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Calcium in PDB 4h8u: Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B

Enzymatic activity of Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B

All present enzymatic activity of Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B:
5.4.11.99;

Protein crystallography data

The structure of Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B, PDB code: 4h8u was solved by A.Lipski, R.Haser, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.40 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.370, 73.680, 82.670, 66.15, 74.29, 72.42
R / Rfree (%) 18.9 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B (pdb code 4h8u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B, PDB code: 4h8u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4h8u

Go back to Calcium Binding Sites List in 4h8u
Calcium binding site 1 out of 2 in the Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:17.5
occ:1.00
 O A:HOH1031 2.2 27.3 1.0
OD1 A:ASN24 2.3 22.1 1.0
OD2 A:ASP30 2.4 13.8 1.0
OD1 A:ASP22 2.4 12.2 1.0
OD1 A:ASP26 2.5 21.0 1.0
O A:ILE28 2.5 14.8 1.0
O A:HOH749 2.5 19.6 1.0
CG A:ASP26 3.2 21.4 1.0
CG A:ASP22 3.3 13.3 1.0
CG A:ASN24 3.4 21.7 1.0
OD2 A:ASP26 3.4 23.8 1.0
CG A:ASP30 3.5 13.5 1.0
C A:ILE28 3.6 14.3 1.0
CB A:ASP30 3.9 12.2 1.0
OD2 A:ASP22 3.9 13.2 1.0
ND2 A:ASN24 4.0 21.5 1.0
N A:ASN24 4.1 18.4 1.0
N A:THR23 4.1 16.3 1.0
CB A:ASP22 4.2 13.5 1.0
N A:ILE28 4.2 16.5 1.0
CA A:ASP22 4.2 13.9 1.0
CA A:ILE28 4.3 16.0 1.0
O A:GLU75 4.5 15.9 1.0
CB A:ASN24 4.5 22.0 1.0
C A:GLY29 4.5 10.7 1.0
CB A:ASP26 4.5 21.2 1.0
CB A:ILE28 4.6 16.1 1.0
OD1 A:ASP30 4.6 12.0 1.0
N A:ASP26 4.6 21.1 1.0
O A:GLY29 4.6 10.3 1.0
N A:GLY29 4.7 13.6 1.0
CA A:ASN24 4.7 21.3 1.0
N A:ASP30 4.7 11.0 1.0
C A:ASP22 4.7 15.3 1.0
O A:HOH1190 4.7 26.0 1.0
CA A:GLY29 4.8 11.2 1.0
O A:HOH1389 4.8 44.5 1.0
CA A:ASP30 4.9 12.6 1.0
C A:ASN24 4.9 21.5 1.0
CA A:ASP26 5.0 18.1 1.0
N A:GLY25 5.0 20.6 1.0

Calcium binding site 2 out of 2 in 4h8u

Go back to Calcium Binding Sites List in 4h8u
Calcium binding site 2 out of 2 in the Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutb Inactive Double Mutant D200A-D415N Soaked with Sucrose and Having As Bound Ligands Sucrose in Molecule A and the Reaction Product Trehalulose in Molecule B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:17.9
occ:1.00
 O B:ILE28 2.3 13.9 1.0
OD1 B:ASP22 2.4 15.6 1.0
OD2 B:ASP30 2.4 15.2 1.0
O B:HOH2362 2.4 17.8 1.0
O B:HOH2222 2.4 17.4 1.0
OD1 B:ASN24 2.5 20.7 1.0
OD1 B:ASP26 2.6 15.2 1.0
CG B:ASP26 3.2 15.1 1.0
CG B:ASP22 3.3 14.2 1.0
OD2 B:ASP26 3.3 16.9 1.0
CG B:ASP30 3.4 13.7 1.0
CG B:ASN24 3.5 20.9 1.0
C B:ILE28 3.5 14.9 1.0
CB B:ASP30 3.7 13.0 1.0
OD2 B:ASP22 4.0 15.5 1.0
ND2 B:ASN24 4.1 21.7 1.0
CA B:ASP22 4.1 14.1 1.0
CB B:ASP22 4.1 14.9 1.0
N B:THR23 4.1 17.4 1.0
N B:ILE28 4.2 16.4 1.0
N B:ASN24 4.2 17.3 1.0
CA B:ILE28 4.3 14.8 1.0
C B:GLY29 4.3 11.2 1.0
O B:GLU75 4.4 14.2 1.0
O B:GLY29 4.4 11.1 1.0
CB B:ILE28 4.5 14.2 1.0
N B:GLY29 4.5 13.5 1.0
N B:ASP30 4.5 11.4 1.0
OD1 B:ASP30 4.5 14.4 1.0
CB B:ASN24 4.6 20.1 1.0
CB B:ASP26 4.6 15.2 1.0
CA B:GLY29 4.6 11.2 1.0
C B:ASP22 4.6 16.9 1.0
N B:ASP26 4.7 16.7 1.0
CA B:ASP30 4.7 12.4 1.0
CA B:ASN24 4.8 20.0 1.0
O B:HOH2586 4.8 32.5 1.0
CG2 B:ILE28 4.8 12.7 1.0
N B:GLY27 5.0 15.6 1.0
C B:ASN24 5.0 19.9 1.0

Reference:

A.Lipski, H.Watzlawick, S.Ravaud, X.Robert, R.Haser, R.Mattes, N.Aghajari. Insights Into Product Binding in Sucrose Isomerases From Crystal Structures of Mutb From Rhizobium Sp. To Be Published.
Page generated: Tue Jul 8 22:38:10 2025

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