Zinc in PDB 3qym: Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site

The structure of Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site, PDB code: 3qym was solved by O.Herzberg, C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.72 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.872, 180.198, 104.379, 90.00, 92.62, 90.00
R / Rfree (%)	24.5 / 27.1

The binding sites of Zinc atom in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site (pdb code 3qym). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site, PDB code: 3qym:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:0.6 occ:1.00 ND1 A:HIS208 2.1 0.6 1.0 SG A:CYS269 2.3 0.7 1.0 SG A:CYS205 2.3 0.8 1.0 SG A:CYS273 2.3 0.2 1.0 CE1 A:HIS208 3.0 0.8 1.0 CG A:HIS208 3.2 0.0 1.0 CB A:CYS273 3.3 0.3 1.0 CB A:CYS269 3.5 0.7 1.0 CB A:CYS205 3.6 0.1 1.0 CB A:HIS208 3.6 0.2 1.0 CA A:CYS269 4.0 0.2 1.0 N A:CYS205 4.1 0.2 1.0 NE2 A:HIS208 4.2 0.7 1.0 CD2 A:HIS208 4.3 0.4 1.0 CA A:CYS205 4.4 0.3 1.0 N A:HIS208 4.5 0.4 1.0 N A:ASN270 4.6 0.2 1.0 O A:MET268 4.6 0.5 1.0 C A:CYS269 4.6 0.2 1.0 CA A:HIS208 4.7 0.5 1.0 CA A:CYS273 4.7 0.4 1.0 O A:CYS205 5.0 0.3 1.0 C A:CYS205 5.0 0.6 1.0

Zinc binding site 2 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:0.8 occ:1.00 ND1 B:HIS208 2.1 0.0 1.0 SG B:CYS269 2.3 0.7 1.0 SG B:CYS273 2.3 0.1 1.0 SG B:CYS205 2.3 90.7 1.0 CE1 B:HIS208 3.0 0.4 1.0 CG B:HIS208 3.2 0.2 1.0 CB B:CYS273 3.3 0.0 1.0 CB B:CYS269 3.5 0.8 1.0 CB B:HIS208 3.6 0.2 1.0 CB B:CYS205 3.6 0.1 1.0 CA B:CYS269 3.9 0.0 1.0 N B:CYS205 4.1 96.1 1.0 NE2 B:HIS208 4.1 0.1 1.0 CD2 B:HIS208 4.2 0.0 1.0 CA B:CYS205 4.4 0.0 1.0 N B:HIS208 4.5 0.1 1.0 N B:ASN270 4.5 0.1 1.0 O B:MET268 4.6 0.8 1.0 C B:CYS269 4.6 0.6 1.0 CA B:HIS208 4.7 0.0 1.0 CA B:CYS273 4.7 0.6 1.0

Zinc binding site 3 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:99.8 occ:1.00 ND1 C:HIS208 2.1 1.0 1.0 SG C:CYS269 2.3 91.9 1.0 SG C:CYS273 2.3 94.6 1.0 SG C:CYS205 2.3 85.0 1.0 CE1 C:HIS208 3.0 0.4 1.0 CG C:HIS208 3.2 0.7 1.0 CB C:CYS273 3.3 0.9 1.0 CB C:CYS269 3.5 0.1 1.0 CB C:HIS208 3.6 75.8 1.0 CB C:CYS205 3.6 0.3 1.0 CA C:CYS269 3.9 77.9 1.0 N C:CYS205 4.1 79.8 1.0 NE2 C:HIS208 4.1 0.3 1.0 CD2 C:HIS208 4.3 90.9 1.0 CA C:CYS205 4.4 82.1 1.0 N C:HIS208 4.5 0.8 1.0 N C:ASN270 4.5 0.1 1.0 O C:MET268 4.6 0.9 1.0 C C:CYS269 4.6 91.6 1.0 CA C:HIS208 4.7 0.3 1.0 CA C:CYS273 4.7 0.2 1.0

Zinc binding site 4 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:0.0 occ:1.00 ND1 D:HIS208 2.1 0.2 1.0 SG D:CYS269 2.3 99.7 1.0 SG D:CYS273 2.3 0.7 1.0 SG D:CYS205 2.3 95.9 1.0 CE1 D:HIS208 3.0 0.0 1.0 CG D:HIS208 3.2 0.9 1.0 CB D:CYS273 3.3 0.1 1.0 CB D:CYS269 3.5 0.5 1.0 CB D:HIS208 3.6 85.8 1.0 CB D:CYS205 3.6 0.8 1.0 CA D:CYS269 3.9 94.0 1.0 N D:CYS205 4.1 75.8 1.0 NE2 D:HIS208 4.1 1.0 1.0 CD2 D:HIS208 4.3 97.5 1.0 CA D:CYS205 4.4 82.7 1.0 N D:HIS208 4.5 0.1 1.0 N D:ASN270 4.5 0.6 1.0 O D:MET268 4.6 0.8 1.0 C D:CYS269 4.6 0.2 1.0 CA D:HIS208 4.7 0.8 1.0 CA D:CYS273 4.7 0.8 1.0

