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Calcium in PDB 2pwf: Crystal Structure of the Mutb D200A Mutant in Complex with Glucose

Enzymatic activity of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose

All present enzymatic activity of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose:
5.4.99.11;

Protein crystallography data

The structure of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose, PDB code: 2pwf was solved by S.Ravaud, X.Robert, R.Haser, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.85 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.980, 85.810, 122.140, 81.77, 81.43, 89.94
R / Rfree (%) 19.8 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Mutb D200A Mutant in Complex with Glucose (pdb code 2pwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Mutb D200A Mutant in Complex with Glucose, PDB code: 2pwf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2pwf

Go back to Calcium Binding Sites List in 2pwf
Calcium binding site 1 out of 4 in the Crystal Structure of the Mutb D200A Mutant in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7000

b:15.0
occ:1.00
 OD1 A:ASP22 2.2 15.2 1.0
OD1 A:ASN24 2.3 22.5 1.0
O A:ILE28 2.3 10.4 1.0
OD2 A:ASP30 2.4 13.5 1.0
OD1 A:ASP26 2.4 12.7 1.0
O A:HOH4531 2.4 23.4 1.0
O A:HOH4715 2.6 26.6 1.0
CG A:ASP22 3.2 16.1 1.0
CG A:ASP26 3.2 15.2 1.0
CG A:ASN24 3.4 21.9 1.0
CG A:ASP30 3.5 12.7 1.0
OD2 A:ASP26 3.6 18.3 1.0
C A:ILE28 3.6 12.2 1.0
CB A:ASP30 4.0 11.9 1.0
OD2 A:ASP22 4.0 18.3 1.0
CB A:ASP22 4.0 16.0 1.0
ND2 A:ASN24 4.1 20.5 1.0
N A:ASN24 4.2 16.7 1.0
CA A:ASP22 4.2 14.1 1.0
N A:ILE28 4.2 13.7 1.0
N A:THR23 4.2 15.8 1.0
CA A:ILE28 4.3 11.9 1.0
O A:GLU75 4.4 14.8 1.0
C A:GLY29 4.4 9.8 1.0
O A:GLY29 4.5 11.6 1.0
CB A:ASN24 4.5 19.4 1.0
N A:ASP26 4.5 13.4 1.0
CB A:ASP26 4.5 16.0 1.0
N A:GLY29 4.6 9.9 1.0
CB A:ILE28 4.6 11.5 1.0
OD1 A:ASP30 4.6 11.4 1.0
C A:ASP22 4.7 14.6 1.0
N A:ASP30 4.7 9.9 1.0
CA A:ASN24 4.7 17.8 1.0
CA A:GLY29 4.7 10.3 1.0
O A:HOH5510 4.7 30.1 1.0
C A:ASN24 4.9 17.4 1.0
N A:GLY25 4.9 15.4 1.0
CA A:ASP26 5.0 13.8 1.0
CA A:ASP30 5.0 10.0 1.0

Calcium binding site 2 out of 4 in 2pwf

Go back to Calcium Binding Sites List in 2pwf
Calcium binding site 2 out of 4 in the Crystal Structure of the Mutb D200A Mutant in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7001

b:17.2
occ:1.00
 OD1 B:ASP22 2.3 19.0 1.0
O B:HOH4405 2.3 29.1 1.0
OD1 B:ASN24 2.4 23.3 1.0
O B:ILE28 2.4 18.5 1.0
OD1 B:ASP26 2.5 14.1 1.0
OD2 B:ASP30 2.5 17.9 1.0
O B:HOH4097 2.6 23.1 1.0
CG B:ASP26 3.3 17.0 1.0
CG B:ASP22 3.3 19.0 1.0
CG B:ASN24 3.5 21.9 1.0
CG B:ASP30 3.6 15.9 1.0
OD2 B:ASP26 3.6 18.2 1.0
C B:ILE28 3.6 17.4 1.0
CB B:ASP30 4.0 16.2 1.0
OD2 B:ASP22 4.1 19.9 1.0
ND2 B:ASN24 4.1 23.0 1.0
N B:ASN24 4.2 21.3 1.0
N B:THR23 4.2 20.7 1.0
CB B:ASP22 4.2 19.2 1.0
CA B:ASP22 4.3 16.8 1.0
N B:ILE28 4.3 15.2 1.0
O B:GLU75 4.3 15.2 1.0
C B:GLY29 4.4 14.6 1.0
CA B:ILE28 4.4 17.1 1.0
O B:GLY29 4.4 15.0 1.0
N B:ASP26 4.5 17.6 1.0
CB B:ASN24 4.5 21.3 1.0
CB B:ASP26 4.6 16.3 1.0
N B:GLY29 4.6 15.5 1.0
CB B:ILE28 4.6 15.9 1.0
OD1 B:ASP30 4.7 15.9 1.0
O B:HOH4625 4.7 35.8 1.0
N B:ASP30 4.7 15.2 1.0
CA B:GLY29 4.7 14.3 1.0
C B:ASP22 4.7 19.8 1.0
CA B:ASN24 4.8 20.9 1.0
O B:HOH5173 4.8 36.4 1.0
C B:ASN24 4.9 19.9 1.0
CA B:ASP26 5.0 18.4 1.0
CA B:ASP30 5.0 15.1 1.0

