Zinc in PDB 5e6b: Glucocorticoid Receptor Dna Binding Domain - Relb Nf-Kb Response Element Complex

The structure of Glucocorticoid Receptor Dna Binding Domain - Relb Nf-Kb Response Element Complex, PDB code: 5e6b 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)	32.46 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.185, 97.045, 103.329, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.7

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain - Relb Nf-Kb Response Element Complex (pdb code 5e6b). 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 - Relb Nf-Kb Response Element Complex, PDB code: 5e6b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Relb 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 - Relb Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:32.4 occ:1.00 SG A:CYS424 2.3 33.0 1.0 SG A:CYS441 2.4 33.0 1.0 SG A:CYS421 2.4 33.6 1.0 SG A:CYS438 2.4 37.0 1.0 CB A:CYS441 3.2 28.7 1.0 CB A:CYS421 3.3 35.5 1.0 CB A:CYS424 3.4 32.9 1.0 CB A:CYS438 3.5 34.9 1.0 N A:CYS424 3.6 34.0 1.0 N A:CYS438 3.9 33.2 1.0 CA A:CYS424 4.0 36.9 1.0 CA A:CYS438 4.3 38.3 1.0 N A:CYS441 4.3 32.6 1.0 NH1 A:ARG470 4.3 34.5 1.0 CA A:CYS441 4.3 36.8 1.0 CB A:VAL423 4.4 35.5 1.0 OG A:SER440 4.5 37.1 1.0 C A:CYS424 4.7 36.6 1.0 C A:VAL423 4.7 36.8 1.0 CB A:ASP426 4.7 42.2 1.0 CA A:CYS421 4.7 40.7 1.0 O A:CYS438 4.8 35.1 1.0 N A:SER425 4.8 37.4 1.0 C A:CYS438 4.9 36.0 1.0 NH2 A:ARG477 4.9 29.6 1.0 CG1 A:VAL423 4.9 30.3 1.0 CA A:VAL423 4.9 32.5 1.0 N A:ASP426 4.9 40.8 1.0 C A:THR437 5.0 36.6 1.0 N A:VAL423 5.0 34.6 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Relb 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 - Relb Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:28.4 occ:1.00 SG A:CYS476 2.3 27.0 1.0 SG A:CYS473 2.3 31.9 1.0 SG A:CYS457 2.3 30.9 1.0 SG A:CYS463 2.4 29.1 1.0 CB A:CYS463 3.0 26.3 1.0 CB A:CYS473 3.3 29.7 1.0 CB A:CYS476 3.4 30.4 1.0 CB A:CYS457 3.4 34.0 1.0 O A:HOH709 3.7 31.8 1.0 N A:CYS463 4.1 33.5 1.0 CA A:CYS457 4.2 36.9 1.0 CA A:CYS463 4.2 30.8 1.0 N A:CYS476 4.2 25.6 1.0 CA A:ASN461 4.2 32.2 1.0 CA A:CYS476 4.4 27.9 1.0 N A:ASN461 4.5 31.3 1.0 O A:HOH732 4.5 38.1 1.0 N A:GLY459 4.7 33.8 1.0 CA A:CYS473 4.7 28.5 1.0 C A:ASN461 4.8 33.2 1.0 N A:ALA458 4.8 31.4 1.0 O A:HOH702 4.8 35.9 1.0 C A:CYS457 4.9 35.2 1.0 O A:HOH712 4.9 36.1 1.0 N A:ASP462 5.0 30.8 1.0 CA A:GLY459 5.0 34.6 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Relb 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 - Relb Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:28.1 occ:1.00 SG B:CYS476 2.3 29.2 1.0 SG B:CYS473 2.3 32.0 1.0 SG B:CYS457 2.4 29.5 1.0 SG B:CYS463 2.4 28.5 1.0 CB B:CYS463 3.0 31.2 1.0 CB B:CYS473 3.3 31.8 1.0 CB B:CYS476 3.3 32.9 1.0 CB B:CYS457 3.4 27.5 1.0 O B:HOH712 3.8 29.6 1.0 N B:CYS463 4.0 37.2 1.0 CA B:CYS463 4.1 35.3 1.0 N B:CYS476 4.2 32.7 1.0 O B:HOH702 4.2 34.4 1.0 CA B:CYS457 4.2 31.5 1.0 CA B:ASN461 4.3 32.0 1.0 CA B:CYS476 4.4 32.8 1.0 N B:ASN461 4.6 32.3 1.0 O A:HOH732 4.7 38.1 1.0 CA B:CYS473 4.7 35.4 1.0 C B:ASN461 4.8 36.1 1.0 N B:GLY459 4.8 32.0 1.0 OD1 B:ASN461 4.8 33.8 1.0 N B:ALA458 4.9 29.5 1.0 N B:ASP462 4.9 37.1 1.0 C B:CYS457 4.9 32.3 1.0 O B:HOH709 5.0 37.2 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - Relb 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 - Relb Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:43.9 occ:1.00 SG B:CYS424 2.2 41.2 1.0 SG B:CYS441 2.3 43.3 1.0 SG B:CYS421 2.4 46.6 1.0 SG B:CYS438 2.4 46.6 1.0 CB B:CYS421 3.2 46.0 1.0 CB B:CYS441 3.3 38.4 1.0 CB B:CYS424 3.3 42.0 1.0 N B:CYS424 3.6 42.6 1.0 CB B:CYS438 3.6 44.7 1.0 N B:CYS438 4.0 48.3 1.0 CA B:CYS424 4.0 44.2 1.0 NH1 B:ARG470 4.3 41.9 1.0 CA B:CYS438 4.3 48.6 1.0 CB B:VAL423 4.3 45.6 1.0 N B:CYS441 4.4 39.9 1.0 CA B:CYS441 4.4 43.2 1.0 OG B:SER440 4.4 43.7 1.0 C B:CYS424 4.6 47.0 1.0 CB B:ASP426 4.6 50.8 1.0 C B:VAL423 4.7 48.3 1.0 CA B:CYS421 4.7 52.7 1.0 N B:SER425 4.7 48.2 1.0 N B:ASP426 4.8 54.7 1.0 O B:CYS438 4.8 44.1 1.0 CA B:VAL423 4.9 46.1 1.0 C B:CYS438 4.9 43.9 1.0 CG1 B:VAL423 4.9 44.2 1.0 NH2 B:ARG477 5.0 41.3 1.0 N B:VAL423 5.0 46.6 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