Zinc in PDB 5e6c: Glucocorticoid Receptor Dna Binding Domain - CCL2 Nf-Kb Response Element Complex

The structure of Glucocorticoid Receptor Dna Binding Domain - CCL2 Nf-Kb Response Element Complex, PDB code: 5e6c 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)	35.52 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.083, 97.407, 103.852, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27.1

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain - CCL2 Nf-Kb Response Element Complex (pdb code 5e6c). 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 - CCL2 Nf-Kb Response Element Complex, PDB code: 5e6c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - CCL2 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 - CCL2 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:49.9 occ:1.00 SG A:CYS421 2.1 39.4 1.0 SG A:CYS441 2.2 45.7 1.0 SG A:CYS424 2.3 55.4 1.0 SG A:CYS438 2.3 55.4 1.0 CB A:CYS441 3.1 42.6 1.0 CB A:CYS421 3.1 54.3 1.0 CB A:CYS424 3.4 49.7 1.0 CB A:CYS438 3.6 52.4 1.0 N A:CYS424 3.6 53.7 1.0 N A:CYS438 4.0 51.6 1.0 CA A:CYS424 4.0 50.2 1.0 N A:CYS441 4.1 35.9 1.0 OG A:SER440 4.2 51.2 1.0 CA A:CYS441 4.2 45.0 1.0 CA A:CYS438 4.3 51.3 1.0 NH1 A:ARG470 4.5 49.1 1.0 CB A:ASP426 4.5 54.4 1.0 CB A:VAL423 4.5 42.4 1.0 CA A:CYS421 4.5 53.8 1.0 C A:CYS424 4.6 54.8 1.0 C A:VAL423 4.7 48.1 1.0 NH2 A:ARG477 4.7 44.6 1.0 N A:SER425 4.9 58.9 1.0 N A:ASP426 4.9 57.0 1.0 O A:CYS438 4.9 48.7 1.0 C A:CYS438 4.9 50.3 1.0 CA A:VAL423 5.0 49.0 1.0 CD A:ARG470 5.0 48.2 1.0 N A:VAL423 5.0 46.5 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - CCL2 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 - CCL2 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:33.5 occ:1.00 SG A:CYS476 2.2 30.9 1.0 SG A:CYS473 2.3 36.3 1.0 SG A:CYS457 2.3 34.6 1.0 SG A:CYS463 2.4 30.9 1.0 CB A:CYS463 3.2 33.7 1.0 CB A:CYS473 3.4 35.4 1.0 CB A:CYS476 3.4 32.4 1.0 CB A:CYS457 3.4 34.7 1.0 O A:HOH705 3.9 30.4 1.0 N A:CYS463 4.0 34.8 1.0 CA A:CYS457 4.1 37.2 1.0 CA A:CYS463 4.2 37.6 1.0 N A:CYS476 4.2 30.5 1.0 CA A:ASN461 4.3 38.3 1.0 CA A:CYS476 4.4 30.5 1.0 N A:ASN461 4.4 39.0 1.0 N A:ASP462 4.6 36.0 1.0 N A:ALA458 4.7 36.1 1.0 C A:ASN461 4.7 38.7 1.0 O A:HOH706 4.8 36.2 1.0 CA A:CYS473 4.8 35.9 1.0 C A:CYS457 4.8 39.4 1.0 N A:GLY459 4.8 34.9 1.0 CB A:ALA475 5.0 26.9 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - CCL2 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 - CCL2 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:34.3 occ:1.00 SG B:CYS457 2.3 31.2 1.0 SG B:CYS473 2.3 33.8 1.0 SG B:CYS476 2.3 31.5 1.0 SG B:CYS463 2.3 32.4 1.0 CB B:CYS463 3.2 32.4 1.0 CB B:CYS457 3.3 29.5 1.0 CB B:CYS476 3.3 30.5 1.0 CB B:CYS473 3.4 39.4 1.0 N B:CYS463 4.0 37.1 1.0 CA B:CYS457 4.0 33.9 1.0 O B:HOH702 4.1 31.5 1.0 N B:CYS476 4.1 33.0 1.0 O B:HOH706 4.1 32.8 1.0 CA B:CYS463 4.2 36.5 1.0 CA B:CYS476 4.3 30.0 1.0 CA B:ASN461 4.5 33.7 1.0 N B:ASN461 4.6 27.8 1.0 N B:ASP462 4.6 31.2 1.0 N B:ALA458 4.7 30.4 1.0 CA B:CYS473 4.8 36.2 1.0 C B:CYS457 4.8 32.6 1.0 C B:ASN461 4.9 32.6 1.0 N B:GLY459 4.9 27.3 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - CCL2 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 - CCL2 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:49.0 occ:1.00 SG B:CYS424 2.2 48.9 1.0 SG B:CYS441 2.3 46.8 1.0 SG B:CYS438 2.3 47.0 1.0 SG B:CYS421 2.3 48.2 1.0 CB B:CYS441 3.1 48.7 1.0 CB B:CYS421 3.2 55.5 1.0 CB B:CYS424 3.4 48.1 1.0 CB B:CYS438 3.5 52.1 1.0 N B:CYS424 3.7 48.0 1.0 N B:CYS438 3.9 52.2 1.0 CA B:CYS424 4.1 46.5 1.0 NH1 B:ARG470 4.2 56.7 1.0 N B:CYS441 4.3 43.7 1.0 CA B:CYS438 4.3 48.4 1.0 CA B:CYS441 4.3 46.3 1.0 CB B:VAL423 4.4 45.4 1.0 CB B:ASP426 4.6 51.5 1.0 C B:VAL423 4.7 49.8 1.0 CA B:CYS421 4.7 54.8 1.0 C B:CYS424 4.7 53.1 1.0 CD B:ARG470 4.8 47.2 1.0 NH2 B:ARG477 4.9 41.4 1.0 N B:ASP426 4.9 51.8 1.0 C B:CYS438 4.9 49.6 1.0 OG B:SER440 4.9 55.5 1.0 CG1 B:VAL423 4.9 47.2 1.0 N B:SER425 4.9 55.0 1.0 CA B:VAL423 4.9 44.8 1.0 N B:VAL423 5.0 46.5 1.0 O B:CYS438 5.0 49.2 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