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Calcium in PDB 3aib: Crystal Structure of Glucansucrase

Enzymatic activity of Crystal Structure of Glucansucrase

All present enzymatic activity of Crystal Structure of Glucansucrase:
2.4.1.5;

Protein crystallography data

The structure of Crystal Structure of Glucansucrase, PDB code: 3aib was solved by K.Ito, S.Ito, T.Shimamura, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.67 / 3.09
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 295.420, 213.940, 220.980, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Glucansucrase (pdb code 3aib). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Glucansucrase, PDB code: 3aib:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3aib

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Calcium binding site 1 out of 8 in the Crystal Structure of Glucansucrase


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 Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4001

b:29.4
occ:1.00
OD1 A:ASP959 2.1 29.2 1.0
O A:ASN481 2.2 28.3 1.0
O A:GLU431 2.4 29.7 1.0
OE2 A:GLU431 2.4 29.5 1.0
OD1 A:ASP437 2.4 30.6 1.0
OD2 A:ASP437 2.7 30.9 1.0
CG A:ASP437 2.9 31.1 1.0
CD A:GLU431 3.3 29.6 1.0
CG A:ASP959 3.4 29.2 1.0
C A:ASN481 3.4 27.7 1.0
C A:GLU431 3.5 29.9 1.0
CG A:GLU431 3.9 30.3 1.0
O A:ASP959 4.0 30.5 1.0
OD2 A:ASP959 4.1 29.5 1.0
CA A:GLU431 4.2 29.6 1.0
CG1 A:VAL482 4.2 27.9 1.0
CA A:VAL482 4.2 27.7 1.0
N A:VAL482 4.2 27.4 1.0
CB A:ASN481 4.3 27.7 1.0
OE1 A:GLU431 4.3 29.3 1.0
CA A:ASN481 4.4 27.4 1.0
CB A:ASP437 4.4 32.1 1.0
CB A:ASP959 4.4 28.8 1.0
O A:VAL438 4.6 30.9 1.0
N A:PHE432 4.6 30.5 1.0
CB A:GLU431 4.7 30.2 1.0
CA A:ASP959 4.7 29.3 1.0
C A:ASP959 4.8 30.2 1.0
ND2 A:ASN1049 4.8 31.4 1.0
CB A:VAL482 4.8 27.6 1.0
CA A:PHE432 4.9 31.0 1.0

Calcium binding site 2 out of 8 in 3aib

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Calcium binding site 2 out of 8 in the Crystal Structure of Glucansucrase


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 Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4001

b:32.5
occ:1.00
OD1 B:ASP959 2.2 31.8 1.0
OE2 B:GLU431 2.3 33.0 1.0
O B:ASN481 2.3 31.6 1.0
OD1 B:ASP437 2.6 33.6 1.0
O B:GLU431 2.6 33.6 1.0
OD2 B:ASP437 2.7 34.1 1.0
CG B:ASP437 2.9 34.2 1.0
CD B:GLU431 3.4 33.6 1.0
CG B:ASP959 3.5 31.7 1.0
C B:ASN481 3.5 31.3 1.0
C B:GLU431 3.6 34.2 1.0
O B:ASP959 4.0 32.3 1.0
OD2 B:ASP959 4.1 32.2 1.0
CG B:GLU431 4.2 34.7 1.0
CA B:VAL482 4.2 30.9 1.0
CA B:GLU431 4.2 34.2 1.0
CG1 B:VAL482 4.3 30.4 1.0
OE1 B:GLU431 4.3 33.5 1.0
N B:VAL482 4.4 31.0 1.0
CB B:ASP437 4.4 35.2 1.0
CB B:ASN481 4.4 31.6 1.0
O B:VAL438 4.5 32.9 1.0
CA B:ASN481 4.5 31.5 1.0
CB B:ASP959 4.5 31.1 1.0
ND2 B:ASN1049 4.5 34.5 1.0
N B:PHE432 4.7 35.2 1.0
CB B:GLU431 4.8 35.0 1.0
CB B:VAL482 4.8 30.4 1.0
C B:ASP959 4.8 31.9 1.0
CA B:ASP959 4.8 31.1 1.0
CA B:PHE432 4.9 35.5 1.0

