Zinc in PDB 5e6a: Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex

The structure of Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex, PDB code: 5e6a was solved by W.H.Hudson, E.A.Rye, A.G.Herbst, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.11 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.993, 95.497, 103.634, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 26.6

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex (pdb code 5e6a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex, PDB code: 5e6a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:37.3 occ:1.00 SG A:CYS424 2.3 40.3 1.0 SG A:CYS441 2.3 36.3 1.0 SG A:CYS421 2.4 38.6 1.0 SG A:CYS438 2.5 40.2 1.0 CB A:CYS441 3.3 38.2 1.0 CB A:CYS424 3.4 37.9 1.0 CB A:CYS421 3.5 44.1 1.0 N A:CYS424 3.5 40.4 1.0 CB A:CYS438 3.5 41.8 1.0 N A:CYS438 3.9 41.5 1.0 CA A:CYS424 4.0 43.9 1.0 CB A:VAL423 4.2 39.5 1.0 CA A:CYS438 4.3 42.1 1.0 NH1 A:ARG470 4.3 39.3 1.0 N A:CYS441 4.3 36.2 1.0 CA A:CYS441 4.4 39.1 1.0 OG A:SER440 4.4 41.5 1.0 C A:VAL423 4.6 41.9 1.0 C A:CYS424 4.7 41.1 1.0 CB A:ASP426 4.7 45.9 1.0 N A:SER425 4.8 42.9 1.0 NH2 A:ARG477 4.8 38.4 1.0 CG1 A:VAL423 4.8 38.7 1.0 CA A:VAL423 4.8 40.3 1.0 N A:VAL423 4.9 39.7 1.0 O A:CYS438 4.9 39.3 1.0 N A:ASP426 4.9 43.5 1.0 C A:CYS438 4.9 40.4 1.0 CA A:CYS421 4.9 46.6 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:32.9 occ:1.00 SG A:CYS476 2.3 32.5 1.0 SG A:CYS463 2.3 37.2 1.0 SG A:CYS473 2.4 36.0 1.0 SG A:CYS457 2.4 37.1 1.0 CB A:CYS463 3.1 36.0 1.0 CB A:CYS473 3.4 33.9 1.0 CB A:CYS476 3.4 35.6 1.0 CB A:CYS457 3.4 40.1 1.0 O A:HOH716 3.7 38.7 1.0 N A:CYS463 4.1 39.4 1.0 CA A:CYS463 4.2 39.0 1.0 CA A:CYS457 4.2 41.1 1.0 N A:CYS476 4.2 35.2 1.0 CA A:ASN461 4.2 42.3 1.0 CA A:CYS476 4.4 35.5 1.0 O A:HOH701 4.4 42.3 1.0 N A:ASN461 4.5 41.6 1.0 O A:HOH718 4.6 40.6 1.0 C A:ASN461 4.7 39.1 1.0 N A:GLY459 4.8 39.3 1.0 CA A:CYS473 4.8 37.7 1.0 N A:ALA458 4.9 39.9 1.0 N A:ASP462 4.9 41.1 1.0 C A:CYS457 4.9 41.0 1.0 O A:HOH707 5.0 39.0 1.0 CB A:ALA475 5.0 41.6 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:32.8 occ:1.00 SG B:CYS476 2.3 37.0 1.0 SG B:CYS463 2.3 34.3 1.0 SG B:CYS473 2.3 36.8 1.0 SG B:CYS457 2.3 33.4 1.0 CB B:CYS463 3.0 37.8 1.0 CB B:CYS457 3.3 34.3 1.0 CB B:CYS473 3.4 36.3 1.0 CB B:CYS476 3.4 38.2 1.0 O B:HOH713 3.7 35.1 1.0 N B:CYS463 4.1 41.9 1.0 O B:HOH702 4.1 38.8 1.0 CA B:CYS457 4.1 33.8 1.0 CA B:CYS463 4.1 39.2 1.0 N B:CYS476 4.2 36.7 1.0 CA B:ASN461 4.3 40.8 1.0 CA B:CYS476 4.4 40.1 1.0 N B:ASN461 4.6 40.1 1.0 OD1 B:ASN461 4.7 38.2 1.0 O A:HOH718 4.7 40.6 1.0 C B:ASN461 4.8 40.3 1.0 CA B:CYS473 4.8 40.5 1.0 N B:GLY459 4.9 37.2 1.0 N B:ASP462 4.9 42.9 1.0 N B:ALA458 4.9 32.5 1.0 C B:CYS457 5.0 33.7 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glucocorticoid Receptor Dna Binding Domain - Plau Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:44.0 occ:1.00 SG B:CYS424 2.3 47.4 1.0 SG B:CYS441 2.3 39.0 1.0 SG B:CYS421 2.4 43.9 1.0 SG B:CYS438 2.4 43.5 1.0 CB B:CYS441 3.2 44.2 1.0 CB B:CYS421 3.3 49.1 1.0 CB B:CYS424 3.4 46.2 1.0 CB B:CYS438 3.5 49.1 1.0 N B:CYS424 3.6 43.9 1.0 N B:CYS438 3.9 48.1 1.0 CA B:CYS424 4.0 47.8 1.0 CA B:CYS438 4.2 47.4 1.0 N B:CYS441 4.3 40.5 1.0 NH1 B:ARG470 4.3 46.4 1.0 OG B:SER440 4.3 42.9 1.0 CB B:VAL423 4.3 45.2 1.0 CA B:CYS441 4.3 40.5 1.0 C B:CYS424 4.7 48.8 1.0 C B:VAL423 4.7 46.2 1.0 CB B:ASP426 4.7 50.4 1.0 CA B:CYS421 4.8 49.2 1.0 O B:CYS438 4.8 46.9 1.0 N B:SER425 4.8 48.5 1.0 C B:CYS438 4.9 44.7 1.0 NH2 B:ARG477 4.9 41.4 1.0 CG1 B:VAL423 4.9 43.2 1.0 CA B:VAL423 4.9 45.8 1.0 N B:ASP426 4.9 49.6 1.0 N B:VAL423 5.0 45.1 1.0

W.H.Hudson, I.M.S.Vera, J.C.Nwachukwu, E.R.Weikum, A.G.Herbst, Q.Yang, D.L.Bain, K.W.Nettles, D.J.Kojetin, E.A.Ortlund. Cryptic Glucocorticoid Receptor-Binding Sites Pervade Genomic Nf-Kappa B Response Elements. Nat Commun V. 9 1337 2018.
ISSN: ESSN 2041-1723
PubMed: 29626214
DOI: 10.1038/S41467-018-03780-1