Zinc in PDB 6fj5: New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg)

The structure of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg), PDB code: 6fj5 was solved by D.Golovenko, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.517, 98.024, 73.171, 90.00, 93.39, 90.00
R / Rfree (%)	19.9 / 24.4

The binding sites of Zinc atom in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg) (pdb code 6fj5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg), PDB code: 6fj5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:18.5 occ:1.00 ND1 A:HIS179 2.1 9.3 1.0 SG A:CYS176 2.3 15.8 1.0 SG A:CYS242 2.4 16.2 1.0 SG A:CYS238 2.5 15.9 1.0 CE1 A:HIS179 3.0 25.4 1.0 CB A:CYS242 3.0 19.9 1.0 CG A:HIS179 3.1 13.1 1.0 CB A:CYS238 3.2 14.8 1.0 CB A:CYS176 3.3 11.3 1.0 CB A:HIS179 3.5 11.5 1.0 CA A:CYS238 3.8 14.5 1.0 N A:CYS176 4.0 6.4 1.0 NE2 A:HIS179 4.1 9.0 1.0 CD2 A:HIS179 4.2 15.1 1.0 CA A:CYS176 4.2 6.5 1.0 N A:HIS179 4.4 8.5 1.0 CA A:CYS242 4.4 17.1 1.0 N A:ASN239 4.6 14.7 1.0 O A:MET237 4.6 14.8 1.0 CA A:HIS179 4.6 21.1 1.0 O A:HOH479 4.7 11.1 1.0 C A:CYS238 4.7 14.4 1.0 CE D:MET243 4.7 17.4 1.0 C A:CYS176 4.9 14.2 1.0 O A:HOH525 4.9 18.4 1.0 O A:CYS176 4.9 21.6 1.0 SD D:MET243 4.9 38.4 1.0 N A:CYS238 5.0 14.2 1.0

Zinc binding site 2 out of 4 in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.6 occ:1.00 ND1 B:HIS179 2.2 20.6 1.0 SG B:CYS176 2.3 21.1 1.0 SG B:CYS242 2.3 14.6 1.0 SG B:CYS238 2.4 14.4 1.0 CB B:CYS242 3.1 14.7 1.0 CG B:HIS179 3.1 21.1 1.0 CE1 B:HIS179 3.1 20.4 1.0 CB B:CYS238 3.3 13.5 1.0 CB B:CYS176 3.4 21.1 1.0 CB B:HIS179 3.4 21.4 1.0 CA B:CYS238 3.9 16.9 1.0 N B:CYS176 4.0 21.0 1.0 NE2 B:HIS179 4.2 20.8 1.0 CD2 B:HIS179 4.3 21.6 1.0 CA B:CYS176 4.3 21.4 1.0 N B:HIS179 4.4 22.3 1.0 CA B:CYS242 4.5 15.1 1.0 CA B:HIS179 4.5 22.2 1.0 O B:MET237 4.6 18.8 1.0 N B:ASN239 4.6 13.4 1.0 O B:HOH483 4.7 13.8 1.0 C B:CYS238 4.8 18.5 1.0 CE C:MET243 4.8 29.3 1.0 SD C:MET243 4.9 35.9 1.0 O B:CYS176 4.9 22.2 1.0 C B:CYS176 4.9 27.0 1.0 O B:HOH519 4.9 23.3 1.0 N B:CYS238 5.0 23.8 1.0

Zinc binding site 3 out of 4 in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:15.9 occ:1.00 ND1 C:HIS179 1.9 18.6 1.0 SG C:CYS238 2.3 15.6 1.0 SG C:CYS176 2.4 19.5 1.0 SG C:CYS242 2.4 16.8 1.0 CE1 C:HIS179 2.8 18.5 1.0 CG C:HIS179 3.0 20.7 1.0 CB C:CYS238 3.1 15.6 1.0 CB C:CYS242 3.2 16.9 1.0 CB C:CYS176 3.4 19.5 1.0 CB C:HIS179 3.5 19.3 1.0 CA C:CYS238 3.8 15.5 1.0 NE2 C:HIS179 3.9 18.8 1.0 N C:CYS176 4.0 19.2 1.0 CD2 C:HIS179 4.1 19.1 1.0 CA C:CYS176 4.3 19.8 1.0 N C:HIS179 4.4 20.7 1.0 O C:MET237 4.5 17.4 1.0 CA C:HIS179 4.6 20.3 1.0 N C:ASN239 4.6 16.0 1.0 O C:HOH474 4.6 12.9 1.0 CA C:CYS242 4.6 18.3 1.0 CE B:MET243 4.6 27.8 1.0 C C:CYS238 4.7 15.6 1.0 O C:CYS176 4.8 20.5 1.0 N C:CYS238 4.9 15.2 1.0 C C:CYS176 4.9 20.6 1.0

Zinc binding site 4 out of 4 in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-Agg-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:16.1 occ:1.00 ND1 D:HIS179 2.0 13.2 1.0 SG D:CYS238 2.4 11.7 1.0 SG D:CYS176 2.4 16.1 1.0 SG D:CYS242 2.4 12.2 1.0 CE1 D:HIS179 2.8 13.5 1.0 CB D:CYS238 3.1 10.8 1.0 CG D:HIS179 3.1 27.7 1.0 CB D:CYS242 3.2 12.5 1.0 CB D:CYS176 3.4 16.1 1.0 CB D:HIS179 3.6 14.4 1.0 CA D:CYS238 3.8 10.7 1.0 N D:CYS176 4.0 12.5 1.0 NE2 D:HIS179 4.0 21.7 1.0 CD2 D:HIS179 4.2 14.1 1.0 CA D:CYS176 4.3 13.1 1.0 N D:HIS179 4.4 15.3 1.0 N D:ASN239 4.5 11.3 1.0 CE A:MET243 4.5 22.4 1.0 O D:HOH491 4.6 10.6 1.0 O D:MET237 4.6 20.0 1.0 CA D:CYS242 4.6 16.8 1.0 CA D:HIS179 4.7 20.6 1.0 C D:CYS238 4.7 17.8 1.0 O D:CYS176 4.8 13.8 1.0 C D:CYS176 4.9 20.3 1.0 N D:CYS238 4.9 10.3 1.0

D.Golovenko, B.Brauning, P.Vyas, T.E.Haran, H.Rozenberg, Z.Shakked. New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins. Structure V. 26 1237 2018.
ISSN: ISSN 1878-4186
PubMed: 30057026
DOI: 10.1016/J.STR.2018.06.006