Calcium binding site 3 out of 8 in 3aib

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Calcium binding site 3 out of 8 in the Crystal Structure of Glucansucrase


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 Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4001

b:29.7
occ:1.00
O C:ASN481 2.1 29.1 1.0
OD1 C:ASP437 2.4 30.3 1.0
O C:GLU431 2.4 29.8 1.0
OE2 C:GLU431 2.4 30.2 1.0
OD1 C:ASP959 2.4 29.3 1.0
OD2 C:ASP437 3.0 30.8 1.0
CG C:ASP437 3.0 30.7 1.0
CD C:GLU431 3.1 30.2 1.0
C C:ASN481 3.3 28.7 1.0
C C:GLU431 3.5 29.9 1.0
CG C:ASP959 3.6 29.3 1.0
CG C:GLU431 3.7 30.5 1.0
OE1 C:GLU431 3.9 30.1 1.0
CA C:GLU431 4.0 29.8 1.0
CA C:VAL482 4.1 29.0 1.0
N C:VAL482 4.1 28.7 1.0
O C:ASP959 4.1 30.2 1.0
CG1 C:VAL482 4.2 29.0 1.0
OD2 C:ASP959 4.2 29.4 1.0
O C:HOH166 4.3 30.3 1.0
CB C:ASN481 4.3 28.4 1.0
CA C:ASN481 4.4 28.4 1.0
CB C:GLU431 4.5 30.3 1.0
CB C:ASP437 4.5 31.2 1.0
O C:VAL438 4.6 31.1 1.0
N C:PHE432 4.6 30.2 1.0
CB C:ASP959 4.7 29.2 1.0
CB C:VAL482 4.7 29.0 1.0
CA C:ASP959 4.8 29.5 1.0
ND2 C:ASN1049 4.8 31.5 1.0
C C:ASP959 4.9 30.0 1.0
CA C:PHE432 4.9 30.4 1.0

Calcium binding site 4 out of 8 in 3aib

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Calcium binding site 4 out of 8 in the Crystal Structure of Glucansucrase


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 Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4001

b:30.8
occ:1.00
OE2 D:GLU431 2.1 31.1 1.0
OD1 D:ASP959 2.3 30.2 1.0
O D:ASN481 2.4 29.7 1.0
O D:GLU431 2.5 31.2 1.0
OD2 D:ASP437 2.6 32.4 1.0
OD1 D:ASP437 2.7 32.1 1.0
CG D:ASP437 3.0 32.6 1.0
CD D:GLU431 3.2 31.4 1.0
CG D:ASP959 3.5 30.1 1.0
C D:ASN481 3.6 29.1 1.0
C D:GLU431 3.7 31.5 1.0
CG D:GLU431 3.8 32.2 1.0
O D:ASP959 3.9 31.4 1.0
OD2 D:ASP959 4.2 30.4 1.0
OE1 D:GLU431 4.2 31.1 1.0
CG1 D:VAL482 4.2 28.9 1.0
CA D:GLU431 4.3 31.4 1.0
CA D:VAL482 4.3 29.0 1.0
CB D:ASP437 4.4 33.6 1.0
N D:VAL482 4.4 28.7 1.0
O D:VAL438 4.4 32.3 1.0
CB D:ASN481 4.5 28.9 1.0
CB D:ASP959 4.5 29.7 1.0
CA D:ASN481 4.5 28.8 1.0
CB D:GLU431 4.7 32.1 1.0
CA D:ASP959 4.7 30.1 1.0
C D:ASP959 4.7 31.0 1.0
O D:HOH87 4.7 30.9 1.0
N D:PHE432 4.8 32.1 1.0
CB D:VAL482 4.8 28.8 1.0
ND2 D:ASN1049 4.9 33.3 1.0
CA D:ASP437 5.0 33.6 1.0

Calcium binding site 5 out of 8 in 3aib

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Calcium binding site 5 out of 8 in the Crystal Structure of Glucansucrase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca4001

b:28.3
occ:1.00
OD1 G:ASP437 2.0 29.1 1.0
O G:ASN481 2.2 27.5 1.0
OE2 G:GLU431 2.3 28.4 1.0
OD1 G:ASP959 2.4 28.0 1.0
O G:GLU431 2.5 28.8 1.0
CG G:ASP437 2.8 29.6 1.0
OD2 G:ASP437 3.0 29.6 1.0
CD G:GLU431 3.3 28.5 1.0
C G:ASN481 3.4 27.1 1.0
C G:GLU431 3.6 29.1 1.0
CG G:ASP959 3.6 28.1 1.0
CG G:GLU431 3.9 29.1 1.0
O G:ASP959 4.1 28.9 1.0
CA G:GLU431 4.1 28.8 1.0
CA G:VAL482 4.1 26.8 1.0
N G:VAL482 4.2 26.7 1.0
CB G:ASP437 4.2 30.3 1.0
OE1 G:GLU431 4.2 28.2 1.0
CG1 G:VAL482 4.2 26.9 1.0
OD2 G:ASP959 4.3 28.5 1.0
CB G:ASN481 4.3 27.3 1.0
CA G:ASN481 4.4 27.0 1.0
O G:VAL438 4.5 29.1 1.0
CB G:GLU431 4.6 29.2 1.0
CB G:ASP959 4.7 27.8 1.0
N G:PHE432 4.7 29.7 1.0
CB G:VAL482 4.8 26.6 1.0
ND2 G:ASN1049 4.8 29.7 1.0
CA G:ASP959 4.8 28.0 1.0
C G:ASP959 4.8 28.6 1.0
CA G:ASP437 4.9 30.4 1.0

Calcium binding site 6 out of 8 in 3aib

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Calcium binding site 6 out of 8 in the Crystal Structure of Glucansucrase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca4001

b:32.3
occ:1.00
OE2 E:GLU431 2.2 32.6 1.0
O E:ASN481 2.3 30.6 1.0
OD1 E:ASP959 2.4 31.3 1.0
OD1 E:ASP437 2.4 33.8 1.0
O E:GLU431 2.5 32.6 1.0
OD2 E:ASP437 2.7 34.5 1.0
CG E:ASP437 2.9 34.6 1.0
CD E:GLU431 3.2 32.8 1.0
C E:ASN481 3.5 29.8 1.0
CG E:ASP959 3.5 31.3 1.0
C E:GLU431 3.6 32.8 1.0
CG E:GLU431 3.8 33.7 1.0
O E:ASP959 4.1 33.5 1.0
OD2 E:ASP959 4.2 31.6 1.0
CA E:GLU431 4.2 32.4 1.0
OE1 E:GLU431 4.2 32.5 1.0
CA E:VAL482 4.3 29.9 1.0
N E:VAL482 4.3 29.4 1.0
CB E:ASP437 4.4 35.9 1.0
CB E:ASN481 4.4 29.4 1.0
O E:VAL438 4.4 34.7 1.0
CG1 E:VAL482 4.5 29.8 1.0
CA E:ASN481 4.5 29.3 1.0
CB E:ASP959 4.6 31.0 1.0
CB E:GLU431 4.7 33.4 1.0
CA E:ASP959 4.7 31.7 1.0
N E:PHE432 4.8 33.5 1.0
C E:ASP959 4.8 33.0 1.0
CB E:VAL482 4.9 29.7 1.0
CA E:ASP437 5.0 36.2 1.0

