Zinc in PDB 5va7: Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition Element Complex

The structure of Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition Element Complex, PDB code: 5va7 was solved by E.R.Weikum, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.79 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.143, 96.855, 104.554, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.7

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition Element Complex (pdb code 5va7). 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 - IL11 Ap-1 Recognition Element Complex, PDB code: 5va7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition 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 - IL11 Ap-1 Recognition Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:36.8 occ:1.00 SG A:CYS421 2.2 36.4 1.0 O A:HOH702 2.3 97.7 1.0 SG A:CYS424 2.3 39.8 1.0 SG A:CYS441 2.3 34.9 1.0 SG A:CYS438 2.3 42.9 1.0 CB A:CYS441 3.2 37.4 1.0 CB A:CYS421 3.2 40.5 1.0 CB A:CYS424 3.5 41.7 1.0 CB A:CYS438 3.6 41.7 1.0 N A:CYS424 3.7 38.8 1.0 N A:CYS438 4.0 38.2 1.0 CA A:CYS424 4.1 41.4 1.0 CA A:CYS438 4.3 41.3 1.0 N A:CYS441 4.3 36.8 1.0 CA A:CYS441 4.3 39.8 1.0 NH1 A:ARG470 4.4 44.0 1.0 CB A:VAL423 4.4 36.8 1.0 C A:VAL423 4.6 40.1 1.0 CB A:ASP426 4.7 45.5 1.0 CA A:CYS421 4.7 41.0 1.0 C A:CYS424 4.7 41.2 1.0 OG A:SER440 4.8 45.2 1.0 O A:CYS438 4.9 39.7 1.0 N A:SER425 4.9 39.4 1.0 CA A:VAL423 4.9 38.2 1.0 N A:VAL423 4.9 35.4 1.0 C A:CYS438 4.9 43.2 1.0 NH2 A:ARG477 4.9 36.3 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition 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 - IL11 Ap-1 Recognition Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:33.3 occ:1.00 SG A:CYS473 2.3 34.2 1.0 SG A:CYS457 2.3 31.5 1.0 SG A:CYS463 2.3 31.9 1.0 SG A:CYS476 2.4 34.0 1.0 CB A:CYS463 3.1 33.4 1.0 CB A:CYS457 3.2 35.4 1.0 CB A:CYS473 3.3 32.4 1.0 CB A:CYS476 3.4 30.5 1.0 O A:HOH707 3.9 34.6 1.0 N A:CYS463 4.0 36.7 1.0 CA A:CYS457 4.0 37.8 1.0 CA A:CYS463 4.1 35.8 1.0 N A:CYS476 4.2 29.5 1.0 CA A:CYS476 4.4 28.8 1.0 CA A:ASN461 4.4 38.6 1.0 O A:HOH721 4.4 40.2 1.0 N A:ASN461 4.5 37.2 1.0 O A:HOH710 4.6 38.0 1.0 N A:ALA458 4.6 37.4 1.0 CA A:CYS473 4.7 35.6 1.0 C A:CYS457 4.7 38.5 1.0 N A:GLY459 4.7 36.1 1.0 N A:ASP462 4.7 36.0 1.0 O A:HOH714 4.8 37.8 1.0 C A:ASN461 4.9 36.2 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition 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 - IL11 Ap-1 Recognition Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:34.8 occ:1.00 SG B:CYS476 2.3 35.7 1.0 SG B:CYS457 2.3 31.0 1.0 SG B:CYS473 2.3 34.2 1.0 SG B:CYS463 2.4 35.0 1.0 CB B:CYS463 3.3 32.7 1.0 CB B:CYS457 3.3 33.0 1.0 CB B:CYS473 3.3 37.0 1.0 CB B:CYS476 3.4 34.0 1.0 N B:CYS463 4.0 36.2 1.0 CA B:CYS457 4.0 34.4 1.0 O B:HOH704 4.0 33.6 1.0 CA B:CYS463 4.2 36.8 1.0 N B:CYS476 4.3 36.5 1.0 CA B:CYS476 4.4 34.7 1.0 N B:ASP462 4.5 35.4 1.0 CA B:ASN461 4.5 33.9 1.0 N B:ASN461 4.6 32.0 1.0 N B:ALA458 4.7 32.2 1.0 CA B:CYS473 4.8 38.0 1.0 C B:CYS457 4.8 35.8 1.0 C B:ASN461 4.8 36.7 1.0 N B:GLY459 4.9 31.2 1.0 O B:HOH713 4.9 36.0 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL11 Ap-1 Recognition 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 - IL11 Ap-1 Recognition Element Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:46.3 occ:1.00 SG B:CYS421 2.2 46.0 1.0 SG B:CYS441 2.3 43.8 1.0 SG B:CYS424 2.4 48.6 1.0 SG B:CYS438 2.4 51.7 1.0 CB B:CYS421 3.1 52.0 1.0 CB B:CYS441 3.2 45.4 1.0 CB B:CYS424 3.4 47.2 1.0 CB B:CYS438 3.6 51.1 1.0 N B:CYS424 3.7 46.4 1.0 N B:CYS438 3.9 50.5 1.0 CA B:CYS424 4.1 47.0 1.0 N B:CYS441 4.2 37.6 1.0 CA B:CYS441 4.3 42.4 1.0 NH1 B:ARG470 4.3 48.2 1.0 CA B:CYS438 4.3 52.4 1.0 CB B:VAL423 4.4 46.8 1.0 OG B:SER440 4.6 49.1 1.0 CA B:CYS421 4.6 53.5 1.0 CB B:ASP426 4.6 58.5 1.0 C B:CYS424 4.7 51.0 1.0 C B:VAL423 4.7 49.5 1.0 N B:SER425 4.9 53.2 1.0 CG1 B:VAL423 4.9 46.0 1.0 CA B:VAL423 4.9 49.9 1.0 C B:CYS438 5.0 51.7 1.0 N B:ASP426 5.0 54.3 1.0 N B:VAL423 5.0 47.6 1.0

E.R.Weikum, I.M.S.De Vera, J.C.Nwachukwu, W.H.Hudson, K.W.Nettles, D.J.Kojetin, E.A.Ortlund. Tethering Not Required: the Glucocorticoid Receptor Binds Directly to Activator Protein-1 Recognition Motifs to Repress Inflammatory Genes. Nucleic Acids Res. V. 45 8596 2017.
ISSN: ESSN 1362-4962
PubMed: 28591827
DOI: 10.1093/NAR/GKX509