Zinc in PDB 7eeu: Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic

The structure of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic, PDB code: 7eeu was solved by Y.F.Xing, M.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.39 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.815, 95.575, 99.646, 89.62, 89.85, 75.79
R / Rfree (%)	23.4 / 26.4

The structure of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic also contains other interesting chemical elements:

Arsenic

(As)

8 atoms

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic (pdb code 7eeu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic, PDB code: 7eeu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:71.9 occ:1.00 ND1 A:HIS179 2.1 70.6 1.0 SG A:CYS176 2.2 64.0 1.0 SG A:CYS242 2.3 64.6 1.0 SG A:CYS238 2.3 67.5 1.0 CE1 A:HIS179 3.0 61.9 1.0 CG A:HIS179 3.1 62.2 1.0 CB A:CYS242 3.1 65.7 1.0 CB A:CYS176 3.2 71.9 1.0 CB A:CYS238 3.3 63.6 1.0 CB A:HIS179 3.4 67.1 1.0 N A:CYS176 3.9 67.5 1.0 CA A:CYS238 3.9 54.0 1.0 NE2 A:HIS179 4.1 59.8 1.0 CA A:CYS176 4.1 69.4 1.0 CD2 A:HIS179 4.2 54.3 1.0 N A:ASN239 4.5 68.0 1.0 CA A:CYS242 4.6 62.5 1.0 N A:HIS179 4.6 65.0 1.0 CA A:HIS179 4.7 70.2 1.0 C A:CYS238 4.7 61.8 1.0 O A:MET237 4.7 59.5 1.0 C A:CYS176 4.9 69.3 1.0 CE C:MET243 4.9 77.8 1.0 O A:ASN239 4.9 73.4 1.0 O A:CYS176 4.9 79.5 1.0

Zinc binding site 2 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:69.3 occ:1.00 ND1 B:HIS179 2.0 74.0 1.0 SG B:CYS176 2.3 61.7 1.0 SG B:CYS238 2.3 67.6 1.0 SG B:CYS242 2.3 63.4 1.0 CE1 B:HIS179 2.9 65.8 1.0 CG B:HIS179 3.0 63.7 1.0 CB B:CYS242 3.2 61.0 1.0 CB B:CYS238 3.3 60.0 1.0 CB B:CYS176 3.3 64.7 1.0 CB B:HIS179 3.4 60.7 1.0 CA B:CYS238 3.9 52.1 1.0 N B:CYS176 3.9 76.0 1.0 NE2 B:HIS179 4.0 65.5 1.0 CD2 B:HIS179 4.1 59.9 1.0 CA B:CYS176 4.2 65.6 1.0 N B:ASN239 4.5 64.3 1.0 N B:HIS179 4.6 67.9 1.0 CA B:HIS179 4.6 62.7 1.0 O B:MET237 4.6 45.6 1.0 C B:CYS238 4.7 55.8 1.0 CA B:CYS242 4.7 58.1 1.0 C B:CYS176 4.9 68.5 1.0 O B:ASN239 4.9 59.9 1.0 O B:CYS176 5.0 72.5 1.0

Zinc binding site 3 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:60.6 occ:1.00 ND1 C:HIS179 2.1 72.3 1.0 SG C:CYS176 2.2 61.3 1.0 SG C:CYS238 2.3 57.0 1.0 SG C:CYS242 2.4 59.2 1.0 CG C:HIS179 3.1 63.1 1.0 CE1 C:HIS179 3.1 69.7 1.0 CB C:CYS242 3.2 60.0 1.0 CB C:CYS176 3.2 64.2 1.0 CB C:CYS238 3.3 57.4 1.0 CB C:HIS179 3.4 57.1 1.0 N C:CYS176 3.8 61.6 1.0 CA C:CYS238 3.9 52.0 1.0 CA C:CYS176 4.1 57.3 1.0 NE2 C:HIS179 4.2 64.5 1.0 CD2 C:HIS179 4.2 55.2 1.0 N C:HIS179 4.6 70.1 1.0 N C:ASN239 4.6 54.1 1.0 CA C:HIS179 4.6 67.2 1.0 CA C:CYS242 4.6 55.4 1.0 O C:MET237 4.7 49.6 1.0 C C:CYS238 4.8 54.2 1.0 C C:CYS176 4.8 59.1 1.0 O C:CYS176 4.9 69.5 1.0 C C:ARG175 5.0 62.8 1.0 O C:ASN239 5.0 61.1 1.0

