Chlorine in PDB 5kce: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative, PDB code: 5kce was solved by J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, V.Dharmarajan, D.Goswami, I.Kastrati, S.Novick, J.Nowak, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Min, J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, 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)	41.16 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.577, 75.326, 57.996, 90.00, 110.82, 90.00
R / Rfree (%)	19.2 / 25

The binding sites of Chlorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative (pdb code 5kce). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative, PDB code: 5kce:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative


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 An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:47.2 occ:0.78 CL1 A:OB3601 0.0 47.2 0.8 C24 A:OB3602 0.4 44.8 0.2 C25 A:OB3602 0.9 42.6 0.2 C23 A:OB3602 1.5 43.1 0.2 C21 A:OB3601 1.7 39.1 0.8 C19 A:OB3602 2.0 36.0 0.2 C22 A:OB3602 2.4 41.0 0.2 C21 A:OB3602 2.5 39.3 0.2 C22 A:OB3601 2.5 39.5 0.8 C19 A:OB3601 2.6 35.7 0.8 N01 A:OB3601 3.0 30.5 0.8 N01 A:OB3602 3.0 31.9 0.2 C20 A:OB3601 3.1 34.0 0.8 SD A:MET528 3.2 53.3 0.5 C04 A:OB3602 3.6 28.2 0.2 C04 A:OB3601 3.6 26.9 0.8 SD A:MET343 3.6 66.6 1.0 C20 A:OB3602 3.7 32.5 0.2 C03 A:OB3602 3.8 28.2 0.2 C03 A:OB3601 3.8 28.3 0.8 C23 A:OB3601 3.8 45.9 0.8 CE A:MET343 3.8 64.0 1.0 C25 A:OB3601 3.8 43.1 0.8 CE A:MET528 3.8 35.0 0.5 C11 A:OB3601 4.0 35.4 0.8 C11 A:OB3602 4.0 35.1 0.2 CD2 A:LEU525 4.1 42.3 1.0 C05 A:OB3602 4.2 29.1 0.2 C05 A:OB3601 4.2 29.0 0.8 CL1 A:OB3602 4.2 47.2 0.2 S01 A:OB3601 4.2 35.8 0.8 S01 A:OB3602 4.2 37.0 0.2 C24 A:OB3601 4.3 44.0 0.8 C17 A:OB3601 4.5 32.2 0.8 C02 A:OB3602 4.5 28.4 0.2 C02 A:OB3601 4.5 28.6 0.8 C17 A:OB3602 4.5 33.2 0.2 O04 A:OB3602 4.5 36.7 0.2 O04 A:OB3601 4.6 38.0 0.8 C07 A:OB3601 4.6 34.1 0.8 C07 A:OB3602 4.6 32.1 0.2 C06 A:OB3601 4.8 26.9 0.8 C06 A:OB3602 4.8 27.3 0.2 SD A:MET421 4.8 46.6 1.0 CG A:MET528 4.9 36.7 0.5 CG A:LEU525 4.9 43.1 1.0 C01 A:OB3602 5.0 27.4 0.2 C01 A:OB3601 5.0 26.1 0.8 CG A:MET528 5.0 36.9 0.5

Chlorine binding site 2 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative


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 An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:47.2 occ:0.22 CL1 A:OB3602 0.0 47.2 0.2 C24 A:OB3601 0.6 44.0 0.8 C25 A:OB3601 0.7 43.1 0.8 C21 A:OB3602 1.7 39.3 0.2 C23 A:OB3601 1.8 45.9 0.8 C19 A:OB3601 1.9 35.7 0.8 C22 A:OB3602 2.4 41.0 0.2 C22 A:OB3601 2.5 39.5 0.8 C21 A:OB3601 2.5 39.1 0.8 C19 A:OB3602 2.7 36.0 0.2 N01 A:OB3601 2.9 30.5 0.8 N01 A:OB3602 3.2 31.9 0.2 CB A:HIS524 3.4 31.1 1.0 CG A:HIS524 3.4 36.6 1.0 S01 A:OB3601 3.6 35.8 0.8 S01 A:OB3602 3.7 37.0 0.2 C23 A:OB3602 3.7 43.1 0.2 O A:GLY420 3.7 40.5 1.0 O04 A:OB3602 3.7 36.7 0.2 CD2 A:HIS524 3.7 38.3 1.0 CA A:MET421 3.7 27.8 1.0 O04 A:OB3601 3.8 38.0 0.8 C A:GLY420 3.8 43.2 1.0 C25 A:OB3602 3.9 42.6 0.2 N A:MET421 3.9 34.0 1.0 C20 A:OB3601 4.0 34.0 0.8 ND1 A:HIS524 4.1 39.4 1.0 CG1 A:ILE424 4.1 38.0 1.0 CL1 A:OB3601 4.2 47.2 0.8 CB A:MET421 4.2 30.8 1.0 C20 A:OB3602 4.2 32.5 0.2 C24 A:OB3602 4.3 44.8 0.2 O05 A:OB3601 4.4 39.8 0.8 O A:GLU419 4.4 49.2 1.0 O05 A:OB3602 4.4 39.3 0.2 CG A:MET421 4.5 34.3 1.0 NE2 A:HIS524 4.5 38.5 1.0 CE1 A:HIS524 4.7 37.7 1.0 CA A:GLY420 4.7 43.6 1.0 CA A:HIS524 4.9 32.3 1.0 C A:MET421 5.0 26.3 1.0 CB A:ILE424 5.0 33.4 1.0 CA A:GLY521 5.0 29.5 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative


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 An N-Methyl, 2-Chlorobenzyl Obhs-N Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:47.3 occ:0.93 CL1 B:OB3601 0.0 47.3 0.9 C21 B:OB3601 1.7 52.6 0.9 C22 B:OB3601 2.6 55.0 0.9 C19 B:OB3601 2.7 50.7 0.9 N01 B:OB3601 3.0 42.0 0.9 C20 B:OB3601 3.2 41.1 0.9 SD B:MET343 3.5 60.5 1.0 CE B:MET343 3.7 30.9 1.0 C04 B:OB3601 3.7 33.7 0.9 C23 B:OB3601 3.9 56.9 0.9 C11 B:OB3601 3.9 32.6 0.9 C25 B:OB3601 3.9 56.5 0.9 C03 B:OB3601 4.2 33.4 0.9 S01 B:OB3601 4.2 36.7 0.9 C24 B:OB3601 4.4 59.1 0.9 C05 B:OB3601 4.5 32.5 0.9 C17 B:OB3601 4.5 29.8 0.9 O04 B:OB3601 4.5 44.3 0.9 C07 B:OB3601 4.7 32.3 0.9 O03 B:OB3601 4.8 36.0 0.9 SD B:MET528 5.0 0.5 1.0 CD2 B:LEU525 5.0 45.5 1.0

S.Srinivasan, J.C.Nwachukwu, N.E.Bruno, V.Dharmarajan, D.Goswami, I.Kastrati, S.Novick, J.Nowak, V.Cavett, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Min, J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, J.A.Katzenellenbogen, K.W.Nettles. Full Antagonism of the Estrogen Receptor Without A Prototypical Ligand Side Chain. Nat. Chem. Biol. V. 13 111 2017.
ISSN: ESSN 1552-4469
PubMed: 27870835
DOI: 10.1038/NCHEMBIO.2236