Zinc in PDB 6tvn: Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase

Enzymatic activity of Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase

All present enzymatic activity of Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase, PDB code: 6tvn 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) 66.45 / 2.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.775, 65.400, 79.752, 90.00, 101.34, 90.00
R / Rfree (%) 22.5 / 25.7

Other elements in 6tvn:

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

Bromine (Br) 4 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase (pdb code 6tvn). 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-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase, PDB code: 6tvn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6tvn

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Zinc binding site 1 out of 4 in the Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase


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-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:47.0
occ:1.00
 ND1 A:HIS143 2.3 44.5 1.0
SG A:CYS154 2.5 57.6 1.0
SG A:CYS165 2.5 57.9 1.0
SG A:CYS155 2.5 56.2 1.0
CB A:CYS165 2.9 54.6 1.0
CE1 A:HIS143 3.2 44.6 1.0
CB A:CYS155 3.2 52.8 1.0
CG A:HIS143 3.2 43.0 1.0
CB A:HIS143 3.5 39.3 1.0
CB A:CYS154 3.7 53.3 1.0
N A:CYS155 3.7 53.6 1.0
CA A:HIS143 3.7 39.3 1.0
N A:CYS165 3.8 56.2 1.0
CA A:CYS165 4.0 55.2 1.0
CA A:CYS155 4.1 53.3 1.0
C A:CYS154 4.2 56.3 1.0
CB A:TYR152 4.2 45.7 1.0
NE2 A:HIS143 4.3 45.3 1.0
CD2 A:HIS143 4.3 46.0 1.0
CA A:CYS154 4.4 52.4 1.0
CD A:PRO144 4.5 44.7 1.0
CG A:TYR152 4.5 46.0 1.0
N A:CYS154 4.7 51.5 1.0
C A:HIS143 4.7 46.6 1.0
N A:HIS143 4.8 39.7 1.0
O A:TYR142 4.8 43.9 1.0
C A:GLY164 4.9 59.1 1.0
CD1 A:TYR152 4.9 46.8 1.0
O A:CYS154 4.9 55.7 1.0
N A:PRO144 4.9 43.6 1.0
C A:CYS165 4.9 62.8 1.0

Zinc binding site 2 out of 4 in 6tvn

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Zinc binding site 2 out of 4 in the Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase


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-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:47.5
occ:1.00
 ND1 B:HIS143 2.2 45.2 1.0
SG B:CYS154 2.5 64.4 1.0
SG B:CYS155 2.5 61.7 1.0
SG B:CYS165 2.5 64.6 1.0
CE1 B:HIS143 3.1 45.1 1.0
CB B:CYS165 3.2 60.8 1.0
CG B:HIS143 3.2 44.0 1.0
CB B:CYS155 3.3 58.2 1.0
CB B:HIS143 3.5 40.8 1.0
CB B:CYS154 3.7 59.8 1.0
N B:CYS155 3.7 59.2 1.0
CA B:HIS143 3.8 40.9 1.0
N B:CYS165 3.9 60.8 1.0
CB B:TYR152 4.1 43.2 1.0
CA B:CYS155 4.2 58.5 1.0
NE2 B:HIS143 4.2 45.5 1.0
CA B:CYS165 4.2 60.2 1.0
CD2 B:HIS143 4.3 45.6 1.0
C B:CYS154 4.3 62.3 1.0
CD B:PRO144 4.4 40.0 1.0
CG B:TYR152 4.4 40.9 1.0
CA B:CYS154 4.5 58.6 1.0
N B:HIS143 4.8 42.6 1.0
N B:CYS154 4.8 56.8 1.0
CD1 B:TYR152 4.8 41.2 1.0
C B:HIS143 4.8 45.0 1.0
O B:TYR142 4.9 46.0 1.0
CD2 B:TYR152 4.9 41.5 1.0
NE2 B:GLN157 5.0 60.3 1.0
C B:GLY164 5.0 62.5 1.0
N B:PRO144 5.0 40.5 1.0

