Zinc in PDB 3g6q: Gr Dna Binding Domain:FKBP5 Binding Site Complex-9

The structure of Gr Dna Binding Domain:FKBP5 Binding Site Complex-9, PDB code: 3g6q was solved by M.A.Pufall, K.R.Yamamoto, S.H.Meijsing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.042, 38.866, 95.521, 90.00, 122.07, 90.00
R / Rfree (%)	17.2 / 21.4

The binding sites of Zinc atom in the Gr Dna Binding Domain:FKBP5 Binding Site Complex-9 (pdb code 3g6q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Gr Dna Binding Domain:FKBP5 Binding Site Complex-9, PDB code: 3g6q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Gr Dna Binding Domain:FKBP5 Binding Site Complex-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gr Dna Binding Domain:FKBP5 Binding Site Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn526 b:74.0 occ:1.00 SG B:CYS440 2.4 82.2 1.0 SG B:CYS460 2.4 69.2 1.0 SG B:CYS443 2.4 69.1 1.0 SG B:CYS457 2.5 73.9 1.0 CB B:CYS440 3.2 82.9 1.0 CB B:CYS460 3.4 74.6 1.0 CB B:CYS443 3.5 92.6 1.0 CB B:CYS457 3.5 79.2 1.0 N B:CYS443 3.7 84.0 1.0 N B:CYS457 3.9 77.1 1.0 CA B:CYS443 4.1 87.5 1.0 NH1 B:ARG489 4.2 78.8 1.0 CA B:CYS457 4.3 71.8 1.0 N B:CYS460 4.3 73.1 1.0 CB B:ASP445 4.3 91.0 1.0 CA B:CYS460 4.5 70.3 1.0 CB B:VAL442 4.5 71.4 1.0 CA B:CYS440 4.7 81.4 1.0 C B:CYS443 4.7 86.0 1.0 N B:SER444 4.7 90.6 1.0 N B:ASP445 4.7 95.3 1.0 C B:VAL442 4.8 78.0 1.0 NH2 B:ARG496 4.9 64.8 1.0 C B:CYS457 4.9 69.2 1.0 C B:THR456 5.0 82.8 1.0

Zinc binding site 2 out of 4 in the Gr Dna Binding Domain:FKBP5 Binding Site Complex-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gr Dna Binding Domain:FKBP5 Binding Site Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn527 b:49.0 occ:1.00 SG B:CYS476 2.3 42.5 1.0 SG B:CYS492 2.4 43.6 1.0 SG B:CYS482 2.4 43.3 1.0 SG B:CYS495 2.4 49.0 1.0 CB B:CYS482 3.2 56.0 1.0 CB B:CYS476 3.3 32.6 1.0 CB B:CYS495 3.4 31.1 1.0 CB B:CYS492 3.4 42.4 1.0 O B:HOH2 3.7 48.0 1.0 CA B:CYS476 4.0 33.1 1.0 N B:CYS482 4.0 47.1 1.0 CA B:CYS482 4.2 45.8 1.0 O B:HOH29 4.3 44.7 1.0 N B:CYS495 4.4 48.3 1.0 CA B:CYS495 4.5 37.5 1.0 N B:ASN480 4.6 43.1 1.0 N B:ALA477 4.6 32.8 1.0 CA B:ASN480 4.6 40.1 1.0 C B:CYS476 4.8 38.2 1.0 N B:GLY478 4.8 43.1 1.0 CA B:CYS492 4.8 46.6 1.0 O B:HOH12 4.9 69.9 1.0 N B:ASP481 4.9 42.3 1.0 C B:ASN480 4.9 46.8 1.0

Zinc binding site 3 out of 4 in the Gr Dna Binding Domain:FKBP5 Binding Site Complex-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gr Dna Binding Domain:FKBP5 Binding Site Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn526 b:49.8 occ:1.00 SG A:CYS460 2.2 46.1 1.0 SG A:CYS457 2.3 48.4 1.0 SG A:CYS443 2.4 54.5 1.0 SG A:CYS440 2.5 41.9 1.0 CB A:CYS440 3.2 34.2 1.0 CB A:CYS460 3.2 42.0 1.0 CB A:CYS443 3.3 44.0 1.0 CB A:CYS457 3.6 59.4 1.0 N A:CYS443 3.7 48.2 1.0 N A:CYS457 3.9 48.1 1.0 CA A:CYS443 4.0 46.5 1.0 CA A:CYS457 4.3 43.9 1.0 NH1 A:ARG489 4.3 42.0 1.0 N A:CYS460 4.3 48.0 1.0 CA A:CYS460 4.4 43.6 1.0 CB A:ASP445 4.5 63.4 1.0 OG A:SER459 4.5 53.1 1.0 CB A:VAL442 4.5 39.6 1.0 C A:CYS443 4.6 60.6 1.0 C A:VAL442 4.7 54.1 1.0 N A:SER444 4.7 57.7 1.0 CA A:CYS440 4.7 43.6 1.0 N A:ASP445 4.7 56.4 1.0 O A:CYS457 4.8 42.2 1.0 C A:CYS457 4.8 41.0 1.0 NH2 A:ARG496 4.9 39.1 1.0 C A:THR456 5.0 53.5 1.0 CA A:VAL442 5.0 46.4 1.0

Zinc binding site 4 out of 4 in the Gr Dna Binding Domain:FKBP5 Binding Site Complex-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Gr Dna Binding Domain:FKBP5 Binding Site Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn527 b:47.1 occ:1.00 SG A:CYS482 2.3 42.3 1.0 SG A:CYS492 2.3 43.9 1.0 SG A:CYS495 2.5 42.8 1.0 SG A:CYS476 2.5 45.1 1.0 CB A:CYS482 3.1 51.7 1.0 CB A:CYS492 3.2 34.8 1.0 CB A:CYS476 3.3 33.5 1.0 CB A:CYS495 3.4 18.1 1.0 O A:HOH1 3.8 46.4 1.0 CA A:CYS476 3.9 42.1 1.0 N A:CYS482 4.1 43.2 1.0 CA A:CYS482 4.2 35.8 1.0 N A:CYS495 4.2 32.6 1.0 CA A:CYS495 4.5 39.0 1.0 CA A:ASN480 4.5 43.0 1.0 O A:HOH4 4.5 43.9 1.0 N A:ASN480 4.6 52.3 1.0 N A:ALA477 4.6 43.3 1.0 CA A:CYS492 4.7 40.8 1.0 O A:HOH13 4.7 60.3 1.0 C A:CYS476 4.7 50.2 1.0 N A:ASP481 4.8 36.0 1.0 N A:GLY478 4.9 47.6 1.0 CB A:ALA494 4.9 39.1 1.0 C A:ASN480 5.0 40.0 1.0

S.H.Meijsing, M.A.Pufall, A.Y.So, D.L.Bates, L.Chen, K.R.Yamamoto. Dna Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity. Science V. 324 407 2009.
ISSN: ISSN 0036-8075
PubMed: 19372434
DOI: 10.1126/SCIENCE.1164265