Zinc binding site 5 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn901 b:0.6 occ:1.00 ND1 E:HIS208 2.1 0.8 1.0 SG E:CYS269 2.3 81.8 1.0 SG E:CYS205 2.3 84.8 1.0 SG E:CYS273 2.4 87.1 1.0 CE1 E:HIS208 3.0 0.8 1.0 CG E:HIS208 3.2 0.8 1.0 CB E:CYS273 3.3 0.5 1.0 CB E:CYS269 3.5 1.0 1.0 CB E:CYS205 3.5 0.6 1.0 CB E:HIS208 3.5 81.7 1.0 CA E:CYS269 4.0 86.7 1.0 N E:CYS205 4.0 63.4 1.0 NE2 E:HIS208 4.2 0.2 1.0 CD2 E:HIS208 4.3 89.8 1.0 CA E:CYS205 4.4 72.0 1.0 N E:HIS208 4.4 99.9 1.0 O E:MET268 4.6 1.0 1.0 N E:ASN270 4.6 0.1 1.0 CA E:HIS208 4.6 0.5 1.0 C E:CYS269 4.6 94.2 1.0 CA E:CYS273 4.7 0.0 1.0 O E:CYS205 5.0 93.2 1.0 C E:CYS205 5.0 80.9 1.0

Zinc binding site 6 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn901 b:0.7 occ:1.00 ND1 F:HIS208 2.1 0.3 1.0 SG F:CYS269 2.3 94.1 1.0 SG F:CYS205 2.3 88.4 1.0 SG F:CYS273 2.3 0.4 1.0 CE1 F:HIS208 3.0 0.1 1.0 CG F:HIS208 3.2 0.7 1.0 CB F:CYS273 3.3 0.5 1.0 CB F:CYS269 3.5 0.9 1.0 CB F:CYS205 3.5 0.3 1.0 CB F:HIS208 3.6 89.9 1.0 CA F:CYS269 4.0 93.8 1.0 N F:CYS205 4.1 80.4 1.0 NE2 F:HIS208 4.2 0.5 1.0 CD2 F:HIS208 4.3 98.2 1.0 CA F:CYS205 4.4 91.8 1.0 N F:HIS208 4.5 1.0 1.0 N F:ASN270 4.6 0.8 1.0 O F:MET268 4.6 0.8 1.0 C F:CYS269 4.6 0.4 1.0 CA F:HIS208 4.7 0.0 1.0 CA F:CYS273 4.7 0.9 1.0 O F:CYS205 5.0 0.8 1.0 C F:CYS205 5.0 0.8 1.0

Zinc binding site 7 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn901 b:0.9 occ:1.00 ND1 G:HIS208 2.1 0.2 1.0 SG G:CYS205 2.3 96.3 1.0 SG G:CYS269 2.3 0.7 1.0 SG G:CYS273 2.3 0.6 1.0 CE1 G:HIS208 3.0 0.1 1.0 CG G:HIS208 3.2 1.0 1.0 CB G:CYS273 3.3 0.2 1.0 CB G:CYS205 3.5 0.9 1.0 CB G:HIS208 3.5 0.0 1.0 CB G:CYS269 3.6 0.3 1.0 CA G:CYS269 4.0 1.0 1.0 N G:CYS205 4.1 86.4 1.0 NE2 G:HIS208 4.2 0.5 1.0 CD2 G:HIS208 4.3 0.5 1.0 CA G:CYS205 4.4 97.9 1.0 N G:HIS208 4.4 0.0 1.0 N G:ASN270 4.6 0.5 1.0 O G:MET268 4.6 0.1 1.0 CA G:HIS208 4.6 0.7 1.0 C G:CYS269 4.7 0.9 1.0 CA G:CYS273 4.7 0.3 1.0 O G:CYS205 5.0 98.7 1.0 C G:CYS205 5.0 0.1 1.0

Zinc binding site 8 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn901 b:0.1 occ:1.00 ND1 H:HIS208 2.1 0.3 1.0 SG H:CYS273 2.3 0.4 1.0 SG H:CYS269 2.3 0.7 1.0 SG H:CYS205 2.3 97.7 1.0 CE1 H:HIS208 3.0 0.4 1.0 CG H:HIS208 3.2 0.8 1.0 CB H:CYS273 3.3 0.2 1.0 CB H:CYS269 3.5 0.3 1.0 CB H:HIS208 3.6 92.8 1.0 CB H:CYS205 3.6 0.5 1.0 CA H:CYS269 3.9 100.0 1.0 N H:CYS205 4.1 94.2 1.0 NE2 H:HIS208 4.1 0.4 1.0 CD2 H:HIS208 4.2 0.6 1.0 CA H:CYS205 4.4 98.5 1.0 N H:HIS208 4.5 0.5 1.0 N H:ASN270 4.5 0.6 1.0 O H:MET268 4.6 0.6 1.0 C H:CYS269 4.6 1.0 1.0 CA H:HIS208 4.7 0.5 1.0 CA H:CYS273 4.7 0.0 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