302 3.3 46.1 0.3
HD2 A:PHE110 3.3 64.0 1.0
HH22 A:ARG38 3.4 50.6 1.0
CG A:PHE110 3.4 60.0 1.0
HB3 A:PHE110 3.5 72.3 1.0
HB2 A:PHE110 3.5 72.3 1.0
N1 A:FMN301 3.6 39.0 1.0
O2 A:FMN301 3.6 42.4 1.0
C2 A:FMN301 3.6 49.4 1.0
HD22 A:LEU107 3.6 78.3 1.0
CB A:PHE110 3.7 60.2 1.0
HF A:IYR302 3.9 51.6 0.7
CE2 A:PHE110 3.9 59.3 1.0
HG21 A:THR112 4.0 76.2 1.0
CD1 A:PHE110 4.1 48.8 1.0
CZ A:ARG38 4.2 45.5 1.0
CE A:IYR302 4.2 60.6 0.7
CC A:IYR302 4.2 60.8 0.7
HE A:ARG38 4.2 60.6 1.0
HE2 A:PHE110 4.3 71.1 1.0
CC A:IYR302 4.3 60.9 0.3
HD23 A:LEU107 4.3 78.3 1.0
C10 A:FMN301 4.3 41.9 1.0
N3 A:FMN301 4.3 48.1 1.0
HF A:IYR302 4.3 55.4 0.3
CG A:IYR302 4.3 60.1 0.3
CD2 A:LEU107 4.4 65.2 1.0
CZ A:PHE110 4.5 49.1 1.0
NE A:ARG38 4.5 50.5 1.0
OG1 A:THR112 4.5 59.5 1.0
HD1 A:PHE110 4.5 58.6 1.0
HG23 A:THR112 4.5 76.2 1.0
CE1 A:PHE110 4.6 56.5 1.0
C2' A:FMN301 4.6 42.3 1.0
H1'1 A:FMN301 4.6 47.7 1.0
HD21 A:LEU107 4.7 78.3 1.0
CD A:IYR302 4.7 61.9 0.7
CG2 A:THR112 4.7 63.5 1.0
HN3 A:FMN301 4.7 57.7 1.0
O4' A:FMN301 4.8 40.1 1.0
CH A:IYR302 4.8 62.1 0.3
C4A A:FMN301 4.9 45.1 1.0
C4 A:FMN301 4.9 52.5 1.0
N10 A:FMN301 4.9 38.0 1.0
C1' A:FMN301 4.9 39.7 1.0
HA A:LEU107 5.0 79.4 1.0

Iodine binding site 3 out of 4 in 5ko8

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Iodine binding site 3 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:62.2
occ:0.67
IE B:IYR302 0.0 62.2 0.7
HG B:IYR302 1.1 71.6 0.3
CE B:IYR302 2.0 60.2 0.7
CG B:IYR302 2.1 59.7 0.3
HF B:IYR302 2.3 59.2 0.3
HF B:IYR302 2.8 56.2 0.7
CD B:IYR302 3.0 57.2 0.7
CF B:IYR302 3.0 51.6 0.3
CH B:IYR302 3.0 57.6 0.3
HD B:IYR302 3.0 68.6 0.7
OF B:IYR302 3.0 49.4 0.3
CF B:IYR302 3.0 51.3 0.7
HH B:IYR302 3.1 69.2 0.3
OF B:IYR302 3.4 46.8 0.7
N5 B:FMN301 3.9 41.3 1.0
HE1 B:TRP103 4.0 0.3 1.0
HG21 B:THR173 4.1 70.9 0.7
HZ2 B:TRP103 4.2 1.0 1.0
HG23 B:THR173 4.2 70.9 0.7
C5A B:FMN301 4.2 50.8 1.0
CE B:IYR302 4.3 57.5 0.3
CC B:IYR302 4.3 59.6 0.3
CC B:IYR302 4.3 59.5 0.7
HG1 B:THR173 4.3 69.8 0.3
CG B:IYR302 4.3 57.5 0.7
C4A B:FMN301 4.4 39.4 1.0
H6 B:FMN301 4.4 43.1 1.0
HG22 B:THR173 4.4 70.9 0.7
C6 B:FMN301 4.4 35.9 1.0
CG2 B:THR173 4.5 59.1 0.7
OG1 B:THR173 4.7 58.2 0.3
O4 B:FMN301 4.7 45.6 1.0
HD21 B:LEU107 4.7 85.8 1.0
C4 B:FMN301 4.8 47.5 1.0
CD B:IYR302 4.8 58.0 0.3
NE1 B:TRP103 4.8 96.1 1.0
CH B:IYR302 4.8 57.6 0.7
C9A B:FMN301 4.9 44.1 1.0
CZ2 B:TRP103 5.0 0.5 1.0
C10 B:FMN301 5.0 37.7 1.0

