Zinc in PDB 6l6l: 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: 6l6l 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)	35.23 / 2.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.405, 64.315, 60.776, 90.00, 96.84, 90.00
R / Rfree (%)	21.6 / 25.2

The binding sites of Zinc atom in the Structural Basis of NR4A2 Homodimers Binding to Selective Nur- Responsive Elements (pdb code 6l6l). 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: 6l6l:
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:30.4 occ:1.00 SG A:CYS283 2.3 39.6 1.0 SG A:CYS266 2.3 33.9 1.0 SG A:CYS280 2.4 33.5 1.0 SG A:CYS263 2.6 37.3 1.0 CB A:CYS283 3.1 30.3 1.0 CB A:CYS266 3.4 33.3 1.0 CB A:CYS280 3.5 34.7 1.0 CB A:CYS263 3.6 45.0 1.0 N A:CYS280 3.8 33.6 1.0 N A:CYS266 3.8 44.9 1.0 N A:CYS283 3.8 30.9 1.0 NH1 A:ARG312 4.0 41.7 1.0 CA A:CYS283 4.1 30.0 1.0 CA A:CYS280 4.1 34.3 1.0 CA A:CYS266 4.2 33.6 1.0 CB A:VAL265 4.4 35.5 1.0 O A:CYS280 4.6 39.0 1.0 CG1 A:VAL265 4.6 32.2 1.0 CB A:ASP268 4.6 36.9 1.0 C A:CYS280 4.7 37.4 1.0 C A:VAL265 4.7 45.5 1.0 NH2 A:ARG319 4.8 22.4 1.0 C A:CYS266 4.9 38.9 1.0 C A:THR279 4.9 34.9 1.0 CA A:VAL265 4.9 31.6 1.0 C A:GLY282 4.9 30.9 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:34.2 occ:1.00 SG A:CYS305 2.3 25.8 1.0 SG A:CYS315 2.3 30.6 1.0 SG A:CYS318 2.4 41.4 1.0 SG A:CYS299 2.4 26.9 1.0 CB A:CYS305 3.3 25.6 1.0 CB A:CYS299 3.4 25.3 1.0 CB A:CYS315 3.4 27.5 1.0 CB A:CYS318 3.4 38.1 1.0 N A:CYS305 3.8 26.0 1.0 CA A:CYS299 4.1 28.7 1.0 CA A:LYS303 4.2 30.6 1.0 N A:CYS318 4.2 45.2 1.0 CA A:CYS305 4.2 29.0 1.0 N A:ASN304 4.3 27.1 1.0 CA A:CYS318 4.4 38.1 1.0 N A:LYS303 4.4 41.7 1.0 O A:HOH504 4.4 5.7 1.0 C A:LYS303 4.6 33.4 1.0 CB A:ALA301 4.6 25.3 1.0 CA A:CYS315 4.8 25.5 1.0 C A:CYS299 4.9 26.5 1.0 N A:LEU300 4.9 22.1 1.0 C A:ASN304 4.9 26.8 1.0 N A:ALA301 5.0 31.2 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:31.6 occ:1.00 SG B:CYS283 2.4 55.6 1.0 SG B:CYS266 2.6 36.0 1.0 SG B:CYS280 2.7 42.4 1.0 SG B:CYS263 2.9 48.4 1.0 CB B:CYS283 3.2 25.3 1.0 CB B:CYS263 3.5 36.9 1.0 CB B:CYS280 3.7 34.6 1.0 CB B:CYS266 3.8 37.3 1.0 N B:CYS266 4.0 38.8 1.0 N B:CYS280 4.0 34.7 1.0 N B:CYS283 4.0 27.7 1.0 CA B:CYS283 4.2 26.4 1.0 CA B:CYS280 4.4 34.7 1.0 CB B:VAL265 4.4 39.2 1.0 CA B:CYS266 4.4 38.6 1.0 NH1 B:ARG312 4.4 32.7 1.0 CG1 B:VAL265 4.6 39.0 1.0 C B:VAL265 4.8 39.9 1.0 CB B:ASP268 4.9 35.1 1.0 O B:CYS280 4.9 32.3 1.0 C B:CYS280 4.9 33.3 1.0 NH2 B:ARG319 5.0 24.6 1.0 CA B:VAL265 5.0 40.2 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:28.1 occ:1.00 SG B:CYS315 2.3 27.6 1.0 SG B:CYS299 2.3 49.4 1.0 SG B:CYS305 2.3 38.9 1.0 SG B:CYS318 2.4 32.1 1.0 CB B:CYS299 3.2 43.3 1.0 CB B:CYS305 3.3 38.3 1.0 CB B:CYS318 3.4 30.2 1.0 CB B:CYS315 3.4 29.4 1.0 N B:CYS305 3.9 42.6 1.0 CA B:CYS299 4.0 38.3 1.0 N B:CYS318 4.1 26.3 1.0 CA B:CYS305 4.2 42.0 1.0 CA B:LYS303 4.3 41.3 1.0 CA B:CYS318 4.3 30.2 1.0 N B:ASN304 4.4 56.4 1.0 N B:LYS303 4.5 51.1 1.0 C B:LYS303 4.6 42.6 1.0 CB B:ALA301 4.7 44.4 1.0 CD2 B:TYR317 4.7 28.8 1.0 C B:CYS299 4.8 39.0 1.0 CA B:CYS315 4.8 29.0 1.0 N B:ALA301 4.8 46.8 1.0 N B:LEU300 4.9 39.7 1.0 C B:ASN304 5.0 45.2 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