Calcium binding site 7 out of 8 in 3aib

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Calcium binding site 7 out of 8 in the Crystal Structure of Glucansucrase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca4001

b:40.3
occ:1.00
OD1 F:ASP437 2.1 40.6 1.0
OE1 F:GLU431 2.3 40.2 1.0
O F:ASN481 2.3 40.0 1.0
OD1 F:ASP959 2.3 40.6 1.0
O F:GLU431 2.3 39.8 1.0
CG F:ASP437 3.0 40.7 1.0
OD2 F:ASP437 3.1 40.7 1.0
CD F:GLU431 3.2 40.0 1.0
C F:GLU431 3.5 39.6 1.0
CG F:ASP959 3.5 40.9 1.0
C F:ASN481 3.5 39.9 1.0
CG F:GLU431 3.8 39.9 1.0
CG1 F:VAL482 4.1 40.9 1.0
CA F:GLU431 4.1 39.4 1.0
OD2 F:ASP959 4.2 41.0 1.0
O F:ASP959 4.2 41.6 1.0
OE2 F:GLU431 4.2 39.9 1.0
CA F:VAL482 4.2 40.4 1.0
N F:VAL482 4.4 40.1 1.0
CB F:ASN481 4.4 39.8 1.0
CB F:ASP437 4.4 41.0 1.0
CA F:ASN481 4.5 39.7 1.0
N F:PHE432 4.5 39.6 1.0
O F:VAL438 4.6 41.7 1.0
CB F:GLU431 4.6 39.6 1.0
CB F:ASP959 4.6 41.3 1.0
CB F:VAL482 4.7 40.8 1.0
CA F:PHE432 4.8 39.8 1.0
CA F:ASP959 4.9 41.7 1.0
C F:ASP959 4.9 41.8 1.0
ND2 F:ASN1049 5.0 41.1 1.0

Calcium binding site 8 out of 8 in 3aib

Go back to Calcium Binding Sites List in 3aib
Calcium binding site 8 out of 8 in the Crystal Structure of Glucansucrase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Glucansucrase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca4001

b:32.6
occ:1.00
OE2 H:GLU431 2.3 32.4 1.0
OD1 H:ASP959 2.3 32.3 1.0
OD1 H:ASP437 2.3 34.3 1.0
O H:ASN481 2.3 30.9 1.0
O H:GLU431 2.5 32.6 1.0
OD2 H:ASP437 2.6 34.6 1.0
CG H:ASP437 2.8 35.0 1.0
CD H:GLU431 3.4 32.4 1.0
CG H:ASP959 3.5 32.6 1.0
C H:GLU431 3.6 32.7 1.0
C H:ASN481 3.6 30.1 1.0
CG H:GLU431 3.8 33.2 1.0
CA H:GLU431 4.1 32.0 1.0
OD2 H:ASP959 4.1 33.0 1.0
O H:ASP959 4.2 34.8 1.0
CA H:VAL482 4.3 30.2 1.0
CG1 H:VAL482 4.3 30.8 1.0
CB H:ASP437 4.3 36.3 1.0
N H:VAL482 4.4 29.7 1.0
OE1 H:GLU431 4.4 32.0 1.0
CB H:ASN481 4.5 30.1 1.0
O H:VAL438 4.5 35.0 1.0
CA H:ASN481 4.5 29.6 1.0
CB H:GLU431 4.6 32.8 1.0
CB H:ASP959 4.6 32.5 1.0
N H:PHE432 4.6 33.4 1.0
CA H:ASP959 4.8 33.2 1.0
ND2 H:ASN1049 4.8 35.1 1.0
CB H:VAL482 4.8 30.5 1.0
CA H:PHE432 4.9 34.2 1.0
C H:ASP959 4.9 34.5 1.0
CA H:ASP437 5.0 36.9 1.0

Reference:

K.Ito, S.Ito, T.Shimamura, S.Weyand, Y.Kawarasaki, T.Misaka, K.Abe, T.Kobayashi, A.D.Cameron, S.Iwata. Crystal Structure of Glucansucrase From the Dental Caries Pathogen Streptococcus Mutans. J.Mol.Biol. V. 408 177 2011.
ISSN: ISSN 0022-2836
PubMed: 21354427
DOI: 10.1016/J.JMB.2011.02.028
Page generated: Tue Jul 8 10:46:58 2025

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