Zinc in PDB 3g99: Gr Dna Binding Domain:Pal Complex-9

The structure of Gr Dna Binding Domain:Pal Complex-9, PDB code: 3g99 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)	35.57 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.774, 38.189, 97.064, 90.00, 123.11, 90.00
R / Rfree (%)	19.1 / 23

The structure of Gr Dna Binding Domain:Pal Complex-9 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Zinc atom in the Gr Dna Binding Domain:Pal Complex-9 (pdb code 3g99). 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:Pal Complex-9, PDB code: 3g99:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Gr Dna Binding Domain:Pal 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:Pal Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn526 b:41.7 occ:1.00 SG A:CYS460 2.2 40.1 1.0 SG A:CYS443 2.3 44.4 1.0 SG A:CYS457 2.3 42.1 1.0 SG A:CYS440 2.4 38.1 1.0 CB A:CYS443 3.3 39.5 1.0 CB A:CYS460 3.3 43.5 1.0 CB A:CYS440 3.4 41.8 1.0 CB A:CYS457 3.6 48.2 1.0 N A:CYS443 3.6 44.8 1.0 N A:CYS457 3.8 46.3 1.0 CA A:CYS443 4.0 41.0 1.0 N A:CYS460 4.2 40.0 1.0 CA A:CYS457 4.3 49.0 1.0 CA A:CYS460 4.4 36.1 1.0 NH1 A:ARG489 4.4 42.3 1.0 OG A:SER459 4.4 52.4 1.0 CB A:VAL442 4.5 40.7 1.0 CB A:ASP445 4.6 63.5 1.0 C A:CYS443 4.6 47.6 1.0 C A:VAL442 4.7 47.0 1.0 NH2 A:ARG496 4.7 36.2 1.0 O A:CYS457 4.8 37.7 1.0 CA A:CYS440 4.8 42.0 1.0 C A:CYS457 4.8 45.9 1.0 N A:SER444 4.8 47.3 1.0 CD A:ARG489 4.9 47.9 1.0 CB A:THR456 4.9 44.3 1.0 C A:THR456 4.9 49.8 1.0 N A:ASP445 5.0 57.8 1.0

Zinc binding site 2 out of 4 in the Gr Dna Binding Domain:Pal 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:Pal Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn527 b:36.3 occ:1.00 SG A:CYS482 2.2 38.0 1.0 SG A:CYS476 2.3 35.4 1.0 SG A:CYS495 2.3 35.0 1.0 SG A:CYS492 2.4 36.2 1.0 CB A:CYS482 3.3 40.1 1.0 CB A:CYS492 3.3 34.4 1.0 CB A:CYS476 3.4 38.4 1.0 CB A:CYS495 3.4 33.3 1.0 O B:HOH4 3.9 37.2 1.0 CA A:CYS476 3.9 29.9 1.0 N A:CYS482 4.0 42.1 1.0 N A:CYS495 4.1 31.4 1.0 CA A:CYS482 4.2 39.5 1.0 CA A:CYS495 4.4 28.1 1.0 CA A:ASN480 4.4 45.1 1.0 N A:ASN480 4.5 50.0 1.0 O A:HOH40 4.5 53.9 1.0 O A:HOH10 4.6 38.3 1.0 N A:ASP481 4.6 37.8 1.0 N A:ALA477 4.6 40.2 1.0 O B:HOH7 4.7 40.7 1.0 C A:CYS476 4.7 42.8 1.0 CA A:CYS492 4.7 34.1 1.0 C A:ASN480 4.8 44.8 1.0 N A:GLY478 4.9 40.3 1.0

Zinc binding site 3 out of 4 in the Gr Dna Binding Domain:Pal 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:Pal Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn526 b:65.5 occ:1.00 SG B:CYS457 2.2 69.6 1.0 SG B:CYS460 2.2 65.1 1.0 SG B:CYS443 2.3 62.5 1.0 SG B:CYS440 2.3 71.9 1.0 CB B:CYS443 3.2 55.0 1.0 CB B:CYS460 3.2 69.0 1.0 CB B:CYS440 3.2 80.5 1.0 CB B:CYS457 3.5 57.8 1.0 N B:CYS443 3.7 68.5 1.0 N B:CYS457 3.9 72.5 1.0 CA B:CYS443 4.0 66.7 1.0 NH1 B:ARG489 4.1 70.4 1.0 CA B:CYS457 4.3 64.9 1.0 N B:CYS460 4.3 62.2 1.0 CB B:ASP445 4.3 79.4 1.0 CA B:CYS460 4.3 60.2 1.0 CB B:VAL442 4.4 66.5 1.0 C B:CYS443 4.5 70.5 1.0 N B:ASP445 4.6 73.4 1.0 C B:VAL442 4.7 66.1 1.0 CA B:CYS440 4.7 79.9 1.0 N B:SER444 4.7 70.3 1.0 CD B:ARG489 4.8 52.5 1.0 N B:VAL442 4.9 70.5 1.0 CA B:VAL442 4.9 67.0 1.0 NH2 B:ARG496 4.9 54.6 1.0 C B:CYS457 4.9 66.4 1.0 C B:THR456 5.0 72.6 1.0 O B:CYS457 5.0 69.5 1.0

Zinc binding site 4 out of 4 in the Gr Dna Binding Domain:Pal 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:Pal Complex-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn527 b:38.4 occ:1.00 SG B:CYS476 2.2 34.6 1.0 SG B:CYS482 2.2 38.2 1.0 SG B:CYS492 2.4 36.1 1.0 SG B:CYS495 2.5 43.4 1.0 CB B:CYS492 3.2 29.0 1.0 CB B:CYS482 3.3 41.4 1.0 CB B:CYS495 3.3 34.1 1.0 CB B:CYS476 3.4 27.4 1.0 N B:CYS482 3.9 45.8 1.0 CA B:CYS476 4.0 31.9 1.0 O B:HOH20 4.0 40.4 1.0 O B:HOH9 4.2 38.0 1.0 N B:CYS495 4.2 42.6 1.0 CA B:CYS482 4.2 39.3 1.0 CA B:CYS495 4.3 39.0 1.0 O B:HOH7 4.5 40.7 1.0 CA B:ASN480 4.6 41.0 1.0 N B:ASP481 4.6 30.5 1.0 N B:ASN480 4.6 36.9 1.0 N B:ALA477 4.6 32.5 1.0 O B:HOH14 4.7 44.7 1.0 CA B:CYS492 4.7 35.8 1.0 C B:CYS476 4.8 36.5 1.0 N B:GLY478 4.8 40.0 1.0 C B:ASN480 4.9 40.2 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