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Zinc in PDB 6yyg: Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C

Enzymatic activity of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C

All present enzymatic activity of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C, PDB code: 6yyg was solved by P.Brear, J.Wagstaff, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.05 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.649, 67.195, 79.641, 90, 99.66, 90
R / Rfree (%) 23 / 29.9

Other elements in 6yyg:

The structure of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C (pdb code 6yyg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C, PDB code: 6yyg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6yyg

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Zinc binding site 1 out of 4 in the Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:30.3
occ:1.00
 ND1 A:HIS143 2.3 27.9 1.0
SG A:CYS165 2.5 29.5 1.0
SG A:CYS154 2.5 32.5 1.0
SG A:CYS155 2.5 29.6 1.0
CE1 A:HIS143 3.0 32.0 1.0
CB A:CYS155 3.2 34.3 1.0
CB A:CYS165 3.2 33.3 1.0
CG A:HIS143 3.3 29.4 1.0
N A:CYS155 3.4 35.7 1.0
CB A:CYS154 3.5 33.6 1.0
CB A:HIS143 3.8 26.9 1.0
N A:CYS165 3.9 33.6 1.0
CA A:CYS155 3.9 34.0 1.0
C A:CYS154 4.0 39.0 1.0
CA A:HIS143 4.0 29.1 1.0
CB A:TYR152 4.1 34.5 1.0
NE2 A:HIS143 4.1 25.7 1.0
CA A:CYS165 4.2 32.4 1.0
CD2 A:HIS143 4.2 28.2 1.0
CA A:CYS154 4.2 35.2 1.0
CG A:TYR152 4.4 33.6 1.0
CD A:PRO144 4.5 31.0 1.0
N A:CYS154 4.8 38.0 1.0
NE2 A:GLN157 4.8 38.6 1.0
O A:CYS154 4.8 40.7 1.0
CD1 A:TYR152 4.8 34.9 1.0
CD2 A:TYR152 4.9 32.6 1.0
C A:CYS155 4.9 37.6 1.0
C A:GLY164 5.0 33.3 1.0

Zinc binding site 2 out of 4 in 6yyg

Go back to Zinc Binding Sites List in 6yyg
Zinc binding site 2 out of 4 in the Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:34.0
occ:1.00
 SG B:CYS165 2.0 31.9 1.0
ND1 B:HIS143 2.2 27.1 1.0
SG B:CYS154 2.5 33.3 1.0
SG B:CYS155 2.6 30.6 1.0
CB B:CYS155 3.1 30.8 1.0
CE1 B:HIS143 3.1 30.1 1.0
CB B:CYS165 3.2 37.5 1.0
CG B:HIS143 3.3 30.8 1.0
CB B:CYS154 3.4 34.8 1.0
CB B:HIS143 3.7 29.9 1.0
N B:CYS155 3.7 38.3 1.0
CA B:HIS143 3.8 30.4 1.0
CA B:CYS155 4.0 38.6 1.0
N B:CYS165 4.0 34.9 1.0
CB B:TYR152 4.1 33.6 1.0
C B:CYS154 4.2 37.9 1.0
CA B:CYS165 4.3 35.7 1.0
CA B:CYS154 4.3 37.3 1.0
NE2 B:HIS143 4.3 28.9 1.0
CD B:PRO144 4.3 34.2 1.0
CD2 B:HIS143 4.4 30.8 1.0
CG B:TYR152 4.5 35.1 1.0
N B:CYS154 4.7 33.7 1.0
O B:TYR142 4.8 30.7 1.0
C B:HIS143 4.8 31.8 1.0
CD1 B:TYR152 4.8 33.3 1.0
N B:HIS143 4.9 30.1 1.0
O B:CYS154 4.9 40.0 1.0
N B:PRO144 4.9 33.8 1.0

Zinc binding site 3 out of 4 in 6yyg

Go back to Zinc Binding Sites List in 6yyg
Zinc binding site 3 out of 4 in the Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:47.2
occ:1.00
 ND1 C:HIS143 2.3 39.6 1.0
SG C:CYS165 2.5 40.5 1.0
SG C:CYS154 2.5 49.9 1.0
SG C:CYS155 2.5 51.5 1.0
CE1 C:HIS143 3.1 42.4 1.0
CB C:CYS165 3.2 45.6 1.0
CG C:HIS143 3.3 41.1 1.0
CB C:CYS155 3.3 48.7 1.0
CB C:CYS154 3.5 50.1 1.0
N C:CYS155 3.5 51.3 1.0
CB C:HIS143 3.7 39.8 1.0
CA C:HIS143 3.9 41.2 1.0
N C:CYS165 3.9 49.4 1.0
CA C:CYS155 4.0 51.9 1.0
C C:CYS154 4.1 48.1 1.0
CB C:TYR152 4.1 52.9 1.0
CA C:CYS165 4.2 47.5 1.0
NE2 C:HIS143 4.3 39.7 1.0
CA C:CYS154 4.3 49.7 1.0
CG C:TYR152 4.3 50.1 1.0
CD2 C:HIS143 4.4 40.6 1.0
CD C:PRO144 4.5 46.4 1.0
CD1 C:TYR152 4.7 49.4 1.0
N C:CYS154 4.8 53.9 1.0
CD2 C:TYR152 4.8 49.5 1.0
C C:HIS143 4.9 45.4 1.0
O C:CYS154 4.9 45.1 1.0
O C:TYR142 4.9 39.9 1.0
NE2 C:GLN157 4.9 48.8 1.0
N C:HIS143 5.0 41.2 1.0

Zinc binding site 4 out of 4 in 6yyg

Go back to Zinc Binding Sites List in 6yyg
Zinc binding site 4 out of 4 in the Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 5-(Trifluoromethoxy)Indoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:45.3
occ:1.00
 ND1 D:HIS143 2.0 38.3 1.0
SG D:CYS154 2.2 46.9 1.0
SG D:CYS165 2.4 46.6 1.0
SG D:CYS155 2.4 49.3 1.0
CE1 D:HIS143 2.9 40.4 1.0
CG D:HIS143 3.0 40.2 1.0
CB D:CYS155 3.2 50.1 1.0
CB D:CYS165 3.3 47.5 1.0
CB D:CYS154 3.3 46.6 1.0
CB D:HIS143 3.4 38.6 1.0
CA D:HIS143 3.7 39.5 1.0
N D:CYS155 3.8 49.3 1.0
CB D:TYR152 3.9 47.3 1.0
NE2 D:HIS143 4.1 38.6 1.0
N D:CYS165 4.1 46.9 1.0
C D:CYS154 4.1 50.0 1.0
CA D:CYS155 4.1 49.6 1.0
CD2 D:HIS143 4.1 40.4 1.0
CG D:TYR152 4.1 46.9 1.0
CA D:CYS154 4.1 48.8 1.0
CA D:CYS165 4.3 48.3 1.0
CD1 D:TYR152 4.4 45.5 1.0
N D:CYS154 4.5 47.4 1.0
CD D:PRO144 4.6 42.1 1.0
C D:HIS143 4.8 38.9 1.0
N D:HIS143 4.8 41.0 1.0
CD2 D:TYR152 4.8 42.1 1.0
O D:CYS154 4.9 47.7 1.0
O D:TYR142 5.0 45.0 1.0

Reference:

P.Brear, G.Fischer, M.May, T.Pantelejevs, R.Mathieu, M.Rossmann, J.Wagstaff, B.Blaszczyk, M.Hyvonen. Optimising Crystallographic Systems For Structure-Guided Drug Discovery To Be Published.
Page generated: Tue Oct 29 15:17:57 2024

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