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Calcium in PDB 3aie: Crystal Structure of Glucansucrase From Streptococcus Mutans

Enzymatic activity of Crystal Structure of Glucansucrase From Streptococcus Mutans

All present enzymatic activity of Crystal Structure of Glucansucrase From Streptococcus Mutans:
2.4.1.5;

Protein crystallography data

The structure of Crystal Structure of Glucansucrase From Streptococcus Mutans, PDB code: 3aie 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) 50.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 293.880, 215.416, 218.946, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Glucansucrase From Streptococcus Mutans (pdb code 3aie). 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 From Streptococcus Mutans, PDB code: 3aie:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4001

b:17.8
occ:1.00
 OE2 A:GLU431 2.3 23.2 1.0
OD1 A:ASP437 2.3 22.1 1.0
O A:GLU431 2.3 22.2 1.0
O A:ASN481 2.4 20.4 1.0
OD1 A:ASP959 2.4 21.9 1.0
O A:HOH1150 2.5 15.6 1.0
OD2 A:ASP437 2.7 21.1 1.0
CG A:ASP437 2.9 19.5 1.0
CD A:GLU431 3.3 25.7 1.0
C A:GLU431 3.4 22.6 1.0
CG A:ASP959 3.5 22.9 1.0
C A:ASN481 3.6 21.3 1.0
CG A:GLU431 3.7 23.3 1.0
CA A:GLU431 4.0 22.6 1.0
OD2 A:ASP959 4.2 21.7 1.0
O A:ASP959 4.2 22.6 1.0
O A:HOH156 4.3 17.4 1.0
CA A:VAL482 4.3 20.8 1.0
OE1 A:GLU431 4.4 23.4 1.0
CB A:ASP437 4.4 20.9 1.0
CG1 A:VAL482 4.4 20.1 1.0
CB A:ASN481 4.5 19.7 1.0
N A:VAL482 4.5 18.5 1.0
N A:PHE432 4.6 22.4 1.0
O A:VAL438 4.6 22.4 1.0
CA A:ASN481 4.6 20.9 1.0
CB A:GLU431 4.6 21.4 1.0
CB A:ASP959 4.7 19.4 1.0
ND2 A:ASN1049 4.7 20.4 1.0
CA A:PHE432 4.8 21.5 1.0
CA A:ASP959 4.8 21.7 1.0
C A:ASP959 4.9 22.5 1.0
CB A:VAL482 5.0 23.4 1.0

Calcium binding site 2 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4001

b:20.0
occ:1.00
 O B:ASN481 2.3 29.8 1.0
OE2 B:GLU431 2.4 31.1 1.0
OD1 B:ASP959 2.4 28.9 1.0
O B:HOH1539 2.4 19.1 1.0
OD1 B:ASP437 2.4 29.9 1.0
O B:GLU431 2.4 32.4 1.0
OD2 B:ASP437 2.6 29.9 1.0
CG B:ASP437 2.9 29.4 1.0
CD B:GLU431 3.4 31.9 1.0
C B:ASN481 3.5 31.4 1.0
C B:GLU431 3.6 31.7 1.0
CG B:ASP959 3.6 30.6 1.0
CG B:GLU431 3.8 30.5 1.0
CA B:GLU431 4.2 30.8 1.0
O B:ASP959 4.2 28.9 1.0
OD2 B:ASP959 4.2 31.1 1.0
O B:HOH200 4.3 16.9 1.0
CA B:VAL482 4.4 30.8 1.0
OE1 B:GLU431 4.4 31.6 1.0
CB B:ASN481 4.4 26.3 1.0
CG1 B:VAL482 4.4 25.0 1.0
CB B:ASP437 4.4 28.6 1.0
N B:VAL482 4.4 29.5 1.0
CA B:ASN481 4.5 28.9 1.0
O B:HOH1118 4.6 19.0 1.0
O B:VAL438 4.6 31.0 1.0
N B:PHE432 4.6 30.7 1.0
CB B:GLU431 4.6 32.0 1.0
CB B:ASP959 4.7 25.8 1.0
ND2 B:ASN1049 4.8 28.5 1.0
CA B:PHE432 4.8 30.6 1.0
CA B:ASP959 4.9 29.2 1.0
C B:ASP959 4.9 28.8 1.0
O B:HOH2927 4.9 35.5 1.0
CB B:VAL482 5.0 31.9 1.0

