Zinc in PDB 6x6e: Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs)

The structure of Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs), PDB code: 6x6e was solved by X.Liu, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.99 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.385, 39.089, 97.371, 90, 118.62, 90
R / Rfree (%)	18.1 / 21.2

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs) (pdb code 6x6e). 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 in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs), PDB code: 6x6e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs)


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 in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:42.9 occ:1.00 SG A:CYS421 2.3 44.4 1.0 SG A:CYS441 2.3 42.1 1.0 SG A:CYS424 2.3 48.9 1.0 SG A:CYS438 2.4 47.1 1.0 CB A:CYS441 3.2 39.5 1.0 CB A:CYS421 3.3 44.7 1.0 CB A:CYS424 3.4 50.9 1.0 N A:CYS424 3.7 49.0 1.0 CB A:CYS438 3.7 55.4 1.0 N A:CYS438 4.1 48.3 1.0 CA A:CYS424 4.1 51.9 1.0 N A:CYS441 4.2 39.7 1.0 CA A:CYS441 4.3 36.4 1.0 CB A:VAL423 4.4 41.0 1.0 NH1 A:ARG470 4.4 49.2 1.0 CA A:CYS438 4.4 48.0 1.0 OG A:SER440 4.4 54.4 1.0 CB A:ASP426 4.5 74.1 1.0 C A:VAL423 4.7 58.5 1.0 C A:CYS424 4.7 54.1 1.0 CA A:CYS421 4.7 50.8 1.0 N A:SER425 4.8 51.4 1.0 N A:ASP426 4.9 51.5 1.0 NH2 A:ARG477 4.9 41.8 1.0 CA A:VAL423 4.9 48.6 1.0 O A:CYS438 4.9 41.5 1.0 N A:VAL423 5.0 50.4 1.0 CG1 A:VAL423 5.0 40.4 1.0 C A:CYS438 5.0 42.5 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs)


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 in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:42.6 occ:1.00 SG A:CYS457 2.3 41.0 1.0 SG A:CYS463 2.3 43.5 1.0 SG A:CYS473 2.4 41.4 1.0 SG A:CYS476 2.4 42.2 1.0 CB A:CYS463 3.2 39.3 1.0 CB A:CYS457 3.2 48.1 1.0 CB A:CYS473 3.3 43.1 1.0 CB A:CYS476 3.4 35.3 1.0 O B:HOH601 3.9 38.4 1.0 CA A:CYS457 4.0 53.5 1.0 N A:CYS463 4.0 44.5 1.0 N A:CYS476 4.2 35.2 1.0 CA A:CYS463 4.2 44.4 1.0 CA A:ASN461 4.3 47.2 0.9 CA A:CYS476 4.4 32.5 1.0 N A:ASN461 4.5 42.5 1.0 O A:HOH604 4.5 46.3 1.0 N A:ASP462 4.6 46.6 1.0 C A:ASN461 4.7 48.9 1.0 CA A:CYS473 4.7 42.5 1.0 O A:HOH612 4.8 50.1 1.0 N A:ALA458 4.8 44.9 1.0 N A:GLY459 4.8 48.1 1.0 C A:CYS457 4.8 48.1 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs)


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 in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:57.5 occ:1.00 SG B:CYS438 2.3 61.2 1.0 SG B:CYS421 2.4 64.5 1.0 SG B:CYS424 2.4 60.3 1.0 SG B:CYS441 2.4 65.1 1.0 CB B:CYS441 3.2 63.6 1.0 CB B:CYS421 3.2 63.9 1.0 CB B:CYS424 3.3 56.5 1.0 CB B:CYS438 3.6 64.7 1.0 N B:CYS424 3.7 57.0 1.0 N B:CYS438 3.9 70.1 1.0 CA B:CYS424 4.0 56.6 1.0 N B:CYS441 4.2 57.3 1.0 CA B:CYS441 4.3 62.7 1.0 CA B:CYS438 4.3 67.2 1.0 OG B:SER440 4.3 65.0 1.0 NH1 B:ARG470 4.4 70.2 1.0 CB B:VAL423 4.5 57.2 1.0 C B:CYS424 4.6 62.2 1.0 CB B:ASP426 4.6 68.3 1.0 C B:VAL423 4.7 56.4 1.0 CA B:CYS421 4.7 62.4 1.0 N B:SER425 4.8 66.4 1.0 N B:ASP426 4.9 63.5 1.0 NH2 B:ARG477 4.9 51.4 1.0 C B:CYS438 5.0 68.1 1.0 CA B:VAL423 5.0 57.2 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs)


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 in Complex with Methylated Precursor For A Modern Recognition Element (Methylated Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:43.6 occ:1.00 SG B:CYS473 2.3 41.9 1.0 SG B:CYS457 2.3 41.9 1.0 SG B:CYS463 2.4 43.0 1.0 SG B:CYS476 2.5 43.5 1.0 CB B:CYS463 3.2 49.0 1.0 CB B:CYS457 3.2 41.0 1.0 CB B:CYS473 3.3 41.6 1.0 CB B:CYS476 3.4 42.3 1.0 N B:CYS463 3.9 40.9 1.0 CA B:CYS457 4.0 41.2 1.0 O B:HOH604 4.1 38.8 1.0 CA B:CYS463 4.2 45.7 1.0 N B:CYS476 4.2 40.0 1.0 CA B:CYS476 4.4 43.4 1.0 CA B:ASN461 4.5 37.5 1.0 N B:ASP462 4.6 43.1 1.0 N B:ASN461 4.6 40.2 1.0 CA B:CYS473 4.7 42.4 1.0 N B:ALA458 4.7 42.9 1.0 C B:CYS457 4.8 35.5 1.0 C B:ASN461 4.8 43.7 1.0 N B:GLY459 4.9 44.0 1.0

X.Liu, E.R.Weikum, E.A.Ortlund. Structural Basis For Glucocorticoid Receptor Recognition of Both Unmodified and Methylated Binding Sites, Precursors For A Modern Recognition Element To Be Published.