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Zinc in PDB 2wgx: Human P53 Core Domain Mutant M133L-V203A-Y236F-N239Y-T253I-N268D

Protein crystallography data

The structure of Human P53 Core Domain Mutant M133L-V203A-Y236F-N239Y-T253I-N268D, PDB code: 2wgx was solved by A.C.Joerger, K.H.Khoo, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.61 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.328, 71.075, 104.915, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Human P53 Core Domain Mutant M133L-V203A-Y236F-N239Y-T253I-N268D (pdb code 2wgx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human P53 Core Domain Mutant M133L-V203A-Y236F-N239Y-T253I-N268D, PDB code: 2wgx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2wgx

Go back to Zinc Binding Sites List in 2wgx
Zinc binding site 1 out of 2 in the Human P53 Core Domain Mutant M133L-V203A-Y236F-N239Y-T253I-N268D


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 M133L-V203A-Y236F-N239Y-T253I-N268D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1300

b:13.0
occ:1.00
ND1 B:HIS179 2.0 13.7 1.0
SG B:CYS242 2.3 12.6 1.0
SG B:CYS238 2.3 11.3 1.0
SG B:CYS176 2.4 10.9 1.0
CE1 B:HIS179 3.0 14.6 1.0
CB B:CYS242 3.0 13.2 1.0
CG B:HIS179 3.1 10.6 1.0
CB B:CYS238 3.3 13.5 1.0
CB B:CYS176 3.4 11.8 1.0
CB B:HIS179 3.5 13.2 1.0
CA B:CYS238 3.9 9.9 1.0
O B:HOH2117 3.9 28.6 1.0
N B:CYS176 4.0 9.3 1.0
NE2 B:HIS179 4.1 14.8 1.0
CD2 B:HIS179 4.2 15.2 1.0
CA B:CYS176 4.3 10.7 1.0
N B:HIS179 4.3 13.1 1.0
N B:TYR239 4.4 10.3 1.0
CA B:CYS242 4.5 16.4 1.0
CA B:HIS179 4.6 11.8 1.0
O B:HOH2183 4.6 13.6 1.0
O B:MET237 4.6 10.1 1.0
C B:CYS238 4.7 9.5 1.0
C B:CYS176 5.0 13.9 1.0

Zinc binding site 2 out of 2 in 2wgx

Go back to Zinc Binding Sites List in 2wgx
Zinc binding site 2 out of 2 in the Human P53 Core Domain Mutant M133L-V203A-Y236F-N239Y-T253I-N268D


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 M133L-V203A-Y236F-N239Y-T253I-N268D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1300

b:12.4
occ:1.00
ND1 A:HIS179 2.0 11.4 1.0
SG A:CYS242 2.3 13.1 1.0
SG A:CYS238 2.3 15.5 1.0
SG A:CYS176 2.4 11.4 1.0
CE1 A:HIS179 2.9 12.8 1.0
CG A:HIS179 3.0 8.6 1.0
CB A:CYS242 3.1 14.6 1.0
CB A:CYS176 3.4 12.8 1.0
CB A:HIS179 3.4 11.8 1.0
CB A:CYS238 3.5 17.2 1.0
CA A:CYS238 3.9 11.2 1.0
O A:HOH2118 3.9 28.4 1.0
N A:CYS176 4.0 10.4 1.0
NE2 A:HIS179 4.1 13.2 1.0
CD2 A:HIS179 4.1 12.5 1.0
CA A:CYS176 4.3 9.8 1.0
N A:HIS179 4.3 12.1 1.0
N A:TYR239 4.3 10.4 1.0
CA A:HIS179 4.5 11.6 1.0
CA A:CYS242 4.5 16.3 1.0
O A:HOH2106 4.6 14.3 1.0
C A:CYS238 4.6 12.1 1.0
O A:MET237 4.8 9.9 1.0

Reference:

K.H.Khoo, A.C.Joerger, S.M.V.Freund, A.R.Fersht. Stabilising the Dna-Binding Domain of P53 By Rational Design of Its Hydrophobic Core. Protein Eng.Des.Sel. V. 22 421 2009.
ISSN: ISSN 1741-0126
PubMed: 19515728
DOI: 10.1093/PROTEIN/GZP018
Page generated: Sat Sep 26 04:23:44 2020
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