Zinc in PDB 6fbq: Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0

The structure of Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0, PDB code: 6fbq was solved by A.G.Mcewen, P.Poussin-Courmontagne, J.Osz, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.44 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.333, 44.257, 62.137, 90.00, 98.31, 90.00
R / Rfree (%)	16.3 / 19.8

The binding sites of Zinc atom in the Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0 (pdb code 6fbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0, PDB code: 6fbq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.4 occ:1.00 SG A:CYS152 2.3 16.7 1.0 SG A:CYS138 2.3 16.3 1.0 SG A:CYS135 2.4 16.6 1.0 SG A:CYS155 2.4 16.7 1.0 H A:CYS152 2.9 19.6 1.0 HB2 A:CYS155 2.9 14.6 1.0 H A:CYS138 3.1 17.2 1.0 HB3 A:CYS135 3.3 14.2 1.0 CB A:CYS135 3.3 15.5 1.0 CB A:CYS155 3.3 14.6 1.0 H A:CYS155 3.3 15.2 1.0 HB3 A:CYS138 3.3 12.5 1.0 HB2 A:CYS135 3.4 13.9 1.0 HB3 A:CYS152 3.4 15.8 1.0 CB A:CYS138 3.4 13.4 1.0 CB A:CYS152 3.5 15.3 1.0 HB A:ILE137 3.5 19.5 1.0 HH11 A:ARG184 3.6 14.3 1.0 HB3 A:ASP140 3.7 16.3 1.0 HH21 A:ARG191 3.7 16.7 1.0 N A:CYS138 3.8 16.4 1.0 N A:CYS152 3.9 16.8 1.0 H A:ASP140 4.0 13.1 1.0 HB3 A:CYS155 4.0 13.7 1.0 N A:CYS155 4.1 15.0 1.0 HD2 A:ARG184 4.1 15.2 1.0 CA A:CYS138 4.2 14.6 1.0 CA A:CYS152 4.2 16.6 1.0 NH1 A:ARG184 4.3 14.9 1.0 CA A:CYS155 4.3 14.3 1.0 HB2 A:CYS138 4.3 12.6 1.0 HB2 A:CYS152 4.3 14.3 1.0 H A:ILE137 4.4 14.2 1.0 HG22 A:ILE137 4.4 18.5 1.0 HB2 A:ASP140 4.5 15.4 1.0 HH12 A:ARG184 4.5 13.7 1.0 HA A:SER151 4.5 19.8 1.0 H A:GLY139 4.5 13.4 1.0 CB A:ILE137 4.6 18.0 1.0 CB A:ASP140 4.6 16.7 1.0 HB2 A:SER151 4.6 20.4 1.0 NH2 A:ARG191 4.7 14.8 1.0 CA A:CYS135 4.7 15.0 1.0 HD3 A:ARG184 4.7 19.1 1.0 HA A:CYS155 4.7 11.2 1.0 C A:CYS138 4.8 17.3 1.0 HD13 A:ILE137 4.8 27.0 1.0 HE A:ARG191 4.8 12.5 1.0 C A:ILE137 4.8 18.0 1.0 N A:GLY139 4.8 15.6 1.0 CD A:ARG184 4.9 16.0 1.0 C A:CYS152 4.9 20.2 1.0 N A:ASP140 4.9 15.5 1.0 O A:CYS152 4.9 17.9 1.0 CG2 A:ILE137 4.9 17.8 1.0 C A:SER151 5.0 20.