Zinc binding site 3 out of 4 in 6tvn

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Zinc binding site 3 out of 4 in the Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase


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-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:52.4
occ:1.00
 ND1 C:HIS143 2.2 45.3 1.0
SG C:CYS165 2.4 56.2 1.0
SG C:CYS154 2.5 56.8 1.0
SG C:CYS155 2.5 54.3 1.0
CB C:CYS155 3.1 51.7 1.0
CB C:CYS165 3.1 52.7 1.0
CE1 C:HIS143 3.2 44.4 1.0
CG C:HIS143 3.2 43.6 1.0
CB C:HIS143 3.5 40.6 1.0
CB C:CYS154 3.6 53.0 1.0
N C:CYS155 3.6 53.1 1.0
CA C:HIS143 3.7 41.1 1.0
N C:CYS165 3.8 53.6 1.0
CA C:CYS155 4.0 53.0 1.0
C C:CYS154 4.0 56.3 1.0
CB C:TYR152 4.1 53.2 1.0
CA C:CYS165 4.1 52.8 1.0
NE2 C:HIS143 4.3 44.8 1.0
CA C:CYS154 4.3 53.2 1.0
CD2 C:HIS143 4.3 44.6 1.0
CG C:TYR152 4.4 53.0 1.0
CD C:PRO144 4.5 43.9 1.0
O C:CYS154 4.7 55.9 1.0
N C:CYS154 4.7 54.1 1.0
C C:HIS143 4.7 48.2 1.0
N C:HIS143 4.8 42.4 1.0
CD1 C:TYR152 4.8 54.7 1.0
CD2 C:TYR152 4.8 53.2 1.0
C C:GLY164 4.9 57.1 1.0
N C:PRO144 5.0 44.0 1.0
O C:TYR142 5.0 46.2 1.0

Zinc binding site 4 out of 4 in 6tvn

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Zinc binding site 4 out of 4 in the Crystal Structure of 5-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase


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-Bromoindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:62.1
occ:1.00
 ND1 D:HIS143 2.3 51.7 1.0
CB D:CYS165 2.4 69.4 1.0
SG D:CYS154 2.5 74.2 1.0
SG D:CYS155 2.5 72.4 1.0
SG D:CYS165 2.5 74.0 1.0
CE1 D:HIS143 3.1 50.8 1.0
CB D:CYS155 3.2 68.8 1.0
CA D:CYS165 3.3 68.6 1.0
CG D:HIS143 3.4 50.4 1.0
N D:CYS155 3.6 70.0 1.0
N D:CYS165 3.7 67.5 1.0
CB D:HIS143 3.8 46.9 1.0
CB D:CYS154 3.9 70.4 1.0
CA D:CYS155 4.0 69.0 1.0
CA D:HIS143 4.0 47.2 1.0
CB D:TYR152 4.1 66.9 1.0
C D:CYS154 4.2 74.5 1.0
NE2 D:HIS143 4.3 51.4 1.0
CG D:TYR152 4.4 65.5 1.0
CD2 D:HIS143 4.4 52.3 1.0
CA D:CYS154 4.5 70.0 1.0
CD D:PRO144 4.6 52.1 1.0
C D:CYS165 4.7 70.8 1.0
CD1 D:TYR152 4.7 66.8 1.0
C D:GLY164 4.8 67.7 1.0
O D:TYR142 4.9 51.9 1.0
O D:CYS154 4.9 75.3 1.0
NE2 D:GLN157 4.9 67.8 1.0
CD2 D:TYR152 5.0 65.1 1.0
N D:CYS154 5.0 70.1 1.0

Reference:

P.Brear, G.Fischer, M.May, T.Pantelejevs, R.Mathieu, M.Rossmann, J.Wagstaff, B.Blaszczyk, M.Hyvonen. Crystal Structure of 1-Methylindoline-2,3-Dione Covalently Bound to the pH Domain of Bruton'S Tyrosine Kinase Mutant R28C To Be Published.
Page generated: Wed Dec 16 12:56:14 2020

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