Zinc in PDB 5cc1: S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex

The structure of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex, PDB code: 5cc1 was solved by W.H.Hudson, E.A.Weikum, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.41 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.721, 39.122, 132.099, 90.00, 101.10, 90.00
R / Rfree (%)	24.5 / 27.9

The binding sites of Zinc atom in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex (pdb code 5cc1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex, PDB code: 5cc1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:52.1 occ:1.00 SG A:CYS421 2.2 48.2 1.0 SG A:CYS424 2.3 56.2 1.0 SG A:CYS438 2.4 53.8 1.0 SG A:CYS441 2.4 53.6 1.0 CB A:CYS421 3.2 52.1 1.0 CB A:CYS441 3.3 46.0 1.0 CB A:CYS438 3.4 54.8 1.0 CB A:CYS424 3.5 53.0 1.0 N A:CYS424 3.5 53.2 1.0 N A:CYS438 3.9 56.0 1.0 CA A:CYS424 4.0 54.7 1.0 CA A:CYS438 4.2 55.7 1.0 NH1 A:ARG470 4.3 52.1 1.0 CB A:VAL423 4.4 53.5 1.0 N A:CYS441 4.4 49.6 1.0 CA A:CYS441 4.5 48.5 1.0 CB A:ASP426 4.6 59.7 1.0 C A:VAL423 4.6 58.4 1.0 CA A:CYS421 4.6 53.0 1.0 OG A:SER440 4.7 51.4 1.0 C A:CYS424 4.7 59.0 1.0 N A:GLY425 4.8 60.2 1.0 CA A:VAL423 4.8 54.1 1.0 C A:CYS438 4.9 53.8 1.0 N A:VAL423 4.9 51.1 1.0 O A:CYS438 4.9 54.0 1.0 N A:ASP426 4.9 59.4 1.0 C A:THR437 5.0 55.8 1.0

Zinc binding site 2 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:43.1 occ:1.00 SG A:CYS457 2.2 46.0 1.0 SG A:CYS463 2.3 45.2 1.0 SG A:CYS473 2.3 42.5 1.0 SG A:CYS476 2.3 40.4 1.0 CB A:CYS463 3.2 40.7 1.0 CB A:CYS457 3.3 45.1 1.0 CB A:CYS473 3.4 42.0 1.0 CB A:CYS476 3.5 41.2 1.0 N A:CYS463 4.0 43.4 1.0 CA A:CYS457 4.0 49.3 1.0 CA A:ASN461 4.1 44.9 1.0 CA A:CYS463 4.2 44.5 1.0 N A:CYS476 4.2 41.1 1.0 N A:ASN461 4.3 47.9 1.0 CA A:CYS476 4.5 37.3 1.0 C A:ASN461 4.6 50.9 1.0 N A:ALA458 4.7 45.8 1.0 N A:GLY459 4.7 44.9 1.0 N A:ASP462 4.8 51.3 1.0 CA A:CYS473 4.8 43.8 1.0 C A:CYS457 4.8 48.7 1.0

Zinc binding site 3 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:65.8 occ:1.00 SG B:CYS424 2.2 68.1 1.0 SG B:CYS441 2.3 66.3 1.0 SG B:CYS421 2.4 68.9 1.0 SG B:CYS438 2.4 67.2 1.0 CB B:CYS424 3.2 63.0 1.0 CB B:CYS421 3.2 73.9 1.0 CB B:CYS441 3.3 68.1 1.0 CB B:CYS438 3.4 71.4 1.0 N B:CYS424 3.5 67.0 1.0 CA B:CYS424 3.8 66.5 1.0 N B:CYS438 4.0 68.9 1.0 CA B:CYS438 4.3 68.1 1.0 CB B:VAL423 4.4 64.8 1.0 N B:CYS441 4.4 62.0 1.0 CA B:CYS441 4.4 63.7 1.0 CB B:ASP426 4.5 73.5 1.0 C B:CYS424 4.5 69.9 1.0 OG B:SER440 4.6 67.8 1.0 NH1 B:ARG470 4.6 65.6 1.0 C B:VAL423 4.6 68.5 1.0 N B:GLY425 4.6 70.5 1.0 CA B:CYS421 4.7 74.9 1.0 N B:ASP426 4.7 76.4 1.0 C B:CYS438 4.9 67.2 1.0 CA B:VAL423 4.9 65.5 1.0 O B:CYS438 4.9 69.7 1.0 CG1 B:VAL423 4.9 63.9 1.0 N B:VAL423 5.0 68.3 1.0

Zinc binding site 4 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:45.8 occ:1.00 SG B:CYS457 2.3 47.3 1.0 SG B:CYS463 2.3 49.6 1.0 SG B:CYS473 2.3 45.8 1.0 SG B:CYS476 2.3 46.7 1.0 CB B:CYS463 3.1 49.1 1.0 CB B:CYS457 3.2 44.8 1.0 CB B:CYS473 3.2 42.7 1.0 CB B:CYS476 3.4 48.3 1.0 CA B:CYS457 3.9 42.7 1.0 N B:CYS463 4.0 52.0 1.0 CA B:CYS463 4.2 48.3 1.0 N B:CYS476 4.2 46.7 1.0 CA B:CYS476 4.4 47.6 1.0 CA B:ASN461 4.6 46.4 1.0 CA B:CYS473 4.6 48.1 1.0 N B:ASN461 4.7 44.7 1.0 N B:ALA458 4.7 40.9 1.0 C B:CYS457 4.8 45.2 1.0 N B:ASP462 4.8 52.6 1.0 N B:GLY459 4.8 44.9 1.0 C B:ASN461 4.9 49.9 1.0

