Zinc in PDB 6x6d: Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (Pre-Gbs)

The structure of Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (Pre-Gbs), PDB code: 6x6d 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)	39.46 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.426, 39, 96.791, 90, 118.71, 90
R / Rfree (%)	19 / 21.1

The structure of Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (Pre-Gbs) also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (Pre-Gbs) (pdb code 6x6d). 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 Unmodified Precursor For A Modern Recognition Element (Pre-Gbs), PDB code: 6x6d:
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 Unmodified Precursor For A Modern Recognition Element (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 Unmodified Precursor For A Modern Recognition Element (Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.3 occ:1.00 SG A:CYS424 2.3 49.8 1.0 SG A:CYS421 2.3 43.8 1.0 SG A:CYS438 2.3 47.5 1.0 SG A:CYS441 2.4 48.1 1.0 HB3 A:CYS424 2.9 45.5 1.0 H A:CYS424 2.9 38.7 1.0 HB2 A:CYS441 3.1 41.4 1.0 CB A:CYS424 3.1 47.6 1.0 HB3 A:CYS421 3.2 43.0 1.0 H A:CYS438 3.2 48.5 1.0 CB A:CYS421 3.2 47.5 1.0 HB2 A:CYS421 3.3 43.0 1.0 CB A:CYS441 3.4 44.4 1.0 HB A:VAL423 3.4 53.8 1.0 HB3 A:CYS438 3.5 51.5 1.0 N A:CYS424 3.5 41.9 1.0 CB A:CYS438 3.6 50.9 1.0 H A:CYS441 3.8 39.1 1.0 HH11 A:ARG470 3.8 42.0 1.0 CA A:CYS424 3.9 46.0 1.0 HB2 A:CYS424 3.9 45.5 1.0 HB3 A:ASP426 3.9 68.3 1.0 HB3 A:CYS441 3.9 41.4 1.0 N A:CYS438 4.0 49.9 1.0 HH21 A:ARG477 4.1 41.6 0.6 HG A:SER440 4.1 45.3 1.0 H A:SER425 4.2 46.0 0.0 H A:ASP426 4.2 53.6 1.0 HB2 A:ASP426 4.2 68.3 1.0 HB2 A:CYS438 4.3 51.5 1.0 CB A:VAL423 4.3 45.0 1.0 CA A:CYS438 4.4 51.2 1.0 N A:CYS441 4.4 43.4 1.0 H A:VAL423 4.4 59.9 1.0 OG A:SER440 4.4 46.9 1.0 HB A:THR437 4.4 48.9 1.0 NH1 A:ARG470 4.4 59.0 1.0 HG12 A:VAL423 4.4 57.3 1.0 CA A:CYS441 4.5 42.6 1.0 C A:CYS424 4.5 50.0 1.0 HH12 A:ARG470 4.5 42.0 1.0 CB A:ASP426 4.5 66.4 1.0 HD2 A:ARG470 4.5 44.2 1.0 N A:SER425 4.6 50.9 1.0 C A:VAL423 4.6 49.1 1.0 CA A:CYS421 4.7 49.0 1.0 HA A:CYS424 4.7 42.5 1.0 HA A:THR437 4.7 45.5 1.0 CG1 A:VAL423 4.8 46.1 1.0 HG11 A:VAL423 4.8 57.3 1.0 N A:ASP426 4.8 58.3 1.0 HA A:CYS441 4.9 38.2 1.0 CA A:VAL423 4.9 45.8 1.0 HE A:ARG477 4.9 36.2 1.0 NH2 A:ARG477 4.9 41.0 0.9 N A:VAL423 4.9 51.3 1.0 C A:CYS438 5.0 46.9 1.0 HA A:CYS421 5.0 44.4 1.0 HD3 A:ARG470 5.0 44.2 1.0

Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (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 Unmodified Precursor For A Modern Recognition Element (Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:44.8 occ:1.00 SG A:CYS473 2.2 49.2 1.0 SG A:CYS463 2.3 51.1 1.0 SG A:CYS476 2.4 42.6 1.0 SG A:CYS457 2.4 51.3 1.0 HB2 A:CYS463 2.8 42.8 1.0 HB2 A:CYS457 2.9 48.0 1.0 HB2 A:CYS476 3.1 35.3 1.0 CB A:CYS463 3.2 46.4 1.0 CB A:CYS457 3.2 50.9 1.0 CB A:CYS473 3.3 46.3 1.0 H A:CYS463 3.3 45.1 1.0 CB A:CYS476 3.4 38.5 1.0 HB2 A:CYS473 3.4 41.5 1.0 HB3 A:CYS473 3.4 41.5 1.0 HA A:CYS457 3.5 45.5 1.0 HA A:ASN461 3.7 42.8 1.0 H A:CYS476 3.8 36.7 1.0 HB3 A:CYS463 3.8 42.8 1.0 CA A:CYS457 3.9 51.3 1.0 H A:ASN461 3.9 48.5 1.0 HB3 A:CYS457 4.0 48.0 1.0 N A:CYS463 4.0 46.7 1.0 H A:GLY459 4.0 43.3 1.0 HB3 A:CYS476 4.0 35.3 1.0 HB3 A:ALA475 4.1 36.8 1.0 CA A:CYS463 4.2 46.5 1.0 N A:CYS476 4.3 38.4 1.0 H A:ALA458 4.3 43.6 1.0 H A:ASP462 4.4 48.3 1.0 CA A:ASN461 4.4 48.5 1.0 CA A:CYS476 4.4 37.4 1.0 N A:ASN461 4.5 51.8 1.0 HA A:CYS463 4.7 42.4 1.0 N A:ASP462 4.7 49.0 1.0 CA A:CYS473 4.7 46.9 1.0 N A:ALA458 4.7 53.7 1.0 HA A:CYS476 4.7 35.4 1.0 C A:CYS457 4.7 51.7 1.0 C A:ASN461 4.8 47.8 1.0 N A:GLY459 4.8 56.4 1.0 HA A:CYS473 4.8 42.9 1.0 HA3 A:GLY459 4.9 47.5 1.0 HH21 A:ARG479 5.0 56.5 1.0

Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (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 Unmodified Precursor For A Modern Recognition Element (Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:62.5 occ:1.00 SG B:CYS441 2.3 67.7 1.0 SG B:CYS424 2.3 68.6 1.0 SG B:CYS438 2.4 71.7 1.0 SG B:CYS421 2.5 76.0 1.0 HB2 B:CYS441 2.9 63.0 1.0 HB3 B:CYS424 3.1 62.5 1.0 H B:CYS438 3.1 67.5 1.0 H B:CYS424 3.2 61.8 1.0 CB B:CYS441 3.2 65.2 1.0 HB3 B:CYS421 3.2 72.4 1.0 CB B:CYS424 3.3 65.8 1.0 CB B:CYS421 3.3 77.1 1.0 HB3 B:CYS438 3.4 71.5 1.0 HB2 B:CYS421 3.4 72.4 1.0 HB B:VAL423 3.5 68.5 1.0 CB B:CYS438 3.5 76.2 1.0 H B:CYS441 3.7 58.5 1.0 N B:CYS424 3.7 66.5 1.0 HH11 B:ARG470 3.7 60.0 1.0 HB3 B:CYS441 3.8 63.0 1.0 N B:CYS438 3.9 74.9 1.0 HB3 B:ASP426 4.0 79.5 1.0 CA B:CYS424 4.1 65.7 1.0 HB2 B:CYS424 4.1 62.5 1.0 HG B:SER440 4.1 70.3 1.0 H B:ASP426 4.2 71.9 1.0 HH21 B:ARG477 4.2 56.4 1.0 NH1 B:ARG470 4.3 70.4 1.0 N B:CYS441 4.3 61.2 1.0 HB2 B:CYS438 4.3 71.5 1.0 HH12 B:ARG470 4.3 60.0 1.0 CA B:CYS441 4.3 64.0 1.0 CA B:CYS438 4.3 76.2 1.0 HB B:THR437 4.4 69.9 1.0 H B:VAL423 4.4 69.1 1.0 CB B:VAL423 4.4 68.5 1.0 HB2 B:ASP426 4.5 79.5 1.0 HD2 B:ARG470 4.5 56.6 1.0 OG B:SER440 4.5 65.0 1.0 H B:SER425 4.5 64.7 1.0 HG12 B:VAL423 4.7 68.1 1.0 HA B:CYS441 4.7 61.1 1.0 HA B:THR437 4.7 68.3 1.0 CB B:ASP426 4.7 79.2 1.0 C B:CYS424 4.7 66.8 1.0 C B:VAL423 4.7 65.7 1.0 CA B:CYS421 4.8 77.2 1.0 N B:SER425 4.8 69.4 1.0 HA B:CYS424 4.9 62.0 1.0 N B:ASP426 4.9 74.6 1.0 CG1 B:VAL423 5.0 65.3 1.0 CA B:VAL423 5.0 68.5 1.0 HG11 B:VAL423 5.0 68.1 1.0 HE B:ARG477 5.0 52.2 1.0 C B:CYS438 5.0 75.9 1.0 NH2 B:ARG477 5.0 56.8 1.0

Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Unmodified Precursor For A Modern Recognition Element (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 Unmodified Precursor For A Modern Recognition Element (Pre-Gbs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:47.5 occ:1.00 SG B:CYS473 2.2 48.0 1.0 SG B:CYS457 2.3 47.2 1.0 SG B:CYS463 2.3 51.0 1.0 SG B:CYS476 2.4 50.3 1.0 HB2 B:CYS463 2.8 49.5 1.0 HB2 B:CYS457 3.0 41.5 1.0 CB B:CYS463 3.1 50.8 1.0 CB B:CYS457 3.2 45.4 1.0 HB2 B:CYS476 3.2 47.1 1.0 CB B:CYS473 3.3 51.1 1.0 HB2 B:CYS473 3.3 45.7 1.0 H B:CYS463 3.4 48.4 1.0 HB3 B:CYS473 3.4 45.7 1.0 CB B:CYS476 3.5 51.3 1.0 HA B:CYS457 3.6 38.2 1.0 H B:CYS476 3.7 45.0 1.0 HA B:ASN461 3.8 42.5 1.0 HB3 B:CYS463 3.8 49.5 1.0 O B:HOH602 3.9 41.0 1.0 CA B:CYS457 3.9 45.9 1.0 HB3 B:CYS457 4.0 41.5 1.0 N B:CYS463 4.0 49.5 1.0 H B:GLY459 4.0 40.6 1.0 H B:ASN461 4.1 41.1 1.0 H B:ASP462 4.1 51.1 1.0 HB3 B:CYS476 4.1 47.1 1.0 HB3 B:ALA475 4.2 47.2 1.0 CA B:CYS463 4.2 50.2 1.0 H B:ALA458 4.2 40.1 1.0 N B:CYS476 4.3 47.1 1.0 CA B:CYS476 4.5 48.7 1.0 CA B:ASN461 4.5 45.0 1.0 N B:ASP462 4.5 51.3 1.0 N B:ASN461 4.6 44.2 1.0 H B:ARG460 4.6 39.6 1.0 HA B:CYS463 4.6 49.4 1.0 CA B:CYS473 4.7 51.5 1.0 N B:ALA458 4.7 46.0 1.0 C B:CYS457 4.8 46.0 1.0 HA B:CYS476 4.8 44.0 1.0 HA B:CYS473 4.8 47.2 1.0 N B:GLY459 4.8 45.5 1.0 C B:ASN461 4.8 47.8 1.0 HH21 B:ARG479 4.9 74.1 1.0 HA3 B:GLY459 4.9 41.2 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.