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Calcium in PDB 3tto: Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form

Enzymatic activity of Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form

All present enzymatic activity of Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form:
2.4.1.5;

Protein crystallography data

The structure of Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form, PDB code: 3tto was solved by Y.Brison, T.Pijning, E.Fabre, L.Mourey, S.Morel, G.Potocki-Veronese, P.Monsan, S.Tranier, M.Remaud-Simeon, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.62 / 3.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.840, 140.040, 155.460, 85.36, 90.92, 76.85
R / Rfree (%) 22.4 / 29.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form (pdb code 3tto). 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 Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form, PDB code: 3tto:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3tto

Go back to Calcium Binding Sites List in 3tto
Calcium binding site 1 out of 4 in the Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form


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 Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2866

b:51.3
occ:1.00
 O A:PHE2214 2.5 26.7 1.0
OD1 A:ASP2170 2.6 21.9 1.0
OD2 A:ASP2170 2.6 22.6 1.0
O A:ASP2164 2.8 23.0 1.0
CG A:ASP2170 3.0 22.3 1.0
OD1 A:ASN2693 3.2 24.1 1.0
OD1 A:ASP2164 3.3 27.2 1.0
C A:PHE2214 3.7 26.8 1.0
C A:ASP2164 3.7 24.1 1.0
O A:VAL2171 3.8 23.4 1.0
OD1 A:ASN2801 4.1 24.4 1.0
CA A:ASP2164 4.1 24.7 1.0
ND2 A:ASN2173 4.1 29.9 1.0
CA A:ILE2215 4.1 25.2 1.0
N A:ILE2215 4.4 25.4 1.0
CG A:ASN2693 4.4 24.6 1.0
CG A:ASP2164 4.5 25.9 1.0
CB A:ASP2170 4.5 22.3 1.0
CG2 A:ILE2215 4.5 25.0 1.0
CA A:PHE2214 4.8 27.8 1.0
CB A:ILE2215 4.8 25.6 1.0
N A:PHE2165 4.9 23.8 1.0
O A:ASN2693 4.9 25.8 1.0
CB A:ASP2164 4.9 25.2 1.0
CB A:PHE2214 5.0 28.1 1.0
C A:VAL2171 5.0 24.2 1.0

Calcium binding site 2 out of 4 in 3tto

Go back to Calcium Binding Sites List in 3tto
Calcium binding site 2 out of 4 in the Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form


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 Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2866

b:44.5
occ:1.00
 O B:PHE2214 2.5 20.3 1.0
OD1 B:ASP2170 2.8 19.2 1.0
OD2 B:ASP2170 2.9 19.7 1.0
OD1 B:ASN2693 3.1 21.7 1.0
O B:ASP2164 3.2 24.9 1.0
CG B:ASP2170 3.2 19.5 1.0
O B:VAL2171 3.4 19.2 1.0
C B:PHE2214 3.7 20.2 1.0
ND2 B:ASN2173 3.9 26.0 1.0
OD1 B:ASN2801 3.9 20.2 1.0
OD1 B:ASP2164 3.9 31.5 1.0
CA B:ILE2215 4.0 19.3 1.0
CG2 B:ILE2215 4.1 18.8 1.0
CG B:ASN2693 4.2 21.7 1.0
O B:ASN2693 4.2 21.7 1.0
C B:ASP2164 4.2 26.6 1.0
N B:ILE2215 4.3 19.7 1.0
C B:VAL2171 4.5 19.7 1.0
CB B:ILE2215 4.6 18.9 1.0
CB B:ASP2170 4.6 19.0 1.0
CA B:ASN2693 4.7 21.2 1.0
CA B:ASP2164 4.7 27.9 1.0
N B:VAL2171 4.8 19.1 1.0
CB B:ASN2693 4.9 21.3 1.0
C B:ASN2693 4.9 21.5 1.0
CA B:PHE2214 4.9 20.8 1.0
CG B:ASP2164 5.0 30.0 1.0
CG B:ASN2173 5.0 25.2 1.0
C B:ASP2170 5.0 18.8 1.0
CG B:ASN2801 5.0 19.6 1.0

Calcium binding site 3 out of 4 in 3tto

Go back to Calcium Binding Sites List in 3tto
Calcium binding site 3 out of 4 in the Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form


