Zinc in PDB 3us1: Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites

The structure of Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites, PDB code: 3us1 was solved by C.Chen, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.61 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.954, 101.220, 71.501, 90.00, 122.78, 90.00
R / Rfree (%)	20.2 / 23.4

The binding sites of Zinc atom in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites (pdb code 3us1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites, PDB code: 3us1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:35.5 occ:1.00 ND1 A:HIS208 2.0 16.4 1.0 SG A:CYS205 2.2 31.1 1.0 SG A:CYS273 2.2 24.5 1.0 SG A:CYS269 2.3 29.5 1.0 CE1 A:HIS208 2.8 12.8 1.0 CB A:CYS273 3.0 33.7 1.0 CG A:HIS208 3.1 20.2 1.0 CB A:CYS205 3.4 32.6 1.0 CB A:HIS208 3.7 20.5 1.0 CB A:CYS269 3.7 29.6 1.0 N A:CYS205 3.9 30.6 1.0 NE2 A:HIS208 4.0 18.9 1.0 CA A:CYS269 4.0 25.5 1.0 CD2 A:HIS208 4.2 22.2 1.0 CA A:CYS205 4.2 27.5 1.0 O A:HOH348 4.3 29.7 1.0 N A:HIS208 4.4 25.4 1.0 CA A:CYS273 4.4 35.0 1.0 N A:ASN270 4.5 26.2 1.0 O A:CYS205 4.6 29.6 1.0 CA A:HIS208 4.7 27.3 1.0 O A:MET268 4.7 17.7 1.0 C A:CYS269 4.7 28.1 1.0 C A:CYS205 4.8 28.2 1.0 C A:ARG204 5.0 30.1 1.0

Zinc binding site 2 out of 2 in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair Response Element Containing A Two Base Pair "Gc" Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:49.0 occ:1.00 ND1 D:HIS208 2.1 40.4 1.0 SG D:CYS205 2.2 39.9 1.0 SG D:CYS269 2.3 34.7 1.0 SG D:CYS273 2.3 27.9 1.0 CE1 D:HIS208 2.8 40.2 1.0 CB D:CYS273 2.9 35.4 1.0 CB D:CYS205 3.2 36.2 1.0 CG D:HIS208 3.2 36.8 1.0 CB D:CYS269 3.6 37.6 1.0 CB D:HIS208 3.7 34.7 1.0 CA D:CYS269 3.8 38.1 1.0 N D:CYS205 3.9 26.5 1.0 NE2 D:HIS208 4.0 51.7 1.0 CA D:CYS205 4.1 31.9 1.0 CD2 D:HIS208 4.2 40.7 1.0 N D:ASN270 4.4 49.5 1.0 CA D:CYS273 4.4 35.4 1.0 N D:HIS208 4.5 42.8 1.0 O D:CYS205 4.5 28.3 1.0 C D:CYS269 4.6 40.3 1.0 C D:CYS205 4.7 30.8 1.0 CA D:HIS208 4.8 39.1 1.0 O D:MET268 4.8 41.4 1.0 C D:ARG204 5.0 34.0 1.0

C.Chen, N.Gorlatova, O.Herzberg. Pliable Dna Conformation of Response Elements Bound to Transcription Factor P63. J.Biol.Chem. V. 287 7477 2012.
ISSN: ISSN 0021-9258
PubMed: 22247550
DOI: 10.1074/JBC.M111.315820