Calcium binding site 3 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4001

b:17.9
occ:1.00
 OE2 C:GLU431 2.3 22.4 1.0
OD1 C:ASP959 2.3 24.1 1.0
O C:GLU431 2.4 24.2 1.0
OD1 C:ASP437 2.4 23.0 1.0
O C:ASN481 2.4 23.1 1.0
O C:HOH1241 2.5 16.3 1.0
OD2 C:ASP437 2.6 22.8 1.0
CG C:ASP437 2.8 23.3 1.0
CD C:GLU431 3.4 25.1 1.0
C C:GLU431 3.5 24.4 1.0
CG C:ASP959 3.5 23.5 1.0
C C:ASN481 3.6 23.2 1.0
CG C:GLU431 3.8 23.1 1.0
CA C:GLU431 4.0 24.7 1.0
OD2 C:ASP959 4.2 25.1 1.0
O C:ASP959 4.2 24.7 1.0
CB C:ASP437 4.3 23.8 1.0
CA C:VAL482 4.4 23.5 1.0
CB C:ASN481 4.4 22.4 1.0
OE1 C:GLU431 4.4 24.0 1.0
CG1 C:VAL482 4.5 25.0 1.0
O C:HOH1214 4.5 22.2 1.0
N C:VAL482 4.5 22.3 1.0
O C:VAL438 4.5 24.7 1.0
CA C:ASN481 4.5 23.3 1.0
CB C:GLU431 4.6 24.9 1.0
N C:PHE432 4.6 24.8 1.0
CB C:ASP959 4.7 21.1 1.0
ND2 C:ASN1049 4.7 24.1 1.0
CA C:PHE432 4.8 23.1 1.0
CA C:ASP959 4.9 24.7 1.0
C C:ASP959 5.0 24.6 1.0
CA C:ASP437 5.0 24.1 1.0

Calcium binding site 4 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4001

b:18.0
occ:1.00
 OE2 D:GLU431 2.2 24.0 1.0
O D:ASN481 2.4 24.3 1.0
O D:GLU431 2.4 25.2 1.0
OD1 D:ASP437 2.4 23.1 1.0
OD1 D:ASP959 2.4 21.7 1.0
O D:HOH1662 2.5 19.3 1.0
OD2 D:ASP437 2.7 21.1 1.0
CG D:ASP437 2.9 23.7 1.0
CD D:GLU431 3.3 28.7 1.0
C D:GLU431 3.5 25.0 1.0
C D:ASN481 3.6 23.6 1.0
CG D:ASP959 3.6 23.7 1.0
CG D:GLU431 4.0 21.0 1.0
CA D:GLU431 4.1 24.9 1.0
OD2 D:ASP959 4.2 25.1 1.0
O D:ASP959 4.3 25.4 1.0
O D:HOH164 4.3 20.8 1.0
OE1 D:GLU431 4.3 25.3 1.0
CA D:VAL482 4.3 25.3 1.0
CB D:ASN481 4.4 20.2 1.0
N D:VAL482 4.4 23.1 1.0
CG1 D:VAL482 4.4 21.1 1.0
O D:HOH116 4.4 17.8 1.0
CB D:ASP437 4.4 26.3 1.0
CA D:ASN481 4.5 23.0 1.0
O D:VAL438 4.6 25.9 1.0
N D:PHE432 4.6 24.6 1.0
CB D:GLU431 4.7 24.9 1.0
CB D:ASP959 4.7 21.4 1.0
ND2 D:ASN1049 4.8 21.9 1.0
CA D:PHE432 4.9 24.4 1.0
CA D:ASP959 4.9 24.4 1.0
CB D:VAL482 5.0 24.2 1.0
C D:ASP959 5.0 24.3 1.0

Calcium binding site 5 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca4001

b:18.4
occ:1.00
 OE2 E:GLU431 2.3 24.1 1.0
O E:GLU431 2.3 23.3 1.0
O E:ASN481 2.4 22.2 1.0
OD1 E:ASP437 2.4 25.6 1.0
OD1 E:ASP959 2.4 24.2 1.0
O E:HOH1859 2.5 18.8 1.0
OD2 E:ASP437 2.6 26.6 1.0
CG E:ASP437 2.8 25.6 1.0
CD E:GLU431 3.2 26.0 1.0
C E:GLU431 3.4 24.6 1.0
C E:ASN481 3.6 23.4 1.0
CG E:ASP959 3.6 25.1 1.0
CG E:GLU431 3.7 23.6 1.0
CA E:GLU431 4.0 23.3 1.0
O E:ASP959 4.2 25.0 1.0
OD2 E:ASP959 4.2 25.6 1.0
OE1 E:GLU431 4.3 24.0 1.0
CB E:ASP437 4.3 25.3 1.0
O E:HOH155 4.4 17.9 1.0
CA E:VAL482 4.4 24.5 1.0
CB E:ASN481 4.4 21.8 1.0
N E:VAL482 4.4 21.6 1.0
O E:VAL438 4.5 24.7 1.0
CB E:GLU431 4.5 25.4 1.0
CG1 E:VAL482 4.5 23.2 1.0
CA E:ASN481 4.5 23.2 1.0
N E:PHE432 4.6 23.6 1.0
ND2 E:ASN1049 4.6 20.8 1.0
O E:HOH1367 4.6 22.5 1.0
CB E:ASP959 4.7 22.6 1.0
CA E:PHE432 4.8 23.8 1.0
CA E:ASP959 4.8 23.6 1.0
C E:ASP959 4.9 24.9 1.0

Calcium binding site 6 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca4001

b:16.5
occ:1.00
 OD1 F:ASP437 2.2 27.8 1.0
OE1 F:GLU431 2.3 29.0 1.0
O F:HOH1678 2.4 15.1 1.0
O F:ASN481 2.4 27.1 1.0
O F:GLU431 2.4 26.4 1.0
OD1 F:ASP959 2.4 26.7 1.0
OD2 F:ASP437 2.7 25.2 1.0
CG F:ASP437 2.8 26.4 1.0
CD F:GLU431 3.2 28.8 1.0
C F:GLU431 3.5 27.5 1.0
C F:ASN481 3.6 28.6 1.0
CG F:ASP959 3.6 30.7 1.0
CG F:GLU431 3.7 29.0 1.0
CA F:GLU431 4.1 27.9 1.0
O F:ASP959 4.2 26.2 1.0
OD2 F:ASP959 4.2 28.9 1.0
OE2 F:GLU431 4.3 32.6 1.0
O F:HOH1137 4.3 18.2 1.0
CA F:VAL482 4.3 28.9 1.0
CB F:ASP437 4.4 26.9 1.0
CB F:ASN481 4.4 25.7 1.0
CG1 F:VAL482 4.4 26.4 1.0
N F:VAL482 4.5 28.0 1.0
O F:VAL438 4.5 28.7 1.0
CA F:ASN481 4.5 27.1 1.0
CB F:GLU431 4.6 28.3 1.0
N F:PHE432 4.6 25.0 1.0
CB F:ASP959 4.7 26.8 1.0
CA F:ASP959 4.8 28.2 1.0
ND2 F:ASN1049 4.8 25.7 1.0
CA F:PHE432 4.8 26.3 1.0
C F:ASP959 4.9 28.5 1.0
CA F:ASP437 5.0 28.7 1.0
CB F:VAL482 5.0 29.4 1.0

