Calcium in PDB 3qed: The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases

The structure of The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases, PDB code: 3qed was solved by A.Cartmell, L.S.Mckee, M.Pena, J.Larsbrink, H.Brumer, R.J.Lewis, A.Viks-Nielsen, H.J.Gilbert, J.Marles-Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.17 / 2.99
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	192.650, 192.650, 132.250, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.6

The binding sites of Calcium atom in the The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases (pdb code 3qed). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases, PDB code: 3qed:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca341 b:33.4 occ:1.00 OD1 B:ASN154 2.4 48.6 1.0 O B:ASN154 2.5 51.1 1.0 OD2 B:ASP166 2.5 40.5 1.0 O B:THR157 2.6 57.3 1.0 OD2 B:ASP165 2.6 39.8 1.0 OD1 B:ASP165 2.6 41.3 1.0 OG1 B:THR157 2.9 56.9 1.0 CG B:ASP165 3.0 39.6 1.0 C B:ASN154 3.4 51.1 1.0 CG B:ASN154 3.5 49.4 1.0 CG B:ASP166 3.6 39.4 1.0 CA B:ASN154 3.6 49.9 1.0 C B:THR157 3.7 57.1 1.0 OD1 B:ASP166 4.0 39.1 1.0 CB B:THR157 4.0 57.3 1.0 CA B:THR157 4.1 57.2 1.0 N B:THR157 4.1 57.1 1.0 CB B:ASN154 4.2 49.9 1.0 O B:ILE162 4.2 45.9 1.0 CB B:ASP165 4.5 39.3 1.0 N B:ASP155 4.6 52.5 1.0 ND2 B:ASN154 4.6 48.0 1.0 O B:THR160 4.7 52.4 1.0 O B:THR153 4.7 47.6 1.0 NH2 B:ARG189 4.7 45.6 1.0 CB B:ASP166 4.8 38.6 1.0 N B:THR158 4.8 56.9 1.0 N B:ASN154 4.8 48.6 1.0 N B:ASP166 4.9 38.7 1.0 NH1 B:ARG189 4.9 45.3 1.0

Calcium binding site 2 out of 4 in the The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca348 b:24.4 occ:1.00 OD1 C:ASN154 2.4 16.8 1.0 O C:THR157 2.4 23.1 1.0 OD1 C:ASP165 2.4 18.5 1.0 OD2 C:ASP166 2.5 19.0 1.0 OG1 C:THR157 2.6 22.3 1.0 O C:ASN154 2.7 19.7 1.0 OD2 C:ASP165 2.7 17.7 1.0 CG C:ASP165 2.9 16.6 1.0 C C:THR157 3.5 23.0 1.0 CG C:ASN154 3.5 17.0 1.0 CG C:ASP166 3.6 17.5 1.0 C C:ASN154 3.6 19.6 1.0 CB C:THR157 3.6 23.1 1.0 CA C:ASN154 3.9 18.4 1.0 CA C:THR157 4.0 23.1 1.0 OD1 C:ASP166 4.1 18.2 1.0 N C:THR157 4.2 23.6 1.0 CB C:ASN154 4.3 18.4 1.0 CB C:ASP165 4.4 15.5 1.0 O C:ILE162 4.4 18.6 1.0 ND2 C:ASN154 4.6 16.2 1.0 N C:THR158 4.6 22.6 1.0 CB C:ASP166 4.8 15.6 1.0 N C:ASP155 4.8 20.9 1.0 NH1 C:ARG189 4.9 25.9 1.0 N C:ASP166 4.9 15.5 1.0 CG2 C:THR157 4.9 23.4 1.0 CG2 C:THR160 5.0 19.4 1.0 CA C:THR158 5.0 22.2 1.0

Calcium binding site 3 out of 4 in the The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca349 b:30.2 occ:1.00 OD1 D:ASP165 2.3 23.0 1.0 O D:THR157 2.3 40.6 1.0 OD2 D:ASP166 2.5 23.9 1.0 OG1 D:THR157 2.5 40.3 1.0 OD1 D:ASN154 2.6 34.1 1.0 OD2 D:ASP165 2.7 21.3 1.0 O D:ASN154 2.8 33.9 1.0 CG D:ASP165 2.8 21.8 1.0 CG D:ASP166 3.4 21.4 1.0 C D:THR157 3.4 40.5 1.0 CB D:THR157 3.7 40.8 1.0 C D:ASN154 3.7 34.1 1.0 CG D:ASN154 3.8 32.8 1.0 OD1 D:ASP166 3.8 23.5 1.0 CA D:ASN154 3.9 32.6 1.0 CA D:THR157 4.0 40.7 1.0 N D:THR157 4.2 40.8 1.0 CB D:ASP165 4.3 21.5 1.0 CB D:ASN154 4.5 32.5 1.0 N D:THR158 4.6 40.2 1.0 CB D:ASP166 4.7 19.5 1.0 O D:ILE162 4.7 29.5 1.0 N D:ASP166 4.7 20.2 1.0 NH2 D:ARG189 4.8 26.4 1.0 ND2 D:ASN154 4.8 31.9 1.0 CA D:THR158 4.9 39.8 1.0 CG2 D:THR157 4.9 40.7 1.0 N D:ASP155 5.0 36.0 1.0

Calcium binding site 4 out of 4 in the The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure and Function of An Arabinan-Specific Alpha-1,2- Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca348 b:20.5 occ:1.00 O A:THR157 2.4 16.6 1.0 OD2 A:ASP165 2.4 20.6 1.0 OD1 A:ASN154 2.5 18.6 1.0 OD2 A:ASP166 2.5 16.0 1.0 OD1 A:ASP165 2.6 18.9 1.0 OG1 A:THR157 2.6 15.7 1.0 O A:ASN154 2.7 17.3 1.0 CG A:ASP165 2.8 17.7 1.0 C A:THR157 3.5 16.5 1.0 CG A:ASN154 3.5 15.9 1.0 C A:ASN154 3.6 17.1 1.0 CG A:ASP166 3.6 14.8 1.0 CB A:THR157 3.6 16.8 1.0 CA A:ASN154 3.8 16.4 1.0 CA A:THR157 4.0 16.8 1.0 OD1 A:ASP166 4.2 14.2 1.0 N A:THR157 4.2 17.5 1.0 CB A:ASN154 4.3 16.4 1.0 CB A:ASP165 4.3 15.9 1.0 O A:ILE162 4.5 14.8 1.0 ND2 A:ASN154 4.5 15.3 1.0 N A:THR158 4.6 16.0 1.0 CB A:ASP166 4.7 14.1 1.0 NH1 A:ARG189 4.8 15.7 1.0 N A:ASP155 4.8 18.0 1.0 N A:ASP166 4.8 14.7 1.0 NH2 A:ARG189 4.9 14.3 1.0 CG2 A:THR160 4.9 11.3 1.0 CG2 A:THR157 5.0 16.3 1.0 CA A:THR158 5.0 15.5 1.0

A.Cartmell, L.S.Mckee, M.J.Pena, J.Larsbrink, H.Brumer, S.Kaneko, H.Ichinose, R.J.Lewis, A.Vikso-Nielsen, H.J.Gilbert, J.Marles-Wright. The Structure and Function of An Arabinan-Specific {Alpha}-1,2-Arabinofuranosidase Identified From Screening the Activities of Bacterial GH43 Glycoside Hydrolases. J.Biol.Chem. V. 286 15483 2011.
ISSN: ISSN 0021-9258
PubMed: 21339299
DOI: 10.1074/JBC.M110.215962