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Iodine in PDB 4lnw: Crystal Structure of Tr-Alpha Bound to T3 in A Second Site

Protein crystallography data

The structure of Crystal Structure of Tr-Alpha Bound to T3 in A Second Site, PDB code: 4lnw was solved by A.C.Puhl, R.Aparicio, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.59 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.781, 80.789, 102.562, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.4

Other elements in 4lnw:

The structure of Crystal Structure of Tr-Alpha Bound to T3 in A Second Site also contains other interesting chemical elements:

Arsenic (As) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site (pdb code 4lnw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site, PDB code: 4lnw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 4lnw

Go back to Iodine Binding Sites List in 4lnw
Iodine binding site 1 out of 6 in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site


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 Tr-Alpha Bound to T3 in A Second Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:24.7
occ:1.00
 I1 A:T3501 0.0 24.7 1.0
C5 A:T3501 2.1 19.2 1.0
C3 A:T3501 3.0 20.4 1.0
O A:PHE218 3.1 24.1 1.0
C7 A:T3501 3.1 18.5 1.0
O2 A:T3501 3.2 21.9 1.0
C2 A:T3501 3.6 20.2 1.0
C A:PHE218 3.9 27.2 1.0
CG1 A:ILE221 3.9 30.1 1.0
C4 A:T3501 3.9 17.4 1.0
CB A:ILE222 3.9 26.7 1.0
CG1 A:ILE222 4.0 23.6 1.0
CB A:PHE218 4.1 20.8 1.0
CA A:PHE218 4.2 24.9 1.0
CD1 A:ILE222 4.2 22.6 1.0
CA A:ILE222 4.2 23.3 1.0
CD1 A:LEU276 4.2 22.2 1.0
CD1 A:ILE221 4.2 32.6 1.0
N A:ILE222 4.3 23.8 1.0
C1 A:T3501 4.3 19.0 1.0
C9 A:T3501 4.4 18.7 1.0
C12 A:T3501 4.5 20.1 1.0
C A:ILE221 4.7 25.3 1.0
CG A:PHE218 4.8 21.2 1.0
C11 A:T3501 4.9 19.5 1.0
C6 A:T3501 4.9 16.6 1.0
CD1 A:PHE218 4.9 24.7 1.0
N A:THR219 4.9 22.3 1.0
CB A:LEU276 5.0 25.8 1.0

Iodine binding site 2 out of 6 in 4lnw

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Iodine binding site 2 out of 6 in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site


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 Tr-Alpha Bound to T3 in A Second Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:26.9
occ:1.00
 I2 A:T3501 0.0 26.9 1.0
C6 A:T3501 2.1 16.6 1.0
C8 A:T3501 3.0 21.3 1.0
C4 A:T3501 3.1 17.4 1.0
O1 A:T3501 3.1 21.6 1.0
O A:GLY290 3.6 24.8 1.0
CD1 A:PHE215 3.9 25.6 1.0
CE1 A:PHE215 4.0 25.7 1.0
CA A:GLY291 4.2 21.6 1.0
C10 A:T3501 4.4 21.5 1.0
C2 A:T3501 4.4 20.2 1.0
CB A:PHE218 4.4 20.8 1.0
CE A:MET388 4.4 23.4 0.6
C A:GLY290 4.5 24.5 1.0
CD2 A:LEU292 4.5 24.8 1.0
C A:GLY291 4.5 24.9 1.0
N A:LEU292 4.6 21.6 1.0
CG A:LEU292 4.6 25.8 1.0
CD2 A:PHE218 4.6 25.0 1.0
N A:GLY291 4.7 23.2 1.0
CE A:MET388 4.8 23.6 0.4
CZ A:PHE401 4.8 24.8 1.0
SD A:MET388 4.8 32.9 0.4
C12 A:T3501 4.9 20.1 1.0
CG A:PHE218 5.0 21.2 1.0
CG2 A:THR219 5.0 29.1 1.0
CG A:PHE215 5.0 25.7 1.0

Iodine binding site 3 out of 6 in 4lnw

Go back to Iodine Binding Sites List in 4lnw
Iodine binding site 3 out of 6 in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site


