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Calcium in PDB 2eac: Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin

Enzymatic activity of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin

All present enzymatic activity of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin:
3.2.1.63;

Protein crystallography data

The structure of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin, PDB code: 2eac was solved by M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.668, 111.702, 98.346, 90.00, 95.31, 90.00
R / Rfree (%) 15 / 19.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin (pdb code 2eac). 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 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin, PDB code: 2eac:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2eac

Go back to Calcium Binding Sites List in 2eac
Calcium binding site 1 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin


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 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca899

b:22.4
occ:1.00
 OE1 A:GLU76 2.6 7.8 1.0
O A:SER385 2.7 8.0 1.0
O A:LEU392 2.8 9.5 1.0
O A:GLY56 2.9 9.6 1.0
O A:HOH2022 3.1 8.7 1.0
CG2 A:ILE399 3.4 4.9 1.0
CD A:GLU76 3.7 8.4 1.0
O A:PRO393 3.7 7.6 1.0
CB A:GLU76 3.7 8.3 1.0
C A:LEU392 3.8 8.4 1.0
C A:SER385 3.9 7.7 1.0
CB A:SER390 3.9 11.2 1.0
OG A:SER390 3.9 9.9 1.0
C A:GLY56 4.0 10.1 1.0
C A:PRO393 4.1 8.3 1.0
CG A:GLU76 4.3 6.5 1.0
N A:SER394 4.5 7.4 1.0
N A:LEU392 4.6 9.4 1.0
CA A:LEU392 4.6 9.4 1.0
OE2 A:GLU76 4.7 8.8 1.0
CB A:LEU392 4.7 9.6 1.0
CA A:PRO393 4.7 7.4 1.0
N A:PRO393 4.7 7.6 1.0
N A:SER386 4.7 8.1 1.0
CA A:GLY56 4.7 9.3 1.0
CA A:SER385 4.7 7.7 1.0
CA A:SER386 4.7 8.8 1.0
CA A:SER394 4.8 8.6 1.0
O A:GLY398 4.9 8.4 1.0
CB A:ILE399 5.0 6.4 1.0
N A:LYS57 5.0 10.7 1.0

Calcium binding site 2 out of 4 in 2eac

Go back to Calcium Binding Sites List in 2eac
Calcium binding site 2 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin


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 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:20.4
occ:1.00
 OE2 A:GLU519 2.3 18.4 1.0
OD2 A:ASP689 2.3 15.7 1.0
O A:HOH1897 2.4 12.0 1.0
O A:HOH2031 2.4 15.3 1.0
O A:HOH1889 2.4 9.8 1.0
O A:HOH1798 2.5 15.7 1.0
OE1 A:GLU519 2.7 16.4 1.0
CD A:GLU519 2.8 14.8 1.0
CG A:ASP689 3.4 14.3 1.0
OD1 A:ASP689 3.7 14.7 1.0
O A:HOH2056 3.9 20.9 1.0
NE A:ARG819 4.3 6.0 1.0
O A:HOH1850 4.3 12.8 1.0
CG A:GLU519 4.3 14.2 1.0
OD1 A:ASP588 4.3 13.2 1.0
NE2 A:GLN584 4.4 9.9 1.0
CE2 A:TYR515 4.6 12.2 1.0
OD1 A:ASN796 4.6 12.7 1.0
CB A:ASP689 4.7 13.9 1.0
OE1 A:GLU591 4.7 25.5 1.0
CD A:ARG819 4.8 9.2 1.0
CD2 A:TYR515 4.8 10.5 1.0
OD2 A:ASP588 4.9 13.8 1.0
O A:ASN783 4.9 10.9 1.0
CG A:ASP588 5.0 12.4 1.0
NH2 A:ARG819 5.0 10.3 1.0
CZ A:ARG819 5.0 8.7 1.0

Calcium binding site 3 out of 4 in 2eac

Go back to Calcium Binding Sites List in 2eac
Calcium binding site 3 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin


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 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca899

b:18.7
occ:1.00
 O B:HOH1795 2.2 15.2 1.0
O B:HOH1757 2.4 11.5 1.0
O B:HOH1908 2.4 20.1 1.0
OD2 B:ASP689 2.4 16.0 1.0
OE2 B:GLU519 2.4 19.3 1.0
O B:HOH2015 2.5 20.2 1.0
OE1 B:GLU519 2.6 17.6 1.0
CD B:GLU519 2.9 14.7 1.0
CG B:ASP689 3.4 15.8 1.0
OD1 B:ASP689 3.7 16.3 1.0
O B:HOH2020 3.9 18.3 1.0
NE B:ARG819 4.2 8.8 1.0
O B:HOH1824 4.3 12.8 1.0
OD1 B:ASP588 4.3 16.7 1.0
CG B:GLU519 4.4 14.4 1.0
NE2 B:GLN584 4.4 14.0 1.0
CE2 B:TYR515 4.5 13.8 1.0
OD1 B:ASN796 4.6 11.4 1.0
CD B:ARG819 4.7 8.5 1.0
OE1 B:GLU591 4.8 23.8 1.0
CD2 B:TYR515 4.8 12.6 1.0
O B:ASN783 4.8 10.8 1.0
CB B:ASP689 4.8 15.3 1.0
OD2 B:ASP588 4.9 16.3 1.0
CG B:ASP588 5.0 14.3 1.0
CZ B:ARG819 5.0 9.3 1.0
NH2 B:ARG819 5.0 11.1 1.0

Calcium binding site 4 out of 4 in 2eac

Go back to Calcium Binding Sites List in 2eac
Calcium binding site 4 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin


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 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Deoxyfuconojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca900

b:20.1
occ:1.00
 OE1 B:GLU76 2.7 13.6 1.0
O B:SER385 2.7 11.1 1.0
O B:LEU392 2.8 9.2 1.0
O B:HOH1945 3.0 8.8 1.0
O B:GLY56 3.1 11.7 1.0
CG2 B:ILE399 3.5 9.6 1.0
O B:PRO393 3.6 10.6 1.0
C B:LEU392 3.7 9.4 1.0
CD B:GLU76 3.7 11.4 1.0
CB B:GLU76 3.8 10.6 1.0
CB B:SER390 3.9 11.1 1.0
C B:SER385 3.9 10.1 1.0
C B:PRO393 4.0 10.9 1.0
OG B:SER390 4.0 11.4 1.0
C B:GLY56 4.2 12.6 1.0
N B:SER394 4.4 9.6 1.0
CG B:GLU76 4.4 9.9 1.0
CA B:LEU392 4.5 9.8 1.0
N B:LEU392 4.6 9.9 1.0
CA B:PRO393 4.6 9.9 1.0
CB B:LEU392 4.6 9.4 1.0
N B:PRO393 4.6 9.5 1.0
CA B:SER394 4.7 10.4 1.0
OE2 B:GLU76 4.7 11.9 1.0
N B:SER386 4.7 9.8 1.0
CA B:SER386 4.8 9.6 1.0
CA B:SER385 4.8 9.6 1.0
CA B:GLY56 4.9 11.8 1.0
O B:GLY398 5.0 9.8 1.0

Reference:

M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, R.Kato. Structural Basis on the Catalytic Reaction Mechanism of Novel 1,2-Alpha-L-Fucosidase (Afca) From Bifidobacterium Bifidum J.Biol.Chem. V. 282 18497 2007.
ISSN: ISSN 0021-9258
PubMed: 17459873
DOI: 10.1074/JBC.M702246200
Page generated: Fri Jul 12 10:09:37 2024

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