Atomistry » Zinc » PDB 4lmg-4m2v » 4loe
Atomistry »
  Zinc »
    PDB 4lmg-4m2v »
      4loe »

Zinc in PDB 4loe: Human P53 Core Domain Mutant N239Y

Protein crystallography data

The structure of Human P53 Core Domain Mutant N239Y, PDB code: 4loe was solved by B.D.Wallentine, Y.Wang, H.Luecke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.11 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.877, 71.103, 84.302, 90.00, 90.14, 90.00
R / Rfree (%) 18.6 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Human P53 Core Domain Mutant N239Y (pdb code 4loe). 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 Mutant N239Y, PDB code: 4loe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4loe

Go back to Zinc Binding Sites List in 4loe
Zinc binding site 1 out of 4 in the Human P53 Core Domain Mutant N239Y


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 Mutant N239Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:36.4
occ:1.00
ND1 A:HIS179 2.0 34.5 1.0
SG A:CYS242 2.4 40.2 1.0
SG A:CYS176 2.4 40.8 1.0
SG A:CYS238 2.7 43.7 1.0
CE1 A:HIS179 2.8 36.2 1.0
CG A:HIS179 3.1 35.3 1.0
CB A:CYS242 3.1 35.7 1.0
CB A:CYS176 3.4 35.6 1.0
CB A:HIS179 3.5 38.7 1.0
CB A:CYS238 3.6 47.2 1.0
CA A:CYS238 3.9 36.3 1.0
NE2 A:HIS179 4.0 37.9 1.0
N A:CYS176 4.0 39.0 1.0
CD2 A:HIS179 4.1 38.0 1.0
N A:TYR239 4.2 40.1 1.0
CA A:CYS176 4.3 39.2 1.0
N A:HIS179 4.4 39.4 1.0
CA A:CYS242 4.6 38.0 1.0
C A:CYS238 4.6 36.7 1.0
CA A:HIS179 4.6 37.6 1.0
O A:HOH578 4.6 46.6 1.0
O A:HOH575 4.7 46.5 1.0
O A:CYS176 4.8 41.1 1.0
O A:MET237 4.9 28.7 1.0
C A:CYS176 4.9 41.5 1.0
O A:TYR239 5.0 35.7 1.0

Zinc binding site 2 out of 4 in 4loe

Go back to Zinc Binding Sites List in 4loe
Zinc binding site 2 out of 4 in the Human P53 Core Domain Mutant N239Y


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 Mutant N239Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:41.3
occ:1.00
ND1 B:HIS179 2.0 43.1 1.0
SG B:CYS176 2.4 47.9 1.0
SG B:CYS242 2.4 53.2 1.0
SG B:CYS238 2.6 53.4 1.0
CE1 B:HIS179 2.8 54.8 1.0
CG B:HIS179 3.1 45.0 1.0
CB B:CYS242 3.1 51.6 1.0
CB B:CYS176 3.4 50.4 1.0
CB B:HIS179 3.5 44.3 1.0
CB B:CYS238 3.8 51.5 1.0
CA B:CYS238 3.9 43.6 1.0
N B:CYS176 3.9 45.8 1.0
NE2 B:HIS179 4.0 54.1 1.0
CD2 B:HIS179 4.1 47.8 1.0
N B:TYR239 4.1 52.0 1.0
CA B:CYS176 4.2 46.9 1.0
O D:HOH547 4.2 37.2 1.0
N B:HIS179 4.3 45.2 1.0
C B:CYS238 4.5 50.6 1.0
CA B:HIS179 4.6 42.4 1.0
CA B:CYS242 4.6 55.2 1.0
O B:CYS176 4.9 50.8 1.0
C B:CYS176 4.9 47.4 1.0
O B:TYR239 4.9 50.7 1.0
O B:MET237 5.0 37.2 1.0

Zinc binding site 3 out of 4 in 4loe

Go back to Zinc Binding Sites List in 4loe
Zinc binding site 3 out of 4 in the Human P53 Core Domain Mutant N239Y


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 Mutant N239Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.1
occ:1.00
ND1 C:HIS179 2.0 51.3 1.0
SG C:CYS242 2.3 56.2 1.0
SG C:CYS176 2.4 55.3 1.0
SG C:CYS238 2.5 50.2 1.0
CE1 C:HIS179 2.9 56.0 1.0
CG C:HIS179 3.1 57.6 1.0
CB C:CYS242 3.1 52.6 1.0
CB C:CYS238 3.2 35.4 1.0
CB C:CYS176 3.5 54.4 1.0
CB C:HIS179 3.5 57.0 1.0
CA C:CYS238 3.8 36.9 1.0
N C:CYS176 4.0 45.8 1.0
NE2 C:HIS179 4.0 57.1 1.0
CD2 C:HIS179 4.1 59.5 1.0
CA C:CYS176 4.3 50.5 1.0
N C:TYR239 4.4 38.8 1.0
N C:HIS179 4.5 61.6 1.0
CA C:CYS242 4.5 53.0 1.0
C C:CYS238 4.6 34.3 1.0
CA C:HIS179 4.6 60.5 1.0
O C:HOH586 4.7 48.4 1.0
O C:MET237 4.7 41.7 1.0
O C:CYS176 4.9 55.9 1.0
C C:CYS176 4.9 56.2 1.0
N C:CYS238 5.0 33.6 1.0

Zinc binding site 4 out of 4 in 4loe

Go back to Zinc Binding Sites List in 4loe
Zinc binding site 4 out of 4 in the Human P53 Core Domain Mutant N239Y


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 Mutant N239Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:39.1
occ:1.00
ND1 D:HIS179 1.9 38.5 1.0
SG D:CYS242 2.3 42.1 1.0
SG D:CYS176 2.4 42.0 1.0
SG D:CYS238 2.5 42.3 1.0
CE1 D:HIS179 2.9 44.4 1.0
CG D:HIS179 3.0 43.2 1.0
CB D:CYS242 3.1 39.7 1.0
CB D:CYS176 3.4 38.4 1.0
CB D:HIS179 3.4 40.2 1.0
CB D:CYS238 3.6 34.3 1.0
CA D:CYS238 3.9 34.7 1.0
N D:CYS176 4.0 41.9 1.0
NE2 D:HIS179 4.0 43.6 1.0
CD2 D:HIS179 4.1 43.9 1.0
CA D:CYS176 4.2 38.2 1.0
N D:TYR239 4.3 31.9 1.0
N D:HIS179 4.4 43.6 1.0
CA D:HIS179 4.6 43.8 1.0
CA D:CYS242 4.6 38.5 1.0
O D:HOH632 4.6 55.3 1.0
C D:CYS238 4.6 32.3 1.0
O D:MET237 4.8 31.2 1.0
O D:HOH546 4.8 37.2 1.0
O D:CYS176 4.9 45.7 1.0
C D:CYS176 4.9 42.6 1.0
O D:TYR239 4.9 33.0 1.0

Reference:

B.D.Wallentine, Y.Wang, V.Tretyachenko-Ladokhina, M.Tan, D.F.Senear, H.Luecke. Structures of Oncogenic, Suppressor and Rescued P53 Core-Domain Variants: Mechanisms of Mutant P53 Rescue. Acta Crystallogr.,Sect.D V. 69 2146 2013.
ISSN: ISSN 0907-4449
PubMed: 24100332
DOI: 10.1107/S0907444913020830
Page generated: Sun Oct 27 02:02:45 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy