Chlorine in PDB 5kra: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde, PDB code: 5kra 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)	40.58 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.580, 82.960, 104.970, 90.00, 101.12, 90.00
R / Rfree (%)	20.4 / 24.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde (pdb code 5kra). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 18 binding sites of Chlorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde, PDB code: 5kra:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:0.9 occ:1.00 CL1 A:6WS601 0.0 0.9 1.0 C02 A:6WS601 1.7 57.5 1.0 C18 A:6WS601 2.7 57.6 1.0 C03 A:6WS601 2.7 55.1 1.0 N A:PHE425 3.3 37.8 1.0 O A:MET421 3.5 54.1 1.0 CE A:MET421 3.5 61.0 1.0 CA A:PHE425 3.5 37.5 1.0 CD1 A:PHE425 3.5 48.4 1.0 CB A:ILE424 3.6 42.1 1.0 C A:ILE424 3.7 38.9 1.0 CG2 A:ILE424 3.7 38.5 1.0 CB A:PHE425 3.8 40.8 1.0 CD1 A:LEU428 3.9 28.4 1.0 SD A:MET421 4.0 74.1 1.0 C17 A:6WS601 4.0 54.5 1.0 C04 A:6WS601 4.0 52.9 1.0 CG A:PHE425 4.1 45.2 1.0 CB A:MET421 4.2 59.1 1.0 C A:MET421 4.2 53.0 1.0 O A:ILE424 4.3 39.3 1.0 CA A:ILE424 4.3 40.6 1.0 CA A:MET421 4.3 54.3 1.0 CE1 A:PHE425 4.5 51.5 1.0 C05 A:6WS601 4.5 50.6 1.0 CG A:MET421 4.8 64.5 1.0 O A:HOH755 4.8 63.7 1.0 CG1 A:ILE424 4.8 45.5 1.0 CD1 A:LEU402 5.0 33.0 1.0 N A:ILE424 5.0 40.2 1.0 C A:PHE425 5.0 36.5 1.0

Chlorine binding site 2 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:50.8 occ:1.00 CL2 A:6WS601 0.0 50.8 1.0 C10 A:6WS601 1.7 43.5 1.0 C09 A:6WS601 2.7 43.7 1.0 C12 A:6WS601 2.7 42.2 1.0 OE1 A:GLU353 3.5 46.1 1.0 OE2 A:GLU353 3.5 40.5 1.0 NH2 A:ARG394 3.6 27.0 1.0 CD A:GLU353 3.6 40.7 1.0 C08 A:6WS601 4.0 44.2 1.0 C13 A:6WS601 4.0 42.7 1.0 CD2 A:LEU349 4.2 32.5 1.0 CG A:LEU349 4.4 32.2 1.0 CD2 A:LEU387 4.4 15.4 1.0 C07 A:6WS601 4.5 44.4 1.0 CG A:GLU353 4.6 32.1 1.0 O A:LEU387 4.7 17.6 1.0 CB A:LEU387 4.8 16.4 1.0 CA A:ALA350 4.8 19.6 1.0 CZ A:ARG394 4.8 24.0 1.0 CD1 A:PHE404 4.9 23.7 1.0 CB A:LEU391 4.9 19.0 1.0 CB A:GLU353 4.9 21.4 1.0

Chlorine binding site 3 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:0.9 occ:1.00 CL3 A:6WS601 0.0 0.9 1.0 C14 A:6WS601 1.7 48.2 1.0 C06 A:6WS601 2.7 47.4 1.0 CL4 A:6WS601 3.0 68.3 1.0 C04 A:6WS601 3.0 52.9 1.0 C05 A:6WS601 3.2 50.6 1.0 CD1 A:LEU525 3.5 52.0 1.0 C07 A:6WS601 4.1 44.4 1.0 CD2 A:LEU525 4.2 46.2 1.0 C03 A:6WS601 4.3 55.1 1.0 O A:GLY521 4.3 27.5 1.0 CG A:LEU525 4.4 47.1 1.0 CD2 A:HIS524 4.4 57.8 1.0 C17 A:6WS601 4.5 54.5 1.0 C08 A:6WS601 4.9 44.2 1.0 CB A:LEU525 4.9 39.4 1.0 CD1 A:LEU384 5.0 20.8 1.0

Chlorine binding site 4 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:68.3 occ:1.00 CL4 A:6WS601 0.0 68.3 1.0 C14 A:6WS601 1.7 48.2 1.0 C06 A:6WS601 2.7 47.4 1.0 C07 A:6WS601 2.9 44.4 1.0 CL3 A:6WS601 3.0 0.9 1.0 C08 A:6WS601 3.3 44.2 1.0 CB A:ALA350 3.7 20.4 1.0 C13 A:6WS601 3.7 42.7 1.0 C05 A:6WS601 4.1 50.6 1.0 CD1 A:LEU384 4.2 20.8 1.0 C09 A:6WS601 4.3 43.7 1.0 CD2 A:LEU525 4.4 46.2 1.0 C12 A:6WS601 4.6 42.2 1.0 CD1 A:LEU525 4.7 52.0 1.0 CD1 A:LEU387 4.8 23.5 1.0 CZ3 A:TRP383 4.8 17.7 1.0 C10 A:6WS601 4.8 43.5 1.0 C04 A:6WS601 4.8 52.9 1.0 O A:LEU346 4.9 36.2 1.0

Chlorine binding site 5 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:68.0 occ:1.00 CL1 B:6WT601 0.0 68.0 1.0 C03 B:6WT601 1.7 32.5 1.0 C04 B:6WT601 2.7 35.6 1.0 C02 B:6WT601 2.7 32.7 1.0 OE1 B:GLU353 3.3 38.2 1.0 NH2 B:ARG394 3.5 31.8 1.0 CD B:GLU353 3.7 35.1 1.0 OE2 B:GLU353 4.0 35.5 1.0 C05 B:6WT601 4.0 39.0 1.0 C01 B:6WT601 4.0 35.9 1.0 O B:HOH717 4.2 24.0 1.0 CD2 B:LEU349 4.2 35.7 1.0 CG B:LEU349 4.4 33.7 1.0 CG B:GLU353 4.5 21.3 1.0 CD2 B:LEU387 4.5 25.5 1.0 C06 B:6WT601 4.6 39.0 1.0 CZ B:ARG394 4.7 32.0 1.0 CA B:ALA350 4.7 25.4 1.0 CD1 B:PHE404 4.8 24.7 1.0 O B:PHE404 4.8 28.8 1.0 N B:ALA350 4.9 26.2 1.0 O B:LEU387 4.9 16.1 1.0 CB B:LEU387 5.0 27.9 1.0 CB B:LEU391 5.0 18.2 1.0

Chlorine binding site 6 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:66.3 occ:1.00 CL5 B:6WT601 0.0 66.3 1.0 C08 B:6WT601 1.8 51.6 1.0 C07 B:6WT601 2.8 41.4 1.0 CL4 B:6WT601 2.8 91.3 1.0 CL3 B:6WT601 2.9 95.6 1.0 C06 B:6WT601 3.3 39.0 1.0 C01 B:6WT601 3.3 35.9 1.0 CB B:ALA350 3.8 26.3 1.0 CD1 B:LEU525 4.1 40.1 1.0 C09 B:6WT601 4.1 40.6 1.0 CD1 B:LEU384 4.2 28.8 1.0 C05 B:6WT601 4.4 39.0 1.0 CD2 B:LEU525 4.4 45.1 1.0 C02 B:6WT601 4.4 32.7 1.0 CG B:LEU525 4.6 40.8 1.0 CZ3 B:TRP383 4.7 25.0 1.0 CH2 B:TRP383 4.8 28.7 1.0 C10 B:6WT601 4.9 44.1 1.0 CG2 B:THR347 5.0 49.5 1.0

Chlorine binding site 7 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:95.6 occ:1.00 CL3 B:6WT601 0.0 95.6 1.0 C08 B:6WT601 1.8 51.6 1.0 CL4 B:6WT601 2.8 91.3 1.0 C07 B:6WT601 2.8 41.4 1.0 CL5 B:6WT601 2.9 66.3 1.0 C09 B:6WT601 3.2 40.6 1.0 C14 B:6WT601 3.5 41.9 1.0 CG B:LEU525 3.8 40.8 1.0 CD1 B:LEU525 3.9 40.1 1.0 C06 B:6WT601 4.2 39.0 1.0 CD2 B:LEU525 4.2 45.1 1.0 C10 B:6WT601 4.2 44.1 1.0 O B:GLY521 4.4 33.0 1.0 C13 B:6WT601 4.6 46.0 1.0 CD1 B:LEU384 4.6 28.8 1.0 SD B:MET421 4.8 84.6 1.0 CA B:GLY521 4.8 28.9 1.0 C B:GLY521 4.8 31.4 1.0 C01 B:6WT601 4.8 35.9 1.0 CD2 B:LEU384 4.9 26.4 1.0