Zinc binding site 4 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:65.8 occ:1.00 ND1 D:HIS179 2.1 58.6 1.0 SG D:CYS176 2.2 75.0 1.0 SG D:CYS238 2.3 58.5 1.0 SG D:CYS242 2.3 56.5 1.0 CG D:HIS179 3.1 60.0 1.0 CE1 D:HIS179 3.1 58.5 1.0 CB D:CYS242 3.1 57.5 1.0 CB D:CYS176 3.1 62.4 1.0 CB D:CYS238 3.3 60.6 1.0 CB D:HIS179 3.4 55.5 1.0 N D:CYS176 3.8 64.9 1.0 CA D:CYS238 4.0 46.0 1.0 CA D:CYS176 4.1 58.6 1.0 NE2 D:HIS179 4.2 61.9 1.0 CD2 D:HIS179 4.2 54.3 1.0 N D:HIS179 4.5 62.0 1.0 CA D:CYS242 4.6 64.8 1.0 N D:ASN239 4.6 62.6 1.0 CA D:HIS179 4.6 59.0 1.0 O D:MET237 4.7 51.8 1.0 C D:CYS238 4.8 54.2 1.0 C D:CYS176 4.8 60.5 1.0 CE B:MET243 4.8 79.0 1.0 O D:CYS176 4.9 69.4 1.0 C D:ARG175 5.0 63.0 1.0

Zinc binding site 5 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn302 b:70.8 occ:1.00 ND1 E:HIS179 2.0 65.6 1.0 SG E:CYS176 2.3 71.2 1.0 SG E:CYS238 2.3 68.2 1.0 SG E:CYS242 2.3 71.0 1.0 CE1 E:HIS179 2.9 65.0 1.0 CG E:HIS179 3.0 61.4 1.0 CB E:CYS242 3.3 76.4 1.0 CB E:CYS238 3.3 68.0 1.0 CB E:CYS176 3.3 70.5 1.0 CB E:HIS179 3.3 63.4 1.0 CA E:CYS238 3.9 57.6 1.0 N E:CYS176 3.9 68.5 1.0 NE2 E:HIS179 4.0 61.1 1.0 CD2 E:HIS179 4.1 54.1 1.0 CA E:CYS176 4.2 64.4 1.0 N E:ASN239 4.5 68.4 1.0 N E:HIS179 4.6 62.5 1.0 CA E:HIS179 4.6 68.0 1.0 O E:MET237 4.6 49.6 1.0 CA E:CYS242 4.7 71.9 1.0 C E:CYS238 4.7 66.2 1.0 C E:CYS176 5.0 62.3 1.0 O E:CYS176 5.0 74.9 1.0 O E:ASN239 5.0 75.5 1.0