Iodine binding site 4 out of 4 in 5ko8

Go back to Iodine Binding Sites List in 5ko8
Iodine binding site 4 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:90.2
occ:0.33
IE B:IYR302 0.0 90.2 0.3
HG B:IYR302 1.0 69.0 0.7
CG B:IYR302 2.0 57.5 0.7
CE B:IYR302 2.0 57.5 0.3
HH22 B:ARG38 2.9 61.3 1.0
CF B:IYR302 2.9 51.3 0.7
CH B:IYR302 2.9 57.6 0.7
CD B:IYR302 2.9 58.0 0.3
OF B:IYR302 3.0 46.8 0.7
HD B:IYR302 3.0 69.7 0.3
CF B:IYR302 3.0 51.6 0.3
HH B:IYR302 3.1 69.1 0.7
HG21 B:THR112 3.2 84.6 1.0
HD2 B:PHE110 3.3 77.0 1.0
CD2 B:PHE110 3.3 64.2 1.0
O2' B:FMN301 3.3 42.2 1.0
OF B:IYR302 3.3 49.4 0.3
HO2' B:FMN301 3.3 50.7 1.0
HD22 B:LEU107 3.4 85.8 1.0
CG B:PHE110 3.4 67.2 1.0
HB2 B:PHE110 3.4 79.5 1.0
NH2 B:ARG38 3.5 51.1 1.0
HB3 B:PHE110 3.5 79.5 1.0
O2 B:FMN301 3.6 51.3 1.0
HH12 B:ARG38 3.6 67.8 1.0
C2 B:FMN301 3.6 51.5 1.0
N1 B:FMN301 3.6 39.6 1.0
CB B:PHE110 3.7 66.3 1.0
CE2 B:PHE110 3.9 68.9 1.0
HH21 B:ARG38 3.9 61.3 1.0
HF B:IYR302 3.9 56.2 0.7
HG23 B:THR112 4.0 84.6 1.0
CG2 B:THR112 4.0 70.5 1.0
NH1 B:ARG38 4.1 56.5 1.0
CZ B:ARG38 4.1 59.3 1.0
CD1 B:PHE110 4.1 59.1 1.0
HE2 B:PHE110 4.2 82.7 1.0
CE B:IYR302 4.2 60.2 0.7
CC B:IYR302 4.2 59.5 0.7
CD2 B:LEU107 4.2 71.5 1.0
CC B:IYR302 4.3 59.6 0.3
HF B:IYR302 4.3 59.2 0.3
HD23 B:LEU107 4.3 85.8 1.0
CG B:IYR302 4.3 59.7 0.3
N3 B:FMN301 4.4 49.0 1.0
C10 B:FMN301 4.4 37.7 1.0
CZ B:PHE110 4.5 59.5 1.0
HG22 B:THR112 4.6 84.6 1.0
HD1 B:PHE110 4.6 70.9 1.0
CE1 B:PHE110 4.6 53.1 1.0
C2' B:FMN301 4.6 39.4 1.0
HD21 B:LEU107 4.7 85.8 1.0
OG1 B:THR112 4.7 75.0 1.0
HB3 B:LEU107 4.7 91.7 1.0
H1'1 B:FMN301 4.7 46.1 1.0
CD B:IYR302 4.7 57.2 0.7
HA B:LEU107 4.8 92.6 1.0
O4' B:FMN301 4.8 43.8 1.0
HH11 B:ARG38 4.8 67.8 1.0
CH B:IYR302 4.8 57.6 0.3
HN3 B:FMN301 4.9 58.7 1.0
CB B:THR112 4.9 75.7 1.0

Reference:

N.Ingavat, J.M.Kavran, Z.Sun, S.E.Rokita. Active Site Binding Is Not Sufficient For Reductive Deiodination By Iodotyrosine Deiodinase. Biochemistry V. 56 1130 2017.
ISSN: ISSN 1520-4995
PubMed: 28157283
DOI: 10.1021/ACS.BIOCHEM.6B01308
Page generated: Sun Dec 13 19:39:53 2020

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