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Fluorine in PDB 5krf: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A

Protein crystallography data

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A, PDB code: 5krf was solved by J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, J.Nowak, 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) 45.83 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.361, 80.875, 58.113, 90.00, 109.53, 90.00
R / Rfree (%) 22.6 / 26.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A (pdb code 5krf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A, PDB code: 5krf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5krf

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Fluorine binding site 1 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:41.6
occ:1.00
F01 A:6WL601 0.0 41.6 1.0
C02 A:6WL601 1.3 41.1 1.0
F04 A:6WL601 2.0 41.5 1.0
F03 A:6WL601 2.1 40.5 1.0
C05 A:6WL601 2.3 40.6 1.0
C06 A:6WL601 2.7 40.4 1.0
O A:GLY521 3.4 38.3 1.0
CD2 A:HIS524 3.5 50.9 1.0
C10 A:6WL601 3.6 39.9 1.0
N A:LEU525 3.6 44.9 1.0
CA A:LEU525 3.7 45.4 1.0
CE A:MET343 3.8 39.9 1.0
CE A:MET528 3.8 49.5 1.0
CB A:LEU525 3.8 44.4 1.0
C07 A:6WL601 4.1 40.2 1.0
C12 A:6WL601 4.1 40.8 1.0
C A:HIS524 4.1 46.9 1.0
CG A:HIS524 4.2 49.9 1.0
CB A:HIS524 4.2 47.1 1.0
N11 A:6WL601 4.3 39.5 1.0
C A:GLY521 4.5 38.4 1.0
CD1 A:LEU525 4.6 46.6 1.0
NE2 A:HIS524 4.6 53.8 1.0
O A:HIS524 4.6 48.5 1.0
C09 A:6WL601 4.7 39.3 1.0
SD A:MET528 4.7 74.3 1.0
CA A:HIS524 4.8 46.9 1.0
CG A:LEU525 4.8 45.9 1.0
CA A:GLY521 4.8 37.5 1.0
C08 A:6WL601 4.9 39.4 1.0

Fluorine binding site 2 out of 6 in 5krf

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Fluorine binding site 2 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:40.5
occ:1.00
F03 A:6WL601 0.0 40.5 1.0
C02 A:6WL601 1.3 41.1 1.0
F01 A:6WL601 2.1 41.6 1.0
F04 A:6WL601 2.1 41.5 1.0
C05 A:6WL601 2.4 40.6 1.0
C12 A:6WL601 2.7 40.8 1.0
C10 A:6WL601 3.0 39.9 1.0
CE A:MET343 3.1 39.9 1.0
N11 A:6WL601 3.2 39.5 1.0
CD2 A:HIS524 3.3 50.9 1.0
SD A:MET421 3.4 66.0 1.0
C06 A:6WL601 3.4 40.4 1.0
CE A:MET421 3.9 50.9 1.0
CG A:HIS524 4.2 49.9 1.0
NE2 A:HIS524 4.2 53.8 1.0
SD A:MET343 4.3 53.2 1.0
C09 A:6WL601 4.3 39.3 1.0
N13 A:6WL601 4.4 39.6 1.0
CB A:HIS524 4.5 47.1 1.0
O A:GLY521 4.5 38.3 1.0
C07 A:6WL601 4.6 40.2 1.0
CD1 A:LEU346 4.8 40.9 1.0
CD1 A:ILE424 4.8 54.1 1.0
CG A:MET421 4.9 61.0 1.0
CE A:MET528 5.0 49.5 1.0

Fluorine binding site 3 out of 6 in 5krf

Go back to Fluorine Binding Sites List in 5krf
Fluorine binding site 3 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:41.5
occ:1.00
F04 A:6WL601 0.0 41.5 1.0
C02 A:6WL601 1.3 41.1 1.0
F01 A:6WL601 2.0 41.6 1.0
F03 A:6WL601 2.1 40.5 1.0
C05 A:6WL601 2.3 40.6 1.0
C12 A:6WL601 2.7 40.8 1.0
C10 A:6WL601 2.9 39.9 1.0
O A:GLY521 3.0 38.3 1.0
N11 A:6WL601 3.1 39.5 1.0
C06 A:6WL601 3.3 40.4 1.0
CA A:GLY521 3.4 37.5 1.0
C A:GLY521 3.5 38.4 1.0
C09 A:6WL601 4.2 39.3 1.0
N13 A:6WL601 4.3 39.6 1.0
CD2 A:HIS524 4.4 50.9 1.0
C07 A:6WL601 4.5 40.2 1.0
CB A:HIS524 4.5 47.1 1.0
CD2 A:LEU384 4.6 31.1 1.0
N A:LEU525 4.7 44.9 1.0
CD1 A:ILE424 4.7 54.1 1.0
N A:MET522 4.7 39.4 1.0
N A:GLY521 4.8 37.7 1.0
CE A:MET388 4.8 30.8 1.0
C08 A:6WL601 4.8 39.4 1.0
CB A:LEU525 4.9 44.4 1.0
CG A:HIS524 4.9 49.9 1.0
C14 A:6WL601 4.9 38.6 1.0
SD A:MET421 4.9 66.0 1.0
CE A:MET343 5.0 39.9 1.0

