Zinc in PDB 6l6q: Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements

The structure of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements, PDB code: 6l6q was solved by L.Jiang, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.41 / 2.60
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	35.696, 35.696, 259.273, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 28.9

The binding sites of Zinc atom in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements (pdb code 6l6q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements, PDB code: 6l6q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:32.5 occ:1.00 SG A:CYS266 2.3 47.0 1.0 SG A:CYS283 2.4 46.3 1.0 SG A:CYS263 2.5 56.5 1.0 SG A:CYS280 2.6 46.5 1.0 CB A:CYS266 2.9 46.2 1.0 CB A:CYS283 3.3 46.5 1.0 CB A:CYS280 3.4 46.8 1.0 CG1 A:VAL265 3.6 46.7 1.0 N A:CYS266 3.7 46.8 1.0 CA A:CYS266 3.8 49.9 1.0 CB A:CYS263 3.8 52.7 1.0 N A:CYS280 4.0 47.0 1.0 N A:CYS283 4.2 46.4 1.0 CA A:CYS280 4.3 47.0 1.0 CD A:ARG312 4.3 38.6 1.0 NH1 A:ARG312 4.4 39.0 1.0 CA A:CYS283 4.4 46.4 1.0 C A:CYS266 4.5 46.5 1.0 N A:GLY267 4.6 50.5 1.0 C A:VAL265 4.6 46.6 1.0 CB A:ASP268 4.6 46.7 1.0 NH2 A:ARG319 4.7 37.2 1.0 N A:ASP268 4.8 51.4 1.0 CB A:VAL265 4.8 48.9 1.0

Zinc binding site 2 out of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:38.9 occ:1.00 SG A:CYS299 2.2 74.0 1.0 SG A:CYS318 2.3 67.6 1.0 SG A:CYS305 2.3 41.0 1.0 SG A:CYS315 2.4 39.6 1.0 CB A:CYS305 3.0 40.4 1.0 CB A:CYS299 3.2 65.1 1.0 CB A:CYS318 3.4 39.5 1.0 CB A:CYS315 3.5 37.9 1.0 N A:CYS305 3.9 43.4 1.0 CA A:CYS299 4.1 46.3 1.0 CA A:CYS305 4.1 42.9 1.0 CA A:LYS303 4.2 47.2 1.0 N A:CYS318 4.3 39.1 1.0 N A:LYS303 4.3 49.2 1.0 CA A:CYS318 4.4 39.2 1.0 N A:ASN304 4.5 46.1 1.0 C A:LYS303 4.5 48.0 1.0 C A:CYS299 4.7 49.4 1.0 N A:LEU300 4.8 66.1 1.0 CA A:CYS315 4.9 37.6 1.0 CB A:ALA301 4.9 59.8 1.0 N A:ALA301 4.9 66.8 1.0

Zinc binding site 3 out of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:40.5 occ:1.00 CB B:CYS280 2.2 56.6 1.0 SG B:CYS283 2.6 60.0 1.0 SG B:CYS266 2.6 45.3 1.0 SG B:CYS263 2.8 46.1 1.0 SG B:CYS280 3.2 65.4 1.0 CB B:CYS283 3.4 41.9 1.0 CA B:CYS280 3.5 41.5 1.0 CB B:CYS263 3.5 53.6 1.0 CB B:CYS266 3.6 50.6 1.0 N B:CYS280 3.6 41.7 1.0 NH1 B:ARG312 4.0 51.5 1.0 N B:CYS283 4.0 41.8 1.0 CB B:ASP268 4.2 45.9 1.0 CA B:CYS283 4.3 41.8 1.0 C B:CYS280 4.3 41.4 1.0 CD B:ARG312 4.5 44.4 1.0 N B:CYS266 4.5 45.7 1.0 CA B:CYS266 4.6 45.4 1.0 N B:ASP268 4.7 45.0 1.0 O B:CYS280 4.7 41.4 1.0 CG1 B:VAL265 4.7 51.9 1.0 C B:THR279 4.9 44.1 1.0 CA B:ASP268 5.0 45.6 1.0 CA B:CYS263 5.0 45.0 1.0

Zinc binding site 4 out of 4 in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:58.7 occ:1.00 SG B:CYS315 2.3 58.0 1.0 SG B:CYS318 2.3 67.8 1.0 SG B:CYS305 2.3 51.1 1.0 SG B:CYS299 2.4 62.0 1.0 CB B:CYS305 3.0 45.6 1.0 CB B:CYS318 3.2 52.0 1.0 CB B:CYS315 3.2 52.1 1.0 CB B:CYS299 3.3 64.6 1.0 N B:CYS305 3.9 56.1 1.0 CA B:CYS305 4.1 52.1 1.0 N B:CYS318 4.1 52.4 1.0 CA B:CYS318 4.2 51.8 1.0 CA B:CYS299 4.3 51.3 1.0 CA B:LYS303 4.4 61.5 1.0 N B:LYS303 4.6 64.2 1.0 CA B:CYS315 4.6 47.8 1.0 C B:LYS303 4.7 62.6 1.0 N B:ASN304 4.7 58.0 1.0 C B:CYS299 4.9 48.7 1.0

L.Jiang, S.Dai, J.Li, X.Liang, L.Qu, X.Chen, M.Guo, Z.Chen, L.Chen, H.Wei, Y.Chen. Structural Basis of Binding of Homodimers of the Nuclear Receptor NR4A2 to Selective Nur-Responsive Dna Elements. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31723028
DOI: 10.1074/JBC.RA119.010730