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Iodine in PDB 5tmv: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate

Protein crystallography data

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate, PDB code: 5tmv was solved by J.C.Nwachukwu, R.Erumbi, S.Srinivasan, N.E.Bruno, J.Nowak, T.Izard, D.J.Kojetin, O.Elemento, J.A.Katzenellenbogen, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.23 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.390, 81.520, 58.360, 90.00, 110.61, 90.00
R / Rfree (%) 19.3 / 25.2

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate (pdb code 5tmv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate, PDB code: 5tmv:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 5tmv

Go back to Iodine Binding Sites List in 5tmv
Iodine binding site 1 out of 2 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I601

b:78.8
occ:0.84
I01 A:7FO601 0.0 78.8 0.8
C22 A:7FO601 2.1 50.7 0.8
C23 A:7FO601 2.9 51.8 0.8
C21 A:7FO601 3.0 46.3 0.8
O A:GLU419 3.3 64.7 1.0
C A:GLY420 3.6 75.0 1.0
ND1 A:HIS524 3.6 53.5 1.0
N A:MET421 3.8 71.3 1.0
CG A:HIS524 3.8 49.1 1.0
CB A:HIS524 3.8 45.0 1.0
CA A:GLY420 3.8 75.0 1.0
SD A:MET528 3.9 52.2 1.0
C A:GLU419 4.0 71.5 1.0
O A:GLY420 4.0 77.0 1.0
C24 A:7FO601 4.1 48.0 0.8
CG1 A:VAL418 4.2 69.3 1.0
N A:GLY420 4.2 77.4 1.0
C20 A:7FO601 4.2 46.5 0.8
CA A:MET421 4.3 63.2 1.0
CE1 A:HIS524 4.3 52.9 1.0
CD2 A:HIS524 4.5 50.4 1.0
O A:VAL418 4.6 67.8 1.0
CB A:MET421 4.6 63.6 1.0
CG A:MET528 4.7 53.4 1.0
C19 A:7FO601 4.7 46.8 0.8
C A:VAL418 4.8 69.3 1.0
NE2 A:HIS524 4.8 54.5 1.0
CB A:VAL418 4.9 70.2 1.0
CE A:MET528 4.9 54.1 1.0

Iodine binding site 2 out of 2 in 5tmv

Go back to Iodine Binding Sites List in 5tmv
Iodine binding site 2 out of 2 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Obhs Analog, 4-Iodophenyl (1S,2R,4S)-5,6-Bis(4- Hydroxyphenyl)-7-Oxabicyclo[2.2.1]Hept-5-Ene-2-Sulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I601

b:81.2
occ:0.80
I01 B:7FO601 0.0 81.2 0.8
C22 B:7FO601 2.1 48.8 0.8
C23 B:7FO601 3.0 45.8 0.8
C21 B:7FO601 3.0 46.1 0.8
O B:GLU419 3.2 0.8 1.0
CG1 B:VAL418 3.7 72.8 1.0
SD B:MET528 3.7 83.0 1.0
C B:GLY420 3.8 85.3 1.0
N B:MET421 3.9 83.2 1.0
CB B:HIS524 4.0 53.2 1.0
C B:GLU419 4.0 0.8 1.0
CA B:GLY420 4.1 91.7 1.0
O B:GLY420 4.1 83.2 1.0
CG B:HIS524 4.2 60.6 1.0
C24 B:7FO601 4.2 41.9 0.8
C20 B:7FO601 4.3 40.4 0.8
CA B:MET421 4.3 80.8 1.0
ND1 B:HIS524 4.4 65.4 1.0
CB B:MET421 4.5 82.5 1.0
N B:GLY420 4.5 99.1 1.0
CE B:MET528 4.6 81.9 1.0
CD2 B:HIS524 4.8 61.1 1.0
CG B:MET528 4.8 80.0 1.0
C19 B:7FO601 4.8 38.9 0.8
CB B:VAL418 4.8 77.0 1.0

Reference:

J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, J.Nowak, N.J.Wright, F.Minutolo, E.S.Rangarajan, T.Izard, X.Q.Yao, B.J.Grant, D.J.Kojetin, O.Elemento, J.A.Katzenellenbogen, K.W.Nettles. Systems Structural Biology Analysis of Ligand Effects on Er Alpha Predicts Cellular Response to Environmental Estrogens and Anti-Hormone Therapies. Cell Chem Biol V. 24 35 2017.
ISSN: ESSN 2451-9456
PubMed: 28042045
DOI: 10.1016/J.CHEMBIOL.2016.11.014
Page generated: Sun Aug 11 21:52:56 2024

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