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.4 occ:1.00 SG A:CYS190 2.3 19.1 1.0 SG A:CYS187 2.3 19.1 1.0 SG A:CYS177 2.3 22.0 1.0 SG A:CYS171 2.4 22.4 1.0 HB2 A:CYS177 3.0 19.6 1.0 HB2 A:CYS190 3.0 16.8 1.0 HB2 A:CYS171 3.1 19.1 1.0 HE22 B:GLN210 3.1 45.9 1.0 H A:CYS177 3.2 21.5 1.0 CB A:CYS187 3.2 16.2 1.0 HB3 A:CYS187 3.3 16.5 1.0 CB A:CYS177 3.3 19.8 1.0 CB A:CYS190 3.3 15.6 1.0 HB2 A:CYS187 3.3 16.0 1.0 CB A:CYS171 3.3 20.7 1.0 H A:CYS190 3.4 18.9 1.0 HA A:LYS175 3.5 26.9 0.9 HA A:LYS175 3.6 27.5 0.1 HA A:CYS171 3.8 18.8 1.0 H A:LYS175 3.9 29.6 0.1 H A:LYS175 3.9 29.9 0.9 HD1 A:TYR189 3.9 18.6 1.0 NE2 B:GLN210 4.0 44.7 1.0 N A:CYS177 4.0 22.5 1.0 HB3 A:CYS177 4.1 18.9 1.0 HB3 A:TYR189 4.1 19.2 1.0 HB3 A:CYS190 4.1 15.0 1.0 HE21 B:GLN210 4.1 44.2 1.0 N A:CYS190 4.1 16.3 1.0 CA A:CYS171 4.2 20.7 1.0 H A:ASP176 4.2 28.1 1.0 HB3 A:CYS171 4.2 20.2 1.0 H A:ASP173 4.2 29.4 1.0 CA A:CYS177 4.3 20.9 1.0 CA A:CYS190 4.3 15.3 1.0 O A:HOH467 4.3 28.7 1.0 HB2 A:ASP173 4.3 31.9 1.0 CA A:LYS175 4.4 27.1 0.9 CA A:LYS175 4.4 28.3 0.1 N A:LYS175 4.5 29.8 1.0 N A:ASP176 4.6 27.9 1.0 H A:ARG172 4.7 26.6 1.0 CA A:CYS187 4.7 16.1 1.0 O B:HOH416 4.7 43.5 1.0 HA A:CYS190 4.7 14.7 1.0 C A:LYS175 4.7 31.0 1.0 HA A:CYS177 4.8 21.4 1.0 CD1 A:TYR189 4.9 21.2 1.0 HA A:CYS187 4.9 16.0 1.0 H A:ASN174 4.9 30.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:29.9 occ:1.00 SG B:CYS138 2.3 27.8 1.0 SG B:CYS135 2.3 25.1 1.0 SG B:CYS155 2.4 21.8 1.0 SG B:CYS152 2.4 23.6 1.0 H B:CYS152 2.9 20.9 1.0 H B:CYS138 3.0 25.5 1.0 HB2 B:CYS155 3.1 17.4 1.0 HB3 B:CYS138 3.1 23.6 1.0 HB3 B:CYS135 3.2 24.3 1.0 CB B:CYS135 3.2 24.6 1.0 CB B:CYS138 3.3 26.2 1.0 CB B:CYS155 3.4 17.9 1.0 HB2 B:CYS135 3.4 24.5 1.0 H B:CYS155 3.4 21.3 1.0 HB B:ILE137 3.5 26.6 1.0 HB3 B:CYS152 3.5 21.9 1.0 CB B:CYS152 3.6 20.7 1.0 HH11 B:ARG184 3.6 28.4 1.0 HB3 B:ASP140 3.7 28.2 1.0 N B:CYS138 3.8 27.0 1.0 N B:CYS152 3.9 21.2 1.0 HH21 B:ARG191 3.9 21.9 1.0 HD2 B:ARG184 4.0 34.0 1.0 H B:ASP140 4.0 32.1 1.0 CA B:CYS138 4.1 28.2 1.0 HB3 B:CYS155 4.1 19.6 1.0 N B:CYS155 4.2 18.7 1.0 HB2 B:CYS138 4.2 26.8 1.0 CA B:CYS152 4.3 20.3 1.0 NH1 B:ARG184 4.3 27.6 1.0 H B:ILE137 4.4 25.7 1.0 CA B:CYS155 4.4 16.3 1.0 HB2 B:SER151 4.4 20.8 1.0 HB2 B:CYS152 4.5 18.0 1.0 CB B:ILE137 4.5 28.2 1.0 H B:GLY139 4.5 31.2 1.0 HA B:SER151 4.5 