Calcium binding site 3 out of 4 in 2pwf

Go back to Calcium Binding Sites List in 2pwf
Calcium binding site 3 out of 4 in the Crystal Structure of the Mutb D200A Mutant in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7000

b:16.2
occ:1.00
 OD1 C:ASP22 2.2 17.6 1.0
O C:HOH4531 2.3 36.4 1.0
OD2 C:ASP30 2.3 21.1 1.0
OD1 C:ASN24 2.3 24.3 1.0
O C:ILE28 2.4 16.9 1.0
OD1 C:ASP26 2.5 19.8 1.0
O C:HOH4715 2.5 23.0 1.0
CG C:ASP22 3.2 18.6 1.0
CG C:ASP26 3.3 21.2 1.0
CG C:ASP30 3.4 19.1 1.0
CG C:ASN24 3.4 23.0 1.0
OD2 C:ASP26 3.5 21.8 1.0
C C:ILE28 3.5 16.7 1.0
CB C:ASP30 3.9 14.0 1.0
OD2 C:ASP22 4.0 18.4 1.0
CB C:ASP22 4.1 18.9 1.0
ND2 C:ASN24 4.1 23.6 1.0
N C:ASN24 4.1 22.7 1.0
CA C:ASP22 4.2 19.8 1.0
N C:THR23 4.3 20.0 1.0
C C:GLY29 4.3 14.5 1.0
N C:ILE28 4.3 18.1 1.0
CA C:ILE28 4.4 17.9 1.0
O C:GLU75 4.4 18.1 1.0
CB C:ASN24 4.4 22.9 1.0
O C:GLY29 4.5 13.4 1.0
OD1 C:ASP30 4.5 18.8 1.0
N C:GLY29 4.5 16.4 1.0
N C:ASP30 4.5 14.3 1.0
CB C:ILE28 4.5 18.8 1.0
CB C:ASP26 4.6 20.7 1.0
CA C:GLY29 4.6 14.1 1.0
N C:ASP26 4.6 21.9 1.0
CA C:ASN24 4.7 23.6 1.0
C C:ASP22 4.7 20.8 1.0
O C:HOH5510 4.8 40.8 1.0
CA C:ASP30 4.8 15.1 1.0
C C:ASN24 4.9 24.1 1.0

Calcium binding site 4 out of 4 in 2pwf

Go back to Calcium Binding Sites List in 2pwf
Calcium binding site 4 out of 4 in the Crystal Structure of the Mutb D200A Mutant in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Mutb D200A Mutant in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca7001

b:16.3
occ:1.00
 OD1 D:ASP22 2.2 14.7 1.0
OD1 D:ASN24 2.3 25.6 1.0
O D:HOH4259 2.3 28.9 1.0
OD2 D:ASP30 2.4 16.4 1.0
O D:ILE28 2.4 13.0 1.0
OD1 D:ASP26 2.5 21.2 1.0
O D:HOH4542 2.6 23.1 1.0
CG D:ASP22 3.2 15.9 1.0
CG D:ASP26 3.3 22.7 1.0
CG D:ASN24 3.3 26.4 1.0
OD2 D:ASP26 3.4 23.1 1.0
CG D:ASP30 3.5 13.9 1.0
C D:ILE28 3.6 12.8 1.0
CB D:ASP30 3.9 12.0 1.0
ND2 D:ASN24 3.9 26.5 1.0
CB D:ASP22 4.0 16.9 1.0
OD2 D:ASP22 4.0 14.9 1.0
N D:ASN24 4.1 19.9 1.0
CA D:ASP22 4.2 15.4 1.0
N D:THR23 4.2 17.1 1.0
N D:ILE28 4.3 13.4 1.0
CA D:ILE28 4.4 13.0 1.0
C D:GLY29 4.4 11.6 1.0
O D:GLU75 4.4 15.1 1.0
CB D:ASN24 4.5 23.0 1.0
O D:GLY29 4.5 11.8 1.0
CB D:ILE28 4.5 11.5 1.0
OD1 D:ASP30 4.6 15.0 1.0
N D:ASP26 4.6 18.2 1.0
N D:ASP30 4.6 10.9 1.0
CB D:ASP26 4.6 18.8 1.0
N D:GLY29 4.6 11.3 1.0
C D:ASP22 4.6 17.0 1.0
CA D:GLY29 4.7 11.6 1.0
CA D:ASN24 4.7 21.9 1.0
O D:HOH4503 4.7 34.6 1.0
CA D:ASP30 4.9 12.4 1.0
C D:ASN24 4.9 20.6 1.0
N D:GLY25 4.9 21.6 1.0
CG2 D:ILE28 5.0 10.9 1.0

Reference:

S.Ravaud, X.Robert, H.Watzlawick, R.Haser, R.Mattes, N.Aghajari. Trehalulose Synthase Native and Carbohydrate Complexed Structures Provide Insights Into Sucrose Isomerization. J.Biol.Chem. V. 61 100 2007.
ISSN: ISSN 0021-9258
PubMed: 17597061
DOI: 10.1074/JBC.M704515200
Page generated: Fri Jul 12 15:19:07 2024

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