Zinc in PDB 5e6d: Glucocorticoid Receptor Dna Binding Domain - ICAM1 Nf-Kb Response Element Complex

The structure of Glucocorticoid Receptor Dna Binding Domain - ICAM1 Nf-Kb Response Element Complex, PDB code: 5e6d 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)	32.66 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.059, 97.145, 104.018, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 28.4

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain - ICAM1 Nf-Kb Response Element Complex (pdb code 5e6d). 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 - ICAM1 Nf-Kb Response Element Complex, PDB code: 5e6d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - ICAM1 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 - ICAM1 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:95.3 occ:1.00 SG A:CYS424 2.2 0.8 1.0 SG A:CYS438 2.3 0.0 1.0 SG A:CYS441 2.3 0.4 1.0 SG A:CYS421 2.5 78.2 1.0 CB A:CYS424 2.9 96.9 1.0 CB A:CYS441 3.2 83.4 1.0 CB A:CYS438 3.2 94.0 1.0 N A:CYS424 3.4 88.6 1.0 CB A:CYS421 3.5 0.8 1.0 CA A:CYS424 3.7 85.9 1.0 N A:CYS438 3.7 89.4 1.0 OG A:SER440 3.9 0.6 1.0 CA A:CYS438 4.0 89.8 1.0 N A:CYS441 4.1 68.9 1.0 CA A:CYS441 4.3 87.3 1.0 C A:CYS424 4.3 96.6 1.0 CB A:VAL423 4.6 66.1 1.0 N A:SER425 4.6 0.3 1.0 C A:CYS438 4.6 82.3 1.0 C A:VAL423 4.6 0.1 1.0 O A:CYS438 4.8 89.1 1.0 N A:ASP426 4.8 0.9 1.0 C A:THR437 4.8 91.9 1.0 CB A:ASP426 4.9 91.6 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - ICAM1 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 - ICAM1 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:51.3 occ:1.00 SG A:CYS476 2.1 51.2 1.0 SG A:CYS473 2.3 62.9 1.0 SG A:CYS457 2.3 56.6 1.0 SG A:CYS463 2.3 52.7 1.0 O A:HOH706 2.7 55.9 1.0 CB A:CYS463 3.0 51.7 1.0 CB A:CYS457 3.3 54.6 1.0 CB A:CYS473 3.3 67.1 1.0 CB A:CYS476 3.4 61.0 1.0 N A:CYS463 4.0 72.3 1.0 CA A:CYS457 4.1 64.9 1.0 CA A:CYS463 4.1 60.1 1.0 CA A:ASN461 4.2 72.7 1.0 O A:HOH705 4.3 53.8 1.0 N A:CYS476 4.3 52.9 1.0 N A:ASN461 4.4 68.7 1.0 CA A:CYS476 4.4 53.2 1.0 N A:GLY459 4.6 53.5 1.0 N A:ALA458 4.7 64.5 1.0 C A:CYS457 4.7 56.1 1.0 CA A:CYS473 4.8 67.0 1.0 C A:ASN461 4.8 73.3 1.0 CA A:GLY459 4.9 67.0 1.0 N A:ASP462 5.0 68.5 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - ICAM1 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 - ICAM1 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:54.2 occ:1.00 SG B:CYS476 2.2 62.0 1.0 SG B:CYS457 2.2 55.0 1.0 SG B:CYS463 2.3 55.1 1.0 SG B:CYS473 2.3 65.5 1.0 CB B:CYS463 2.9 56.4 1.0 CB B:CYS473 3.3 57.5 1.0 CB B:CYS476 3.3 65.2 1.0 CB B:CYS457 3.4 63.7 1.0 O B:HOH709 3.7 58.9 1.0 N B:CYS463 3.9 62.4 1.0 CA B:CYS463 4.0 60.7 1.0 CA B:CYS457 4.2 49.3 1.0 N B:CYS476 4.3 55.4 1.0 CA B:ASN461 4.4 49.0 1.0 CA B:CYS476 4.4 67.5 1.0 N B:ASN461 4.5 53.8 1.0 C B:ASN461 4.6 63.3 1.0 CA B:CYS473 4.8 68.1 1.0 N B:GLY459 4.8 56.8 1.0 N B:ALA458 4.9 53.8 1.0 N B:ASP462 4.9 58.4 1.0 CA B:GLY459 5.0 47.5 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - ICAM1 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 - ICAM1 Nf-Kb Response Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:89.9 occ:1.00 SG B:CYS424 2.2 88.8 1.0 SG B:CYS441 2.2 96.6 1.0 SG B:CYS421 2.2 93.0 1.0 SG B:CYS438 2.4 97.3 1.0 CB B:CYS441 2.7 98.7 1.0 CB B:CYS424 3.1 87.0 1.0 CB B:CYS421 3.4 99.6 1.0 N B:CYS424 3.4 87.6 1.0 CB B:CYS438 3.5 0.7 1.0 CA B:CYS424 3.8 87.5 1.0 N B:CYS438 3.8 99.9 1.0 CA B:CYS441 3.9 99.9 1.0 N B:CYS441 4.1 84.7 1.0 OG1 B:THR437 4.2 0.6 1.0 CA B:CYS438 4.2 99.5 1.0 CB B:VAL423 4.3 89.9 1.0 CB B:THR437 4.4 0.3 1.0 C B:VAL423 4.5 95.9 1.0 C B:CYS424 4.5 0.1 1.0 NH1 B:ARG470 4.6 92.5 1.0 CG1 B:VAL423 4.7 97.8 1.0 N B:SER425 4.7 0.7 1.0 NH2 B:ARG477 4.7 80.3 1.0 OG B:SER440 4.8 0.7 1.0 CA B:CYS421 4.8 0.3 1.0 CA B:VAL423 4.8 90.7 1.0 C B:CYS438 4.9 0.4 1.0 C B:THR437 4.9 0.2 1.0 N B:ASP426 4.9 90.0 1.0 N B:VAL423 4.9 97.3 1.0 CB B:ASP426 5.0 100.0 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