23.4 1.0 HB2 B:ASP140 4.6 31.4 1.0 HG22 B:ILE137 4.6 28.5 1.0 HH12 B:ARG184 4.6 28.7 1.0 CB B:ASP140 4.6 30.8 1.0 HD13 B:ILE137 4.7 46.3 1.0 HD3 B:ARG184 4.7 37.4 1.0 CA B:CYS135 4.7 26.8 1.0 C B:ILE137 4.7 30.8 1.0 C B:CYS138 4.7 35.1 1.0 CD B:ARG184 4.8 35.1 1.0 HA B:CYS155 4.8 15.4 1.0 N B:GLY139 4.8 32.6 1.0 NH2 B:ARG191 4.8 21.7 1.0 HE B:ARG191 4.9 24.2 1.0 N B:ASP140 4.9 34.0 1.0 C B:CYS152 5.0 20.4 1.0 O B:CYS152 5.0 18.8 1.0 CA B:ILE137 5.0 27.9 1.0 C B:SER151 5.0 23.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Human Retinoid X Receptor Dna-Binding Domain Bound to the Human Mep DR1 Response Element, pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:51.5 occ:1.00 SG B:CYS190 2.2 38.5 1.0 SG B:CYS177 2.3 48.5 1.0 SG B:CYS171 2.4 46.4 1.0 SG B:CYS187 2.4 39.5 1.0 HB2 B:CYS177 2.9 41.5 1.0 HB2 B:CYS190 3.0 31.5 1.0 H B:CYS177 3.0 47.0 0.5 H B:CYS177 3.0 47.0 0.5 CB B:CYS190 3.2 32.2 1.0 HB2 B:CYS171 3.2 38.9 1.0 CB B:CYS177 3.2 43.6 1.0 HA B:LYS175 3.4 45.4 1.0 HB3 B:CYS187 3.4 37.2 1.0 CB B:CYS187 3.4 36.7 1.0 CB B:CYS171 3.4 41.8 1.0 H B:CYS190 3.5 31.8 1.0 HB2 B:CYS187 3.6 38.0 1.0 HA B:CYS171 3.7 42.2 1.0 H B:LYS175 3.8 48.6 1.0 N B:CYS177 3.8 48.3 1.0 H B:ASP176 3.9 50.6 0.5 H B:ASP176 3.9 50.4 0.5 HD1 B:TYR189 3.9 34.5 1.0 HB3 B:CYS190 4.0 32.6 1.0 O B:HOH464 4.0 26.6 0.5 HB3 B:TYR189 4.0 32.7 1.0 HB3 B:CYS177 4.1 44.5 1.0 HB2 B:ASP173 4.1 58.2 1.0 N B:CYS190 4.1 30.4 1.0 H B:ASP173 4.1 54.4 0.5 H B:ASP173 4.1 54.4 0.5 CA B:CYS177 4.2 46.2 1.0 CA B:CYS171 4.2 42.9 1.0 CA B:LYS175 4.2 47.2 1.0 CA B:CYS190 4.3 29.9 1.0 HB3 B:CYS171 4.3 43.7 1.0 N B:ASP176 4.3 49.3 0.5 N B:ASP176 4.3 49.5 0.5 N B:LYS175 4.4 50.1 1.0 H B:ARG172 4.5 51.1 0.5 H B:ARG172 4.6 50.8 0.5 C B:LYS175 4.6 50.8 1.0 HA B:CYS190 4.6 30.1 1.0 HA B:CYS177 4.8 48.6 1.0 CD1 B:TYR189 4.8 34.9 1.0 CA B:CYS187 4.8 35.1 1.0 C B:ASP176 4.9 54.0 0.5 C B:ASP176 5.0 54.1 0.5 H B:ASN174 5.0 59.1 1.0

J.Osz, A.G.Mcewen, J.Wolf, P.Poussin-Courmontagne, C.Peluso-Iltis, Y.Chebaro, B.Kieffer, N.Rochel. Modulation of Rxr-Dna Complex Assembly By Dna Context. Mol. Cell. Endocrinol. V. 481 44 2019.
ISSN: ISSN 1872-8057
PubMed: 30476562
DOI: 10.1016/J.MCE.2018.11.008