Zinc binding site 5 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn601 b:52.8 occ:1.00 SG W:CYS421 2.1 46.9 1.0 SG W:CYS438 2.3 53.3 1.0 SG W:CYS424 2.4 55.7 1.0 SG W:CYS441 2.4 53.6 1.0 CB W:CYS421 3.2 52.9 1.0 CB W:CYS441 3.3 45.8 1.0 CB W:CYS438 3.4 54.1 1.0 CB W:CYS424 3.4 52.3 1.0 N W:CYS424 3.5 52.9 1.0 N W:CYS438 3.9 55.3 1.0 CA W:CYS424 4.0 54.7 1.0 CA W:CYS438 4.2 55.5 1.0 NH1 W:ARG470 4.3 51.8 1.0 CB W:VAL423 4.3 53.5 1.0 N W:CYS441 4.4 49.8 1.0 CA W:CYS441 4.5 48.3 1.0 CB W:ASP426 4.5 59.5 1.0 C W:VAL423 4.6 58.2 1.0 CA W:CYS421 4.6 52.3 1.0 OG W:SER440 4.6 51.9 1.0 C W:CYS424 4.7 58.6 1.0 N W:GLY425 4.8 60.2 1.0 CA W:VAL423 4.8 53.9 1.0 N W:VAL423 4.9 51.3 1.0 C W:CYS438 4.9 53.6 1.0 O W:CYS438 4.9 54.4 1.0 N W:ASP426 4.9 59.7 1.0

Zinc binding site 6 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn602 b:42.7 occ:1.00 SG W:CYS457 2.3 46.6 1.0 SG W:CYS463 2.3 45.0 1.0 SG W:CYS473 2.3 44.5 1.0 SG W:CYS476 2.3 40.1 1.0 CB W:CYS463 3.2 41.0 1.0 CB W:CYS457 3.3 44.8 1.0 CB W:CYS473 3.4 40.7 1.0 CB W:CYS476 3.5 41.1 1.0 N W:CYS463 4.0 43.8 1.0 CA W:CYS457 4.0 48.7 1.0 CA W:ASN461 4.2 45.6 1.0 CA W:CYS463 4.2 43.5 1.0 N W:CYS476 4.2 41.4 1.0 N W:ASN461 4.3 48.4 1.0 CA W:CYS476 4.4 37.1 1.0 C W:ASN461 4.7 49.9 1.0 N W:ALA458 4.7 46.3 1.0 N W:GLY459 4.7 44.4 1.0 CA W:CYS473 4.8 44.0 1.0 C W:CYS457 4.8 48.9 1.0 N W:ASP462 4.8 50.0 1.0

Zinc binding site 7 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn601 b:65.9 occ:1.00 SG X:CYS424 2.2 68.7 1.0 SG X:CYS441 2.3 66.3 1.0 SG X:CYS421 2.4 69.3 1.0 SG X:CYS438 2.5 67.4 1.0 CB X:CYS424 3.2 63.0 1.0 CB X:CYS421 3.3 73.9 1.0 CB X:CYS441 3.3 68.3 1.0 CB X:CYS438 3.4 71.1 1.0 N X:CYS424 3.5 68.1 1.0 CA X:CYS424 3.9 67.1 1.0 N X:CYS438 4.0 68.9 1.0 CA X:CYS438 4.3 68.0 1.0 CB X:VAL423 4.4 65.0 1.0 N X:CYS441 4.4 61.9 1.0 CA X:CYS441 4.4 63.6 1.0 CB X:ASP426 4.5 73.8 1.0 C X:CYS424 4.5 70.5 1.0 OG X:SER440 4.6 67.8 1.0 NH1 X:ARG470 4.6 65.2 1.0 C X:VAL423 4.6 69.8 1.0 N X:GLY425 4.6 71.5 1.0 N X:ASP426 4.7 76.5 1.0 CA X:CYS421 4.7 74.6 1.0 C X:CYS438 4.9 66.8 1.0 CA X:VAL423 4.9 66.5 1.0 O X:CYS438 4.9 69.4 1.0 CG1 X:VAL423 4.9 64.5 1.0 N X:VAL423 5.0 69.4 1.0

Zinc binding site 8 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn602 b:46.9 occ:1.00 SG X:CYS473 2.2 46.0 1.0 SG X:CYS457 2.2 46.1 1.0 SG X:CYS463 2.3 49.5 1.0 SG X:CYS476 2.3 46.3 1.0 CB X:CYS463 3.1 47.5 1.0 CB X:CYS457 3.2 44.3 1.0 CB X:CYS473 3.2 44.8 1.0 CB X:CYS476 3.4 48.3 1.0 N X:CYS463 3.9 52.1 1.0 CA X:CYS457 4.0 43.8 1.0 CA X:CYS463 4.1 48.7 1.0 N X:CYS476 4.2 46.7 1.0 CA X:CYS476 4.4 47.4 1.0 CA X:ASN461 4.6 46.9 1.0 CA X:CYS473 4.6 48.0 1.0 N X:ASN461 4.7 45.3 1.0 N X:ALA458 4.8 41.2 1.0 N X:ASP462 4.8 52.3 1.0 N X:GLY459 4.8 44.9 1.0 C X:CYS457 4.8 45.6 1.0 C X:ASN461 4.8 50.0 1.0

W.H.Hudson, B.R.Kossmann, I.M.De Vera, S.W.Chuo, E.R.Weikum, G.N.Eick, J.W.Thornton, I.N.Ivanov, D.J.Kojetin, E.A.Ortlund. Distal Substitutions Drive Divergent Dna Specificity Among Paralogous Transcription Factors Through Subdivision of Conformational Space. Proc.Natl.Acad.Sci.Usa V. 113 326 2016.
ISSN: ESSN 1091-6490
PubMed: 26715749
DOI: 10.1073/PNAS.1518960113