Fluorine binding site 4 out of 6 in 5krf

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Fluorine binding site 4 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:37.9
occ:0.88
F01 B:6WL601 0.0 37.9 0.9
C02 B:6WL601 1.3 38.7 0.9
F03 B:6WL601 2.0 38.4 0.9
F04 B:6WL601 2.1 39.3 0.9
C05 B:6WL601 2.3 39.5 0.9
C10 B:6WL601 3.0 39.1 0.9
C12 B:6WL601 3.0 38.9 0.9
O B:GLY521 3.2 44.4 1.0
CA B:GLY521 3.3 42.9 1.0
N11 B:6WL601 3.3 38.9 0.9
C06 B:6WL601 3.3 40.4 0.9
C B:GLY521 3.5 42.1 1.0
C09 B:6WL601 4.3 39.7 0.9
CD2 B:LEU384 4.5 32.4 1.0
CD1 B:ILE424 4.5 47.7 1.0
N13 B:6WL601 4.5 38.8 0.9
C07 B:6WL601 4.6 40.2 0.9
CE B:MET388 4.6 39.1 1.0
CB B:HIS524 4.6 55.1 1.0
N B:GLY521 4.7 43.2 1.0
N B:MET522 4.7 39.5 1.0
CD2 B:HIS524 4.8 57.7 1.0
C08 B:6WL601 5.0 40.2 0.9
N B:LEU525 5.0 49.9 1.0
CD1 B:LEU384 5.0 32.7 1.0

Fluorine binding site 5 out of 6 in 5krf

Go back to Fluorine Binding Sites List in 5krf
Fluorine binding site 5 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:38.4
occ:0.88
F03 B:6WL601 0.0 38.4 0.9
C02 B:6WL601 1.3 38.7 0.9
F01 B:6WL601 2.0 37.9 0.9
F04 B:6WL601 2.1 39.3 0.9
C05 B:6WL601 2.4 39.5 0.9
C06 B:6WL601 2.7 40.4 0.9
O B:GLY521 3.3 44.4 1.0
C10 B:6WL601 3.7 39.1 0.9
CD2 B:HIS524 3.7 57.7 1.0
N B:LEU525 3.7 49.9 1.0
CB B:LEU525 3.9 44.6 1.0
CA B:LEU525 3.9 48.4 1.0
CE B:MET528 4.0 57.6 1.0
C07 B:6WL601 4.1 40.2 0.9
C B:GLY521 4.2 42.1 1.0
CB B:HIS524 4.2 55.1 1.0
C B:HIS524 4.3 52.4 1.0
CG B:HIS524 4.3 57.6 1.0
N11 B:6WL601 4.5 38.9 0.9
CD1 B:LEU525 4.5 45.0 1.0
C12 B:6WL601 4.5 38.9 0.9
CA B:GLY521 4.5 42.9 1.0
C09 B:6WL601 4.8 39.7 0.9
CG B:LEU525 4.8 43.5 1.0
CA B:HIS524 4.8 53.7 1.0
O B:HIS524 4.9 52.7 1.0
NE2 B:HIS524 4.9 59.2 1.0
C08 B:6WL601 4.9 40.2 0.9

Fluorine binding site 6 out of 6 in 5krf

Go back to Fluorine Binding Sites List in 5krf
Fluorine binding site 6 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Dynamic Way Derivative, 1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:39.3
occ:0.88
F04 B:6WL601 0.0 39.3 0.9
C02 B:6WL601 1.3 38.7 0.9
F01 B:6WL601 2.1 37.9 0.9
F03 B:6WL601 2.1 38.4 0.9
C05 B:6WL601 2.4 39.5 0.9
C12 B:6WL601 3.1 38.9 0.9
C10 B:6WL601 3.1 39.1 0.9
N11 B:6WL601 3.4 38.9 0.9
C06 B:6WL601 3.4 40.4 0.9
CD2 B:HIS524 3.7 57.7 1.0
SD B:MET421 3.7 83.8 1.0
CE B:MET421 4.3 69.1 1.0
CG B:HIS524 4.4 57.6 1.0
C09 B:6WL601 4.4 39.7 0.9
NE2 B:HIS524 4.5 59.2 1.0
SD B:MET343 4.6 71.3 1.0
CB B:HIS524 4.6 55.1 1.0
O B:GLY521 4.6 44.4 1.0
N13 B:6WL601 4.6 38.8 0.9
C07 B:6WL601 4.7 40.2 0.9
CD1 B:ILE424 4.8 47.7 1.0
CE B:MET343 5.0 41.1 1.0
CA B:GLY521 5.0 42.9 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: Tue Jul 15 04:53:32 2025

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