Chlorine binding site 8 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:91.3 occ:1.00 CL4 B:6WT601 0.0 91.3 1.0 C08 B:6WT601 1.8 51.6 1.0 C07 B:6WT601 2.8 41.4 1.0 CL3 B:6WT601 2.8 95.6 1.0 CL5 B:6WT601 2.8 66.3 1.0 C09 B:6WT601 3.3 40.6 1.0 C10 B:6WT601 3.3 44.1 1.0 C01 B:6WT601 3.5 35.9 1.0 CE B:MET343 3.6 36.8 1.0 C06 B:6WT601 3.6 39.0 1.0 CG2 B:THR347 3.9 49.5 1.0 CB B:LEU346 4.2 31.2 1.0 C14 B:6WT601 4.4 41.9 1.0 N B:THR347 4.4 38.3 1.0 C11 B:6WT601 4.5 48.6 1.0 C B:LEU346 4.6 37.3 1.0 CA B:THR347 4.6 39.3 1.0 SD B:MET343 4.8 86.6 1.0 C02 B:6WT601 4.8 32.7 1.0 O B:LEU346 4.8 38.7 1.0 CD2 B:LEU525 4.9 45.1 1.0 CB B:THR347 4.9 46.2 1.0 CD1 B:LEU346 5.0 31.9 1.0

Chlorine binding site 9 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:0.5 occ:1.00 CL2 B:6WT601 0.0 0.5 1.0 C12 B:6WT601 1.7 48.3 1.0 C13 B:6WT601 2.7 46.0 1.0 C11 B:6WT601 2.7 48.6 1.0 CD1 B:PHE425 3.3 44.5 1.0 CG B:MET421 3.5 68.9 1.0 CA B:PHE425 3.6 36.4 1.0 N B:PHE425 3.6 43.1 1.0 CB B:PHE425 3.7 38.9 1.0 O B:MET421 3.8 77.7 1.0 CG B:PHE425 3.9 43.4 1.0 CD1 B:LEU428 3.9 29.8 1.0 C10 B:6WT601 4.0 44.1 1.0 C14 B:6WT601 4.1 41.9 1.0 C B:ILE424 4.2 38.8 1.0 CE1 B:PHE425 4.2 48.3 1.0 CG2 B:ILE424 4.3 32.8 1.0 CB B:ILE424 4.4 36.3 1.0 SD B:MET421 4.5 84.6 1.0 C09 B:6WT601 4.6 40.6 1.0 CZ B:PHE404 4.7 27.8 1.0 C B:MET421 4.7 67.9 1.0 CB B:MET421 4.7 67.8 1.0 O B:ILE424 4.7 33.1 1.0 CD1 B:LEU402 4.9 32.4 1.0 CA B:ILE424 4.9 36.2 1.0

Chlorine binding site 10 out of 18 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with Ddt and Dde within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl601 b:0.9 occ:1.00 CL1 E:6WS601 0.0 0.9 1.0 C02 E:6WS601 1.8 57.4 1.0 C18 E:6WS601 2.7 54.6 1.0 C03 E:6WS601 2.7 56.5 1.0 N E:PHE425 3.5 32.7 1.0 O E:MET421 3.5 53.8 1.0 SD E:MET421 3.5 0.3 1.0 CB E:ILE424 3.8 39.0 1.0 CA E:PHE425 3.8 36.5 1.0 C E:ILE424 3.8 36.6 1.0 CD1 E:LEU428 3.9 29.1 1.0 CG2 E:ILE424 3.9 34.7 1.0 C17 E:6WS601 4.0 49.9 1.0 CD1 E:PHE425 4.0 51.9 1.0 C04 E:6WS601 4.0 51.4 1.0 CB E:PHE425 4.1 42.3 1.0 O E:ILE424 4.2 32.7 1.0 CE E:MET421 4.3 60.8 1.0 C E:MET421 4.4 51.4 1.0 CA E:ILE424 4.4 38.9 1.0 CG E:PHE425 4.4 47.6 1.0 CB E:MET421 4.5 48.3 1.0 C05 E:6WS601 4.6 47.4 1.0 CA E:MET421 4.6 50.2 1.0 CG E:MET421 4.7 49.7 1.0 CG1 E:ILE424 4.9 41.3 1.0 CE1 E:PHE425 5.0 57.3 1.0

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