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Zinc in PDB 4ibs: Human P53 Core Domain with Hot Spot Mutation R273H (Form I)

Protein crystallography data

The structure of Human P53 Core Domain with Hot Spot Mutation R273H (Form I), PDB code: 4ibs was solved by H.Rozenberg, A.Eldar, Y.Diskin-Posner, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.05 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.852, 70.179, 83.730, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R273H (Form I) (pdb code 4ibs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human P53 Core Domain with Hot Spot Mutation R273H (Form I), PDB code: 4ibs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ibs

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Zinc binding site 1 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H (Form I)


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 R273H (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.7
occ:1.00
 ND1 A:HIS179 2.1 19.8 1.0
SG A:CYS176 2.4 22.4 1.0
SG A:CYS238 2.4 21.7 1.0
SG A:CYS242 2.5 25.0 1.0
CE1 A:HIS179 2.9 20.9 1.0
CB A:CYS242 3.1 24.4 1.0
CG A:HIS179 3.1 19.5 1.0
CB A:CYS176 3.2 18.6 1.0
CB A:CYS238 3.5 17.9 1.0
CB A:HIS179 3.6 18.0 1.0
N A:CYS176 3.9 16.2 1.0
CA A:CYS238 4.0 17.1 1.0
NE2 A:HIS179 4.1 19.6 1.0
CA A:CYS176 4.1 19.0 1.0
CD2 A:HIS179 4.2 18.0 1.0
N A:ASN239 4.3 16.3 1.0
CA A:CYS242 4.5 26.9 1.0
N A:HIS179 4.5 20.5 1.0
O A:HOH412 4.6 13.0 1.0
CA A:HIS179 4.7 19.5 1.0
C A:CYS238 4.7 16.8 1.0
O A:MET237 4.7 17.5 1.0
O A:CYS176 4.8 18.6 1.0
C A:CYS176 4.8 19.0 1.0
O A:ASN239 5.0 20.2 1.0

Zinc binding site 2 out of 4 in 4ibs

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Zinc binding site 2 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H (Form I)


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 R273H (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:24.3
occ:1.00
 ND1 B:HIS179 2.2 13.4 1.0
SG B:CYS176 2.3 21.5 1.0
SG B:CYS238 2.5 18.1 1.0
SG B:CYS242 2.6 30.5 1.0
CB B:CYS242 2.8 12.7 1.0
CE1 B:HIS179 3.0 24.9 1.0
CB B:CYS176 3.1 17.9 1.0
CG B:HIS179 3.3 18.8 1.0
CB B:CYS238 3.4 20.4 1.0
CB B:HIS179 3.7 17.5 1.0
N B:CYS176 3.8 20.0 1.0
CA B:CYS238 4.0 20.9 1.0
CA B:CYS176 4.1 19.1 1.0
NE2 B:HIS179 4.2 25.1 1.0
O A:HOH476 4.2 19.6 1.0
CA B:CYS242 4.2 20.9 1.0
O B:HOH480 4.3 16.2 1.0
CD2 B:HIS179 4.3 22.9 1.0
N B:ASN239 4.4 20.8 1.0
N B:HIS179 4.6 16.7 1.0
C B:CYS238 4.7 21.0 1.0
CA B:HIS179 4.8 18.0 1.0
O B:MET237 4.8 14.8 1.0
C B:CYS176 4.9 19.0 1.0
O B:ASN239 4.9 21.7 1.0
O B:CYS176 4.9 18.7 1.0
C B:CYS242 5.0 26.6 1.0
C B:ARG175 5.0 18.7 1.0

Zinc binding site 3 out of 4 in 4ibs

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Zinc binding site 3 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H (Form I)


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 R273H (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:20.9
occ:1.00
 ND1 C:HIS179 2.1 19.2 1.0
SG C:CYS176 2.4 24.8 1.0
SG C:CYS238 2.4 21.5 1.0
SG C:CYS242 2.5 26.5 1.0
CB C:CYS242 3.0 15.6 1.0
CE1 C:HIS179 3.0 18.7 1.0
CG C:HIS179 3.1 19.6 1.0
CB C:CYS176 3.4 16.3 1.0
CB C:CYS238 3.4 21.2 1.0
CB C:HIS179 3.5 18.8 1.0
N C:CYS176 3.8 19.3 1.0
CA C:CYS238 4.0 18.5 1.0
NE2 C:HIS179 4.2 19.4 1.0
CA C:CYS176 4.2 19.1 1.0
O C:HOH473 4.2 34.2 1.0
CD2 C:HIS179 4.2 20.7 1.0
CA C:CYS242 4.4 20.0 1.0
N C:ASN239 4.5 20.2 1.0
O C:HOH460 4.5 18.5 1.0
N C:HIS179 4.6 18.6 1.0
CA C:HIS179 4.7 17.6 1.0
C C:CYS238 4.7 18.5 1.0
O C:MET237 4.8 14.3 1.0
O C:CYS176 4.8 21.1 1.0
C C:CYS176 4.9 20.1 1.0
O C:ASN239 5.0 22.3 1.0
C C:ARG175 5.0 19.2 1.0

Zinc binding site 4 out of 4 in 4ibs

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Zinc binding site 4 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H (Form I)


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 R273H (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:29.0
occ:1.00
 ND1 D:HIS179 2.1 19.7 1.0
SG D:CYS176 2.4 21.8 1.0
SG D:CYS242 2.4 25.2 1.0
SG D:CYS238 2.4 25.1 1.0
CB D:CYS242 2.9 20.9 1.0
CE1 D:HIS179 2.9 23.9 1.0
CB D:CYS176 3.1 18.5 1.0
CG D:HIS179 3.3 18.6 1.0
CB D:CYS238 3.5 23.7 1.0
N D:CYS176 3.7 20.0 1.0
CB D:HIS179 3.8 19.7 1.0
CA D:CYS176 4.0 20.0 1.0
CA D:CYS238 4.1 20.0 1.0
NE2 D:HIS179 4.1 22.2 1.0
CD2 D:HIS179 4.3 19.8 1.0
CA D:CYS242 4.3 22.4 1.0
N D:ASN239 4.4 21.9 1.0
C D:CYS238 4.7 21.7 1.0
O D:ASN239 4.7 22.9 1.0
N D:HIS179 4.8 23.9 1.0
O D:CYS176 4.8 19.8 1.0
C D:CYS176 4.8 21.1 1.0
C D:ARG175 4.9 22.4 1.0
CA D:HIS179 4.9 22.5 1.0

Reference:

A.Eldar, H.Rozenberg, Y.Diskin-Posner, R.Rohs, Z.Shakked. Structural Studies of P53 Inactivation By Dna-Contact Mutations and Its Rescue By Suppressor Mutations Via Alternative Protein-Dna Interactions. Nucleic Acids Res. V. 41 8748 2013.
ISSN: ISSN 0305-1048
PubMed: 23863845
DOI: 10.1093/NAR/GKT630
Page generated: Wed Dec 16 05:23:35 2020

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