Zinc in PDB 3g8u: Dna Binding Domain:Gilz 16BP Complex-5

The structure of Dna Binding Domain:Gilz 16BP Complex-5, PDB code: 3g8u 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)	29.20 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.941, 38.605, 98.518, 90.00, 123.51, 90.00
R / Rfree (%)	21 / 23.6

The binding sites of Zinc atom in the Dna Binding Domain:Gilz 16BP Complex-5 (pdb code 3g8u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dna Binding Domain:Gilz 16BP Complex-5, PDB code: 3g8u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Dna Binding Domain:Gilz 16BP Complex-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Binding Domain:Gilz 16BP Complex-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn526 b:57.5 occ:1.00 SG A:CYS443 2.2 56.7 1.0 SG A:CYS457 2.3 60.9 1.0 SG A:CYS460 2.3 53.0 1.0 SG A:CYS440 2.4 56.0 1.0 CB A:CYS443 3.2 48.9 1.0 CB A:CYS440 3.2 55.5 1.0 CB A:CYS460 3.3 43.4 1.0 CB A:CYS457 3.6 71.2 1.0 N A:CYS443 3.7 64.2 1.0 N A:CYS457 3.9 58.7 1.0 CA A:CYS443 4.0 68.1 1.0 N A:CYS460 4.2 42.7 1.0 NH1 A:ARG489 4.3 56.8 1.0 CA A:CYS457 4.3 54.3 1.0 CA A:CYS460 4.3 39.6 1.0 OG A:SER459 4.3 73.7 1.0 CB A:VAL442 4.6 49.6 1.0 CB A:ASP445 4.6 79.1 1.0 C A:CYS443 4.7 78.7 1.0 CA A:CYS440 4.7 64.3 1.0 C A:VAL442 4.8 66.9 1.0 C A:CYS457 4.8 53.0 1.0 O A:CYS457 4.8 48.4 1.0 NH2 A:ARG496 4.8 43.8 1.0 N A:ASP445 4.8 77.8 1.0 N A:SER444 4.9 70.6 1.0 CD A:ARG489 5.0 61.9 1.0

Zinc binding site 2 out of 4 in the Dna Binding Domain:Gilz 16BP Complex-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Binding Domain:Gilz 16BP Complex-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn527 b:38.2 occ:1.00 SG A:CYS482 2.2 39.0 1.0 SG A:CYS492 2.3 37.7 1.0 SG A:CYS495 2.3 38.8 1.0 SG A:CYS476 2.4 38.6 1.0 CB A:CYS482 3.2 48.4 1.0 CB A:CYS495 3.3 37.2 1.0 CB A:CYS476 3.3 35.8 1.0 CB A:CYS492 3.4 34.5 1.0 O B:HOH1 3.9 45.0 1.0 N A:CYS482 3.9 48.5 1.0 CA A:CYS476 4.0 38.7 1.0 N A:CYS495 4.2 32.0 1.0 CA A:CYS482 4.2 44.5 1.0 CA A:CYS495 4.3 30.9 1.0 CA A:ASN480 4.4 51.8 1.0 N A:ASP481 4.5 43.4 1.0 O A:HOH9 4.6 56.9 1.0 N A:ASN480 4.6 46.1 1.0 O A:HOH2 4.7 39.3 1.0 C A:ASN480 4.8 54.6 1.0 O A:HOH3 4.8 46.2 1.0 CA A:CYS492 4.8 33.0 1.0 N A:ALA477 4.8 40.0 1.0 C A:CYS476 4.8 52.0 1.0 N A:GLY478 4.8 44.5 1.0 O A:CYS492 5.0 41.6 1.0

Zinc binding site 3 out of 4 in the Dna Binding Domain:Gilz 16BP Complex-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Binding Domain:Gilz 16BP Complex-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn526 b:88.8 occ:1.00 SG B:CYS440 2.2 86.6 1.0 SG B:CYS443 2.4 81.5 1.0 SG B:CYS460 2.5 80.0 1.0 SG B:CYS457 2.5 79.1 1.0 CB B:CYS443 3.0 81.4 1.0 CB B:CYS440 3.1 0.1 1.0 N B:CYS443 3.3 86.0 1.0 CB B:CYS460 3.4 85.2 1.0 CB B:CYS457 3.4 0.8 1.0 CA B:CYS443 3.6 79.7 1.0 N B:CYS457 4.0 0.0 1.0 C B:CYS443 4.2 96.7 1.0 CB B:VAL442 4.2 71.9 1.0 CA B:CYS457 4.3 1.0 1.0 C B:VAL442 4.4 83.5 1.0 N B:SER444 4.4 0.7 1.0 N B:CYS460 4.4 76.0 1.0 CB B:ASP445 4.5 84.8 1.0 CA B:CYS460 4.5 80.1 1.0 CA B:CYS440 4.5 0.8 1.0 N B:ASP445 4.6 0.3 1.0 CD B:ARG489 4.6 94.1 1.0 OG B:SER459 4.7 78.7 1.0 CA B:VAL442 4.7 80.5 1.0 CG1 B:VAL442 4.9 71.8 1.0 NH2 B:ARG496 4.9 70.5 1.0 N B:VAL442 4.9 84.1 1.0 O B:CYS443 4.9 93.3 1.0 C B:CYS457 4.9 92.0 1.0 O B:CYS457 5.0 94.9 1.0

Zinc binding site 4 out of 4 in the Dna Binding Domain:Gilz 16BP Complex-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dna Binding Domain:Gilz 16BP Complex-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn527 b:43.4 occ:1.00 SG B:CYS476 2.2 40.7 1.0 SG B:CYS482 2.2 45.8 1.0 SG B:CYS492 2.3 42.0 1.0 SG B:CYS495 2.4 48.4 1.0 CB B:CYS476 3.3 37.0 1.0 CB B:CYS482 3.3 52.5 1.0 CB B:CYS495 3.3 43.0 1.0 CB B:CYS492 3.3 39.6 1.0 CA B:CYS476 4.0 27.9 1.0 N B:CYS482 4.0 48.2 1.0 O A:HOH7 4.1 41.5 1.0 O B:HOH15 4.2 42.2 1.0 N B:CYS495 4.2 43.0 1.0 CA B:CYS482 4.2 44.4 1.0 CA B:CYS495 4.3 49.2 1.0 O A:HOH3 4.6 46.2 1.0 CA B:ASN480 4.6 48.1 1.0 N B:ASP481 4.6 41.3 1.0 N B:ASN480 4.6 42.2 1.0 O B:HOH21 4.6 54.7 1.0 N B:ALA477 4.7 30.6 1.0 CA B:CYS492 4.8 40.0 1.0 C B:CYS476 4.8 33.3 1.0 N B:GLY478 4.8 41.5 1.0 C B:ASN480 4.9 48.3 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