Zinc in PDB 3us0: Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites

The structure of Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites, PDB code: 3us0 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)	59.80 / 2.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	141.806, 141.806, 119.604, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 23.9

The binding sites of Zinc atom in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites (pdb code 3us0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites, PDB code: 3us0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" 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 A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:54.4 occ:1.00 ND1 A:HIS208 2.1 47.8 1.0 SG A:CYS273 2.3 49.3 1.0 SG A:CYS269 2.3 57.4 1.0 SG A:CYS205 2.4 58.8 1.0 CG A:HIS208 3.0 43.9 1.0 CE1 A:HIS208 3.1 39.3 1.0 CB A:CYS273 3.2 54.7 1.0 CB A:HIS208 3.3 52.5 1.0 CB A:CYS269 3.4 50.1 1.0 CB A:CYS205 3.5 50.8 1.0 CA A:CYS269 3.9 39.8 1.0 N A:CYS205 4.0 62.1 1.0 CD2 A:HIS208 4.2 51.0 1.0 NE2 A:HIS208 4.2 53.4 1.0 O A:CYS205 4.3 56.1 1.0 CA A:CYS205 4.3 52.9 1.0 N A:HIS208 4.4 66.7 1.0 CA A:HIS208 4.4 62.4 1.0 N A:ASN270 4.5 52.2 1.0 CA A:CYS273 4.6 59.1 1.0 C A:CYS205 4.6 53.4 1.0 O A:MET268 4.7 51.9 1.0 C A:CYS269 4.7 45.8 1.0 CG A:ARG204 4.9 48.3 1.0

Zinc binding site 2 out of 4 in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" 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 A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:51.1 occ:1.00 ND1 B:HIS208 2.1 50.0 1.0 SG B:CYS205 2.3 49.3 1.0 SG B:CYS273 2.3 42.1 1.0 SG B:CYS269 2.4 51.7 1.0 CE1 B:HIS208 3.0 46.3 1.0 CB B:CYS273 3.1 42.2 1.0 CG B:HIS208 3.2 46.3 1.0 CB B:CYS205 3.4 53.5 1.0 CB B:CYS269 3.4 41.9 1.0 CB B:HIS208 3.5 46.0 1.0 N B:CYS205 3.9 49.2 1.0 CA B:CYS269 3.9 45.6 1.0 NE2 B:HIS208 4.2 54.4 1.0 CA B:CYS205 4.2 52.8 1.0 CD2 B:HIS208 4.3 53.4 1.0 CA B:CYS273 4.5 41.0 1.0 N B:ASN270 4.6 46.4 1.0 O B:MET268 4.6 51.0 1.0 N B:HIS208 4.6 60.8 1.0 O B:CYS205 4.7 58.5 1.0 CA B:HIS208 4.7 54.8 1.0 C B:CYS269 4.7 46.7 1.0 O B:HOH329 4.8 42.2 1.0 C B:CYS205 4.8 52.9 1.0

Zinc binding site 3 out of 4 in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:79.7 occ:1.00 ND1 C:HIS208 2.1 69.6 1.0 SG C:CYS273 2.3 55.7 1.0 SG C:CYS269 2.3 75.7 1.0 SG C:CYS205 2.4 81.5 1.0 CE1 C:HIS208 3.1 63.1 1.0 CG C:HIS208 3.1 68.7 1.0 CB C:CYS273 3.4 69.8 1.0 CB C:CYS269 3.4 63.7 1.0 CB C:HIS208 3.4 75.3 1.0 CB C:CYS205 3.5 74.5 1.0 CA C:CYS269 3.9 55.1 1.0 N C:CYS205 3.9 75.0 1.0 NE2 C:HIS208 4.2 67.9 1.0 CA C:CYS205 4.2 74.9 1.0 CD2 C:HIS208 4.2 64.5 1.0 N C:HIS208 4.5 87.2 1.0 O C:MET268 4.5 64.9 1.0 O C:CYS205 4.6 74.9 1.0 CA C:HIS208 4.6 80.0 1.0 CA C:CYS273 4.6 74.1 1.0 N C:ASN270 4.7 59.4 1.0 C C:CYS269 4.7 57.6 1.0 C C:CYS205 4.8 77.9 1.0 CG C:ARG204 4.9 68.5 1.0

Zinc binding site 4 out of 4 in the Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing A Two Base Pair "at" Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:60.0 occ:1.00 ND1 D:HIS208 2.2 68.3 1.0 SG D:CYS205 2.3 55.5 1.0 SG D:CYS273 2.3 48.7 1.0 SG D:CYS269 2.3 51.9 1.0 CE1 D:HIS208 3.0 60.0 1.0 CB D:CYS273 3.1 49.9 1.0 CG D:HIS208 3.2 62.8 1.0 CB D:CYS269 3.3 47.4 1.0 CB D:CYS205 3.5 56.6 1.0 CB D:HIS208 3.6 63.2 1.0 CA D:CYS269 3.8 57.2 1.0 N D:CYS205 3.9 56.7 1.0 NE2 D:HIS208 4.2 68.4 1.0 CA D:CYS205 4.3 59.6 1.0 CD2 D:HIS208 4.3 69.4 1.0 N D:ASN270 4.4 57.0 1.0 N D:HIS208 4.5 76.6 1.0 CA D:CYS273 4.5 48.8 1.0 O D:MET268 4.6 54.8 1.0 O D:CYS205 4.6 67.4 1.0 C D:CYS269 4.7 56.8 1.0 CA D:HIS208 4.7 71.2 1.0 C D:CYS205 4.9 61.2 1.0 N D:CYS269 5.0 57.4 1.0 C D:ARG204 5.0 57.4 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