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

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

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

Protein crystallography data

The structure of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Substrate, PDB code: 2ead 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) 37.60 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.448, 72.743, 129.207, 90.00, 96.68, 90.00
R / Rfree (%) 15.9 / 21

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 Substrate (pdb code 2ead). 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 Substrate, PDB code: 2ead:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2ead

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


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 Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca899

b:24.3
occ:1.00
 OE1 A:GLU76 2.6 12.5 1.0
O A:SER385 2.6 13.9 1.0
O A:LEU392 2.6 12.9 1.0
O A:GLY56 2.8 16.6 1.0
O A:HOH1076 3.1 18.8 1.0
CG2 A:ILE399 3.5 11.1 1.0
CD A:GLU76 3.6 16.2 1.0
C A:LEU392 3.6 12.3 1.0
CB A:GLU76 3.7 15.3 1.0
OG A:SER390 3.8 16.5 1.0
CB A:SER390 3.8 16.2 1.0
O A:PRO393 3.8 12.6 1.0
C A:SER385 3.8 14.2 1.0
C A:GLY56 4.0 16.3 1.0
C A:PRO393 4.1 12.8 1.0
CG A:GLU76 4.2 14.0 1.0
N A:LEU392 4.4 12.6 1.0
CA A:LEU392 4.4 12.3 1.0
N A:SER394 4.5 12.8 1.0
N A:PRO393 4.5 12.9 1.0
CA A:PRO393 4.6 12.9 1.0
OE2 A:GLU76 4.6 14.7 1.0
CA A:SER386 4.6 13.6 1.0
CB A:LEU392 4.6 10.8 1.0
N A:SER386 4.7 13.8 1.0
CA A:GLY56 4.7 16.0 1.0
CA A:SER385 4.8 14.1 1.0
CA A:SER394 4.9 13.0 1.0
CA A:SER390 5.0 16.8 1.0

Calcium binding site 2 out of 4 in 2ead

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Calcium binding site 2 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Substrate


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 Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:13.9
occ:1.00
 O A:HOH1149 2.3 9.8 1.0
O A:HOH948 2.4 13.5 1.0
OD2 A:ASP689 2.4 15.5 1.0
O A:HOH1160 2.4 18.2 1.0
OE1 A:GLU519 2.5 16.2 1.0
O A:HOH962 2.5 11.5 1.0
OE2 A:GLU519 2.6 15.6 1.0
CD A:GLU519 2.8 15.5 1.0
CG A:ASP689 3.4 14.2 1.0
OD1 A:ASP689 3.6 11.9 1.0
O A:HOH1424 4.0 24.6 1.0
O A:HOH901 4.1 11.9 1.0
NE A:ARG819 4.1 15.2 1.0
NE2 A:GLN584 4.1 14.6 1.0
O A:HOH1108 4.2 13.6 1.0
CG A:GLU519 4.3 17.2 1.0
OD1 A:ASP588 4.4 17.3 1.0
OD1 A:ASN796 4.6 20.2 1.0
CD A:ARG819 4.6 14.2 1.0
CE2 A:TYR515 4.7 16.8 1.0
CB A:ASP689 4.7 13.3 1.0
O A:ASN783 4.8 12.8 1.0
OD2 A:ASP588 4.8 13.8 1.0
CD2 A:TYR515 4.8 14.8 1.0
CZ A:ARG819 4.8 13.5 1.0
NH2 A:ARG819 4.8 12.2 1.0
O A:HOH1447 4.8 27.1 1.0
CG A:ASP588 5.0 14.9 1.0

Calcium binding site 3 out of 4 in 2ead

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Calcium binding site 3 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Substrate


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 Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:14.8
occ:1.00
 O B:HOH938 2.4 12.2 1.0
O B:HOH1234 2.4 15.1 1.0
OE2 B:GLU519 2.5 12.8 1.0
O B:HOH993 2.5 12.6 1.0
OD2 B:ASP689 2.5 15.0 1.0
O B:HOH1084 2.5 13.4 1.0
OE1 B:GLU519 2.6 15.4 1.0
CD B:GLU519 2.8 15.7 1.0
CG B:ASP689 3.4 15.6 1.0
OD1 B:ASP689 3.6 16.0 1.0
O B:HOH1029 4.1 13.7 1.0
NE B:ARG819 4.1 15.6 1.0
O B:HOH1638 4.2 35.6 1.0
O B:HOH1167 4.2 13.6 1.0
NE2 B:GLN584 4.3 14.4 1.0
CG B:GLU519 4.3 16.3 1.0
OD1 B:ASP588 4.4 15.4 1.0
OD1 B:ASN796 4.6 14.4 1.0
CE2 B:TYR515 4.6 14.1 1.0
CD B:ARG819 4.7 15.0 1.0
OD2 B:ASP588 4.7 16.4 1.0
CD2 B:TYR515 4.7 13.1 1.0
O B:HOH1478 4.8 27.0 1.0
NH2 B:ARG819 4.8 16.4 1.0
CB B:ASP689 4.8 14.4 1.0
O B:ASN783 4.8 13.5 1.0
OE1 B:GLU591 4.8 24.5 1.0
CZ B:ARG819 4.8 15.1 1.0
CG B:ASP588 4.9 14.9 1.0

Calcium binding site 4 out of 4 in 2ead

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Calcium binding site 4 out of 4 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complex with Substrate


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 Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:20.7
occ:1.00
 OE1 B:GLU76 2.5 14.8 1.0
O B:SER385 2.6 13.9 1.0
O B:LEU392 2.6 14.4 1.0
O B:GLY56 2.9 14.3 1.0
O B:HOH1037 3.0 18.5 1.0
CG2 B:ILE399 3.6 13.2 1.0
CD B:GLU76 3.6 13.8 1.0
O B:PRO393 3.7 14.8 1.0
C B:LEU392 3.7 14.9 1.0
C B:SER385 3.7 14.4 1.0
OG B:SER390 3.8 14.4 1.0
CB B:GLU76 3.8 13.2 1.0
CB B:SER390 3.9 15.7 1.0
C B:PRO393 4.0 14.4 1.0
C B:GLY56 4.0 14.0 1.0
CG B:GLU76 4.3 11.6 1.0
N B:LEU392 4.4 15.0 1.0
OE2 B:GLU76 4.4 13.1 1.0
N B:SER394 4.5 12.4 1.0
CA B:LEU392 4.5 14.8 1.0
CA B:PRO393 4.6 14.6 1.0
N B:PRO393 4.6 14.6 1.0
N B:SER386 4.6 12.9 1.0
CB B:LEU392 4.6 14.8 1.0
CA B:SER385 4.7 14.4 1.0
CA B:SER386 4.7 13.2 1.0
CA B:GLY56 4.8 13.5 1.0
CA B:SER394 4.8 12.9 1.0
O B:GLY398 5.0 11.1 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: Sat Dec 12 03:36:11 2020

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