Zinc in PDB 5uan: Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna

The structure of Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna, PDB code: 5uan was solved by V.Chandra, D.Wu, Y.Kim, F.Rastinejad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 3.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.470, 77.403, 112.113, 90.00, 90.37, 90.00
R / Rfree (%)	22.1 / 27

The binding sites of Zinc atom in the Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna (pdb code 5uan). 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 Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna, PDB code: 5uan:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna


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 Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.6 occ:1.00 SG A:CYS138 2.3 0.9 1.0 SG A:CYS152 2.3 97.4 1.0 SG A:CYS155 2.3 0.0 1.0 SG A:CYS135 2.3 0.4 1.0 CB A:CYS135 3.6 0.1 1.0 CB A:CYS138 3.6 0.5 1.0 CB A:CYS155 3.6 0.5 1.0 CB A:CYS152 3.6 88.9 1.0 N A:CYS138 3.7 0.9 1.0 N A:CYS152 3.8 80.2 1.0 CB A:ILE137 4.1 0.2 1.0 CA A:CYS138 4.1 0.0 1.0 NH1 A:ARG184 4.1 81.9 1.0 CA A:CYS152 4.3 81.5 1.0 CB A:ASP140 4.3 90.6 1.0 N A:CYS155 4.4 90.3 1.0 C A:ILE137 4.6 0.9 1.0 CA A:CYS155 4.6 97.2 1.0 C A:CYS138 4.6 0.4 1.0 N A:ASP140 4.7 0.7 1.0 CA A:ILE137 4.7 0.9 1.0 N A:GLY139 4.8 0.1 1.0 CG2 A:ILE137 4.8 0.4 1.0 C A:SER151 4.8 83.7 1.0 N A:ILE137 4.8 0.8 1.0 CG1 A:ILE137 4.9 92.8 1.0 C A:CYS152 4.9 75.8 1.0 CA A:SER151 4.9 77.2 1.0 CA A:CYS135 5.0 0.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna


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 Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.1 occ:1.00 SG A:CYS187 2.3 0.3 1.0 SG A:CYS177 2.3 0.8 1.0 CB A:CYS187 2.8 0.7 1.0 SG A:CYS190 3.3 0.8 1.0 CB A:CYS177 3.6 0.1 1.0 CA A:CYS187 4.3 0.2 1.0 CB A:CYS190 4.4 1.0 1.0 N A:CYS190 4.8 0.4 1.0 CA A:CYS177 4.9 0.1 1.0 N A:CYS177 4.9 0.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna


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 Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:44.4 occ:1.00 SG B:CYS84 2.3 47.4 1.0 SG B:CYS101 2.3 40.6 1.0 SG B:CYS98 2.3 45.9 1.0 SG B:CYS81 2.3 56.5 1.0 CB B:CYS101 3.2 48.3 1.0 CB B:CYS81 3.5 61.9 1.0 CB B:CYS84 3.6 47.0 1.0 CB B:CYS98 3.7 48.1 1.0 N B:CYS84 3.8 63.2 1.0 N B:CYS98 4.0 56.8 1.0 N B:CYS101 4.2 47.8 1.0 CA B:CYS84 4.3 73.5 1.0 CB B:VAL83 4.3 50.8 1.0 CA B:CYS101 4.4 43.5 1.0 CA B:CYS98 4.4 55.0 1.0 CB B:ASP86 4.6 71.2 1.0 C B:VAL83 4.8 54.2 1.0 C B:CYS84 4.8 71.9 1.0 CA B:CYS81 4.9 60.6 1.0 NH2 B:ARG137 4.9 44.5 1.0 CA B:VAL83 5.0 51.6 1.0 CG1 B:VAL83 5.0 48.9 1.0 NH2 B:ARG130 5.0 73.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna


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 Multi-Domain Rar-Beta-Rxr-Alpha Heterodimer on Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:76.8 occ:0.96 SG B:CYS136 2.3 57.0 1.0 SG B:CYS117 2.3 67.9 1.0 SG B:CYS133 2.3 96.0 1.0 SG B:CYS123 2.3 81.4 1.0 CB B:CYS133 2.4 73.3 1.0 CB B:CYS117 3.4 60.2 1.0 CB B:CYS123 3.4 73.1 1.0 CB B:CYS136 3.6 57.9 1.0 CA B:LYS121 3.9 63.1 1.0 CA B:CYS133 3.9 55.0 1.0 N B:LYS121 4.3 62.8 1.0 N B:CYS123 4.3 77.0 1.0 CA B:CYS117 4.3 54.3 1.0 N B:CYS136 4.4 52.5 1.0 C B:LYS121 4.4 65.4 1.0 CA B:CYS123 4.4 73.0 1.0 CA B:CYS136 4.5 53.9 1.0 N B:CYS133 4.6 57.5 1.0 C B:CYS133 4.7 41.0 1.0 CB B:ARG119 4.7 67.3 1.0 N B:ASN122 4.8 72.6 1.0 N B:ARG119 4.8 74.3 1.0 O B:CYS133 4.9 40.1 1.0 CG B:ARG119 4.9 68.0 1.0 N B:HIS118 4.9 64.0 1.0 O B:LYS121 4.9 59.0 1.0

V.Chandra, D.Wu, S.Li, N.Potluri, Y.Kim, F.Rastinejad. The Quaternary Architecture of Rar Beta-Rxr Alpha Heterodimer Facilitates Domain-Domain Signal Transmission. Nat Commun V. 8 868 2017.
ISSN: ESSN 2041-1723
PubMed: 29021580
DOI: 10.1038/S41467-017-00981-Y