Zinc binding site 6 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn302 b:66.3 occ:1.00 ND1 F:HIS179 2.1 69.9 1.0 SG F:CYS176 2.2 69.5 1.0 SG F:CYS238 2.3 57.9 1.0 SG F:CYS242 2.4 68.5 1.0 CG F:HIS179 3.0 63.2 1.0 CE1 F:HIS179 3.0 66.0 1.0 CB F:CYS242 3.2 69.2 1.0 CB F:CYS176 3.2 65.9 1.0 CB F:CYS238 3.3 54.5 1.0 CB F:HIS179 3.3 62.8 1.0 N F:CYS176 3.8 70.1 1.0 CA F:CYS238 3.9 52.9 1.0 NE2 F:HIS179 4.1 64.2 1.0 CA F:CYS176 4.1 66.5 1.0 CD2 F:HIS179 4.1 59.3 1.0 N F:ASN239 4.6 61.3 1.0 N F:HIS179 4.6 66.1 1.0 CA F:HIS179 4.6 66.4 1.0 O F:MET237 4.6 60.3 1.0 CA F:CYS242 4.7 60.0 1.0 C F:CYS238 4.7 52.4 1.0 C F:CYS176 4.8 70.5 1.0 O F:CYS176 4.9 77.2 1.0 C F:ARG175 5.0 66.3 1.0 O F:ASN239 5.0 74.0 1.0

Zinc binding site 7 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn302 b:64.2 occ:1.00 ND1 G:HIS179 2.2 70.8 1.0 SG G:CYS238 2.2 49.8 1.0 SG G:CYS242 2.3 53.8 1.0 SG G:CYS176 2.3 64.2 1.0 CB G:CYS242 3.0 57.1 1.0 CB G:CYS238 3.1 51.4 1.0 CE1 G:HIS179 3.1 71.5 1.0 CG G:HIS179 3.2 69.0 1.0 CB G:CYS176 3.2 63.7 1.0 CB G:HIS179 3.5 62.4 1.0 N G:CYS176 3.8 66.8 1.0 CA G:CYS238 3.8 49.0 1.0 CA G:CYS176 4.1 64.5 1.0 NE2 G:HIS179 4.2 85.1 1.0 CD2 G:HIS179 4.3 82.5 1.0 N G:ASN239 4.4 52.8 1.0 CA G:CYS242 4.5 54.5 1.0 C G:CYS238 4.6 47.0 1.0 O G:MET237 4.7 53.2 1.0 N G:HIS179 4.7 75.1 1.0 CA G:HIS179 4.8 72.6 1.0 O G:ASN239 4.8 57.9 1.0 C G:CYS176 4.9 72.5 1.0 C G:ARG175 4.9 57.3 1.0 N G:CYS238 5.0 53.7 1.0 O G:CYS176 5.0 81.6 1.0

Zinc binding site 8 out of 8 in the Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:68.7 occ:1.00 ND1 H:HIS179 2.1 77.2 1.0 SG H:CYS176 2.2 69.0 1.0 SG H:CYS242 2.3 60.2 1.0 SG H:CYS238 2.3 57.5 1.0 CB H:CYS242 3.1 62.4 1.0 CE1 H:HIS179 3.1 78.8 1.0 CG H:HIS179 3.1 64.2 1.0 CB H:CYS176 3.2 57.4 1.0 CB H:CYS238 3.2 56.4 1.0 CB H:HIS179 3.5 63.1 1.0 N H:CYS176 3.8 64.9 1.0 CA H:CYS238 3.9 49.9 1.0 CA H:CYS176 4.1 62.8 1.0 NE2 H:HIS179 4.2 84.0 1.0 CD2 H:HIS179 4.2 65.9 1.0 N H:ASN239 4.5 56.1 1.0 CA H:CYS242 4.5 64.6 1.0 CG H:ARG175 4.6 72.6 1.0 C H:CYS238 4.7 52.7 1.0 N H:HIS179 4.7 67.9 1.0 CA H:HIS179 4.7 72.7 1.0 O H:MET237 4.7 49.4 1.0 CE F:MET243 4.8 99.6 1.0 C H:CYS176 4.9 66.9 1.0 O H:ASN239 4.9 95.1 1.0 O H:CYS176 5.0 82.7 1.0

Y.F.Xing, M.Lu. Human P53 Core Domain with Hot Spot Mutation R282W in Complex with the Natural CDKN1A(P21) P53-Response Element and Arsenic To Be Published.