Zinc in PDB 3qyn: Structure of P63 Dna Binding Domain in Complex with A 22 Base Pair A/T Rich Response Element Containing 2 Base Pair 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 2 Base Pair Spacer Between Half Sites, PDB code: 3qyn 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)	61.05 / 2.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	140.984, 140.984, 119.346, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.5

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 2 Base Pair Spacer Between Half Sites (pdb code 3qyn). 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 2 Base Pair Spacer Between Half Sites, PDB code: 3qyn:
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 2 Base Pair 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 2 Base Pair Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:49.5 occ:1.00 ND1 A:HIS208 2.1 43.0 1.0 SG A:CYS273 2.3 48.2 1.0 SG A:CYS269 2.3 51.9 1.0 SG A:CYS205 2.4 52.7 1.0 CG A:HIS208 3.0 39.1 1.0 CE1 A:HIS208 3.2 35.4 1.0 CB A:CYS273 3.2 58.1 1.0 CB A:HIS208 3.2 46.5 1.0 CB A:CYS269 3.3 45.4 1.0 CB A:CYS205 3.5 42.9 1.0 CA A:CYS269 3.8 41.7 1.0 N A:CYS205 3.9 54.9 1.0 CD2 A:HIS208 4.2 47.1 1.0 CA A:CYS205 4.2 44.4 1.0 NE2 A:HIS208 4.2 50.0 1.0 O A:CYS205 4.3 48.8 1.0 N A:HIS208 4.4 58.3 1.0 CA A:HIS208 4.4 55.3 1.0 O A:MET268 4.5 43.1 1.0 N A:ASN270 4.5 40.8 1.0 CA A:CYS273 4.6 60.3 1.0 O A:HOH327 4.6 52.4 1.0 C A:CYS205 4.6 44.8 1.0 C A:CYS269 4.7 43.3 1.0 C A:ARG204 5.0 63.0 1.0 CG A:ARG204 5.0 46.9 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 2 Base Pair 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 2 Base Pair Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:41.3 occ:1.00 ND1 B:HIS208 2.1 43.3 1.0 SG B:CYS273 2.3 33.6 1.0 SG B:CYS205 2.3 43.5 1.0 SG B:CYS269 2.4 45.0 1.0 CE1 B:HIS208 3.0 39.1 1.0 CB B:CYS273 3.1 42.1 1.0 CG B:HIS208 3.2 38.9 1.0 CB B:CYS269 3.3 32.5 1.0 CB B:CYS205 3.4 48.4 1.0 CB B:HIS208 3.6 38.8 1.0 CA B:CYS269 3.8 37.0 1.0 N B:CYS205 3.9 44.4 1.0 NE2 B:HIS208 4.1 46.4 1.0 CD2 B:HIS208 4.3 45.2 1.0 CA B:CYS205 4.3 47.8 1.0 N B:HIS208 4.5 52.9 1.0 CA B:CYS273 4.5 40.4 1.0 N B:ASN270 4.5 33.9 1.0 O B:MET268 4.6 48.0 1.0 CA B:HIS208 4.7 46.6 1.0 C B:CYS269 4.7 37.9 1.0 O B:HOH101 4.7 48.7 1.0 O B:CYS205 4.7 52.1 1.0 C B:CYS205 4.8 47.0 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 2 Base Pair 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 2 Base Pair Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:65.5 occ:1.00 ND1 C:HIS208 2.1 57.5 1.0 SG C:CYS273 2.3 46.5 1.0 SG C:CYS205 2.3 75.2 1.0 SG C:CYS269 2.4 61.3 1.0 CE1 C:HIS208 3.0 52.1 1.0 CG C:HIS208 3.1 56.7 1.0 CB C:CYS273 3.2 52.4 1.0 CB C:CYS269 3.2 46.5 1.0 CB C:CYS205 3.4 66.3 1.0 CB C:HIS208 3.5 62.0 1.0 N C:CYS205 3.8 67.7 1.0 CA C:CYS269 3.9 40.8 1.0 CA C:CYS205 4.2 66.1 1.0 NE2 C:HIS208 4.2 57.8 1.0 CD2 C:HIS208 4.2 53.7 1.0 N C:HIS208 4.4 70.9 1.0 CA C:CYS273 4.6 56.3 1.0 O C:CYS205 4.6 67.0 1.0 CA C:HIS208 4.6 65.4 1.0 O C:MET268 4.6 55.1 1.0 N C:ASN270 4.6 47.6 1.0 C C:CYS205 4.7 68.7 1.0 C C:CYS269 4.8 42.0 1.0 O C:HOH5 4.9 45.1 1.0 CG C:ARG204 4.9 58.3 1.0 C C:ARG204 4.9 64.7 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 2 Base Pair 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 2 Base Pair Spacer Between Half Sites within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:53.9 occ:1.00 ND1 D:HIS208 2.2 56.6 1.0 SG D:CYS205 2.3 42.4 1.0 SG D:CYS273 2.3 41.3 1.0 SG D:CYS269 2.4 49.6 1.0 CB D:CYS273 3.0 44.2 1.0 CE1 D:HIS208 3.1 47.8 1.0 CG D:HIS208 3.2 50.0 1.0 CB D:CYS269 3.2 39.4 1.0 CB D:CYS205 3.4 44.7 1.0 CB D:HIS208 3.6 50.6 1.0 CA D:CYS269 3.8 45.5 1.0 N D:CYS205 3.8 44.6 1.0 CA D:CYS205 4.2 47.6 1.0 NE2 D:HIS208 4.2 55.0 1.0 CD2 D:HIS208 4.3 55.5 1.0 N D:HIS208 4.5 64.0 1.0 CA D:CYS273 4.5 45.4 1.0 N D:ASN270 4.5 47.0 1.0 O D:HOH378 4.5 43.6 1.0 O D:MET268 4.6 50.4 1.0 O D:CYS205 4.6 53.5 1.0 CA D:HIS208 4.7 57.8 1.0 C D:CYS269 4.7 47.3 1.0 C D:CYS205 4.8 48.1 1.0 C D:ARG204 5.0 52.7 1.0 N D:CYS269 5.0 54.5 1.0

C.Chen, N.Gorlatova, Z.Kelman, O.Herzberg. Structures of P63 Dna Binding Domain in Complexes with Half-Site and with Spacer-Containing Full Response Elements. Proc.Natl.Acad.Sci.Usa V. 108 6456 2011.
ISSN: ISSN 0027-8424
PubMed: 21464285
DOI: 10.1073/PNAS.1013657108