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 Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2866

b:30.1
occ:1.00
 O C:PHE2214 2.3 25.5 1.0
OD1 C:ASP2170 2.4 24.8 1.0
OD2 C:ASP2170 2.5 24.9 1.0
OD1 C:ASN2693 2.8 23.8 1.0
CG C:ASP2170 2.8 25.3 1.0
O C:ASP2164 2.8 24.0 1.0
OD1 C:ASP2164 3.4 29.4 1.0
C C:PHE2214 3.5 25.0 1.0
OD1 C:ASN2801 3.8 23.6 1.0
C C:ASP2164 3.8 25.2 1.0
CG C:ASN2693 4.0 25.1 1.0
CA C:ILE2215 4.0 26.4 1.0
O C:VAL2171 4.1 26.8 1.0
ND2 C:ASN2173 4.1 28.3 1.0
CA C:ASP2164 4.2 26.5 1.0
N C:ILE2215 4.2 25.5 1.0
CB C:ASP2170 4.4 25.2 1.0
CG C:ASP2164 4.5 28.3 1.0
O C:ASN2693 4.5 28.0 1.0
CG2 C:ILE2215 4.6 25.7 1.0
CA C:PHE2214 4.6 24.3 1.0
CB C:PHE2214 4.9 24.2 1.0
CB C:ILE2215 4.9 25.9 1.0
ND2 C:ASN2693 4.9 25.1 1.0
CB C:ASP2164 5.0 27.4 1.0
CB C:ASN2693 5.0 25.9 1.0
CG C:ASN2801 5.0 23.6 1.0
N C:PHE2165 5.0 24.4 1.0

Calcium binding site 4 out of 4 in 3tto

Go back to Calcium Binding Sites List in 3tto
Calcium binding site 4 out of 4 in the Crystal Structure of Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form


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 Leuconostoc Mesenteroides Nrrl B-1299 N- Terminally Truncated Dextransucrase Dsr-E in Triclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2866

b:29.9
occ:1.00
 OD1 D:ASP2170 2.2 29.4 1.0
O D:PHE2214 2.3 28.8 1.0
OD2 D:ASP2170 2.4 30.3 1.0
OD1 D:ASN2693 2.5 26.3 1.0
CG D:ASP2170 2.7 29.3 1.0
O D:ASP2164 2.8 28.9 1.0
C D:PHE2214 3.5 27.6 1.0
CG D:ASN2693 3.7 27.9 1.0
OD1 D:ASP2164 3.9 37.1 1.0
O D:VAL2171 3.9 23.1 1.0
C D:ASP2164 3.9 30.4 1.0
O D:ASN2693 4.0 27.7 1.0
CA D:ILE2215 4.2 27.7 1.0
CG2 D:ILE2215 4.2 26.5 1.0
CB D:ASP2170 4.2 28.1 1.0
N D:ILE2215 4.3 27.4 1.0
ND2 D:ASN2173 4.4 28.1 1.0
OD1 D:ASN2801 4.5 24.1 1.0
CA D:ASP2164 4.5 31.9 1.0
CA D:ASN2693 4.6 29.3 1.0
CB D:PHE2214 4.6 27.5 1.0
CA D:PHE2214 4.6 27.2 1.0
CB D:ASN2693 4.6 28.7 1.0
ND2 D:ASN2693 4.6 28.0 1.0
C D:ASN2693 4.7 27.9 1.0
CB D:ILE2215 4.8 27.3 1.0
N D:VAL2171 4.8 25.8 1.0
CG D:ASP2164 5.0 34.5 1.0
CA D:ASP2170 5.0 27.0 1.0

Reference:

Y.Brison, T.Pijning, Y.Malbert, E.Fabre, L.Mourey, S.Morel, G.Potocki-Veronese, P.Monsan, S.Tranier, M.Remaud-Simeon, B.W.Dijkstra. Functional and Structural Characterization of Alpha-(1-2) Branching Sucrase Derived From Dsr-E Glucansucrase J.Biol.Chem. V. 287 7915 2012.
ISSN: ISSN 0021-9258
PubMed: 22262856
DOI: 10.1074/JBC.M111.305078
Page generated: Sat Jul 13 19:55:30 2024

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