Calcium binding site 7 out of 8 in 3aie

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


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca4001

b:16.9
occ:1.00
 OD1 G:ASP437 2.4 21.1 1.0
OE2 G:GLU431 2.4 22.6 1.0
O G:ASN481 2.4 21.1 1.0
O G:GLU431 2.4 21.1 1.0
OD1 G:ASP959 2.4 18.6 1.0
O G:HOH1311 2.4 16.9 1.0
OD2 G:ASP437 2.6 19.6 1.0
CG G:ASP437 2.8 19.6 1.0
CD G:GLU431 3.3 25.5 1.0
C G:GLU431 3.5 20.5 1.0
C G:ASN481 3.6 24.1 1.0
CG G:ASP959 3.6 20.3 1.0
CG G:GLU431 3.8 19.4 1.0
CA G:GLU431 4.1 22.7 1.0
O G:ASP959 4.2 22.1 1.0
OD2 G:ASP959 4.3 21.2 1.0
O G:HOH1163 4.3 16.6 1.0
OE1 G:GLU431 4.3 23.1 1.0
CA G:VAL482 4.4 21.8 1.0
CB G:ASP437 4.4 20.6 1.0
CB G:ASN481 4.4 17.8 1.0
N G:VAL482 4.5 19.6 1.0
CG1 G:VAL482 4.5 20.7 1.0
CA G:ASN481 4.5 21.4 1.0
O G:VAL438 4.5 22.2 1.0
CB G:GLU431 4.6 21.0 1.0
N G:PHE432 4.6 20.0 1.0
O G:HOH1188 4.6 22.5 1.0
CB G:ASP959 4.7 15.6 1.0
ND2 G:ASN1049 4.8 23.5 1.0
CA G:PHE432 4.8 21.3 1.0
CA G:ASP959 4.9 24.8 1.0
C G:ASP959 5.0 21.3 1.0
CB G:VAL482 5.0 19.8 1.0

Calcium binding site 8 out of 8 in 3aie

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Calcium binding site 8 out of 8 in the Crystal Structure of Glucansucrase From Streptococcus Mutans


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 From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca4001

b:18.4
occ:1.00
 OE2 H:GLU431 2.3 26.1 1.0
O H:GLU431 2.3 23.2 1.0
OD1 H:ASP959 2.4 23.9 1.0
OD1 H:ASP437 2.4 21.5 1.0
O H:ASN481 2.4 20.3 1.0
O H:HOH1140 2.5 17.8 1.0
OD2 H:ASP437 2.6 23.3 1.0
CG H:ASP437 2.8 23.4 1.0
CD H:GLU431 3.2 25.2 1.0
C H:GLU431 3.4 20.6 1.0
CG H:ASP959 3.6 22.6 1.0
C H:ASN481 3.6 25.4 1.0
CG H:GLU431 3.7 21.9 1.0
CA H:GLU431 4.0 23.9 1.0
O H:ASP959 4.1 23.9 1.0
OD2 H:ASP959 4.2 24.2 1.0
O H:HOH187 4.3 16.5 1.0
CA H:VAL482 4.3 24.2 1.0
OE1 H:GLU431 4.3 27.5 1.0
CB H:ASP437 4.4 20.6 1.0
N H:VAL482 4.4 22.0 1.0
CG1 H:VAL482 4.5 17.0 1.0
O H:VAL438 4.5 23.7 1.0
CB H:ASN481 4.5 19.6 1.0
CB H:GLU431 4.5 23.0 1.0
N H:PHE432 4.5 22.4 1.0
CA H:ASN481 4.6 22.4 1.0
O H:HOH1187 4.6 19.2 1.0
CB H:ASP959 4.6 22.0 1.0
ND2 H:ASN1049 4.7 21.0 1.0
CA H:ASP959 4.8 24.6 1.0
CA H:PHE432 4.9 22.4 1.0
C H:ASP959 4.9 26.7 1.0
CB H:VAL482 5.0 22.4 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: Sat Jul 13 07:47:06 2024

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