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 Tr-Alpha Bound to T3 in A Second Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:27.3
occ:1.00
 I3 A:T3501 0.0 27.3 1.0
C9 A:T3501 2.1 18.7 1.0
C11 A:T3501 3.1 19.5 1.0
C7 A:T3501 3.1 18.5 1.0
O2 A:T3501 3.3 21.9 1.0
CD1 A:ILE299 3.6 21.3 1.0
C12 A:T3501 3.8 20.1 1.0
C2 A:T3501 3.8 20.2 1.0
CE A:MET256 4.2 23.9 1.0
CD1 A:LEU292 4.2 22.2 1.0
OG A:SER260 4.2 24.5 1.0
CB A:ALA263 4.2 18.7 1.0
CA A:SER260 4.3 19.5 1.0
CD2 A:LEU276 4.4 19.5 1.0
C1 A:T3501 4.4 19.0 1.0
C5 A:T3501 4.4 19.2 1.0
O A:MET259 4.5 16.5 1.0
N A:SER260 4.6 15.5 1.0
C A:MET259 4.7 14.2 1.0
CB A:SER260 4.8 21.4 1.0
SD A:MET256 4.9 23.1 1.0
CD2 A:LEU287 4.9 24.9 1.0
C3 A:T3501 5.0 20.4 1.0
C10 A:T3501 5.0 21.5 1.0

Iodine binding site 4 out of 6 in 4lnw

Go back to Iodine Binding Sites List in 4lnw
Iodine binding site 4 out of 6 in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site


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 Tr-Alpha Bound to T3 in A Second Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:31.1
occ:0.85
 I1 A:T3502 0.0 31.1 0.8
C5 A:T3502 2.1 25.1 0.8
C3 A:T3502 3.0 24.6 0.8
C7 A:T3502 3.1 21.3 0.8
O A:LEU368 3.2 24.6 1.0
O2 A:T3502 3.3 24.5 0.8
CB A:VAL371 3.7 27.4 1.0
CG1 A:VAL371 3.7 30.2 1.0
OG1 A:THR372 3.7 26.8 0.5
C2 A:T3502 3.8 25.4 0.8
CG2 A:THR372 3.9 28.7 0.5
C A:LEU368 4.0 27.5 1.0
C12 A:T3502 4.1 28.0 0.8
CB A:LEU368 4.1 24.2 1.0
CA A:LEU368 4.2 26.8 1.0
O A:HOH917 4.2 31.6 1.0
CD2 A:LEU368 4.3 27.7 1.0
N A:THR372 4.3 28.8 1.0
C1 A:T3502 4.4 24.8 0.8
C9 A:T3502 4.5 21.6 0.8
CG2 A:VAL371 4.5 28.4 1.0
C4 A:T3502 4.6 27.9 0.8
NH1 A:ARG375 4.6 37.6 1.0
C A:VAL371 4.7 30.9 1.0
CA A:VAL371 4.7 28.7 1.0
CG A:LEU368 4.8 27.5 1.0
O4 A:T3502 4.9 27.3 0.8
CB A:THR372 4.9 29.4 0.5
C11 A:T3502 4.9 26.1 0.8
CA A:THR372 5.0 25.8 0.5

Iodine binding site 5 out of 6 in 4lnw

Go back to Iodine Binding Sites List in 4lnw
Iodine binding site 5 out of 6 in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Tr-Alpha Bound to T3 in A Second Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:40.3
occ:0.85
 I2 A:T3502 0.0 40.3 0.8
C6 A:T3502 2.1 29.4 0.8
C4 A:T3502 3.0 27.9 0.8
C8 A:T3502 3.1 32.5 0.8
O1 A:T3502 3.3 33.8 0.8
SD A:MET369 3.8 40.5 0.6
CE A:MET369 4.2 37.7 0.6
C2 A:T3502 4.4 25.4 0.8
C10 A:T3502 4.4 32.1 0.8
CG2 A:THR372 4.7 28.7 0.5
OG1 A:THR372 4.8 26.8 0.5
C12 A:T3502 4.9 28.0 0.8

Iodine binding site 6 out of 6 in 4lnw

Go back to Iodine Binding Sites List in 4lnw
Iodine binding site 6 out of 6 in the Crystal Structure of Tr-Alpha Bound to T3 in A Second Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Tr-Alpha Bound to T3 in A Second Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:28.8
occ:0.85
 I3 A:T3502 0.0 28.8 0.8
C9 A:T3502 2.1 21.6 0.8
C11 A:T3502 3.0 26.1 0.8
C7 A:T3502 3.1 21.3 0.8
O2 A:T3502 3.3 24.5 0.8
C2 A:T3502 3.8 25.4 0.8
C12 A:T3502 4.1 28.0 0.8
O A:HOH896 4.2 52.2 1.0
C1 A:T3502 4.4 24.8 0.8
C5 A:T3502 4.5 25.1 0.8
C4 A:T3502 4.7 27.9 0.8
C3 A:T3502 4.9 24.6 0.8

Reference:

P.C.Souza, A.C.Puhl, L.Martinez, R.Aparicio, A.S.Nascimento, A.C.Figueira, P.Nguyen, P.Webb, M.S.Skaf, I.Polikarpov. Identification of A New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor. Mol.Endocrinol. V. 28 534 2014.
ISSN: ISSN 0888-8809
PubMed: 24552590
DOI: 10.1210/ME.2013-1359
Page generated: Sun Aug 11 18:34:30 2024

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