Calcium in PDB 5xfm: Crystal Structure of Beta-Arabinopyranosidase

The structure of Crystal Structure of Beta-Arabinopyranosidase, PDB code: 5xfm was solved by K.Kato, M.Okuyama, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.78 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.810, 90.510, 128.550, 105.50, 94.80, 96.15
R / Rfree (%)	20.7 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Beta-Arabinopyranosidase (pdb code 5xfm). 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 Beta-Arabinopyranosidase, PDB code: 5xfm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Beta-Arabinopyranosidase


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 Beta-Arabinopyranosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:20.4 occ:1.00 O A:HOH1051 2.4 20.7 1.0 O A:HOH1043 2.4 23.0 1.0 OE2 A:GLU457 2.4 27.0 1.0 O A:HOH1066 2.5 24.7 1.0 OE2 A:GLU179 2.5 21.5 1.0 OE2 A:GLU463 2.6 24.4 1.0 OE1 A:GLU457 2.7 20.9 1.0 O A:HOH914 2.8 19.7 1.0 CD A:GLU457 2.9 25.0 1.0 CD A:GLU463 3.6 31.8 1.0 CD A:GLU179 3.6 20.4 1.0 O A:HOH885 3.8 22.5 1.0 O A:HOH905 3.9 17.2 1.0 OE1 A:GLU463 3.9 30.2 1.0 OE1 A:GLU179 4.0 24.6 1.0 O A:HOH1039 4.3 29.9 1.0 CG A:GLU457 4.4 15.6 1.0 ND1 A:HIS438 4.4 22.3 1.0 N A:GLY439 4.4 20.8 1.0 O A:HOH900 4.6 12.1 1.0 CA A:GLY439 4.6 14.6 1.0 OD1 A:ASP408 4.8 19.5 1.0 CG A:GLU463 4.9 26.3 1.0 CG A:GLU179 4.9 16.1 1.0 OD2 A:ASP408 4.9 17.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Beta-Arabinopyranosidase


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 Beta-Arabinopyranosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:27.9 occ:1.00 O B:HOH1011 2.4 24.6 1.0 OE2 B:GLU463 2.4 36.5 1.0 OE2 B:GLU179 2.5 34.3 1.0 O B:HOH939 2.6 24.4 1.0 OE1 B:GLU457 2.6 28.9 1.0 OE2 B:GLU457 2.7 23.9 1.0 O B:HOH1033 2.9 34.2 1.0 CD B:GLU457 3.0 27.4 1.0 O B:HOH1030 3.1 28.7 1.0 O B:HOH869 3.4 24.1 1.0 CD B:GLU463 3.4 33.7 1.0 CD B:GLU179 3.6 35.5 1.0 OE1 B:GLU463 3.8 31.5 1.0 OE1 B:GLU179 4.0 40.2 1.0 O B:HOH901 4.4 27.4 1.0 ND1 B:HIS438 4.4 29.6 1.0 CG B:GLU457 4.5 26.3 1.0 O B:HOH1040 4.5 32.3 1.0 O B:HOH1045 4.5 28.3 1.0 N B:GLY439 4.6 28.0 1.0 CG B:GLU463 4.8 28.5 1.0 CG B:GLU179 4.8 31.8 1.0 O B:HOH952 4.8 26.5 1.0 CA B:GLY439 4.9 24.1 1.0 OD1 B:ASP408 4.9 22.7 1.0 O B:HOH1061 4.9 37.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Beta-Arabinopyranosidase


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 Beta-Arabinopyranosidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:21.2 occ:1.00 O C:HOH933 2.3 23.9 1.0 OE1 C:GLU457 2.4 20.7 1.0 OE2 C:GLU457 2.5 21.0 1.0 OE2 C:GLU179 2.5 24.0 1.0 O C:HOH849 2.6 18.2 1.0 O C:HOH971 2.7 15.9 1.0 CD C:GLU457 2.8 24.3 1.0 OE1 C:GLU463 2.8 30.6 1.0 O C:HOH1053 3.2 20.2 1.0 CD C:GLU179 3.6 25.9 1.0 O C:HOH1100 3.6 26.8 1.0 CD C:GLU463 3.8 28.8 1.0 O C:HOH932 3.8 23.0 1.0 OE1 C:GLU179 4.0 22.1 1.0 OE2 C:GLU463 4.0 24.0 1.0 O C:HOH884 4.1 17.1 1.0 N C:GLY439 4.3 17.1 1.0 CG C:GLU457 4.3 24.4 1.0 O C:HOH1098 4.3 13.6 1.0 ND1 C:HIS438 4.4 23.2 1.0 O C:HOH976 4.5 19.0 1.0 CA C:GLY439 4.6 15.4 1.0 OD1 C:ASP408 4.7 26.1 1.0 CG C:GLU179 4.9 21.8 1.0 CB C:HIS438 5.0 19.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Beta-Arabinopyranosidase


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 Beta-Arabinopyranosidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:25.7 occ:1.00 O D:HOH955 2.5 23.8 1.0 OE2 D:GLU457 2.6 28.1 1.0 OE2 D:GLU179 2.6 36.9 1.0 O D:HOH837 2.6 26.5 1.0 OE2 D:GLU463 2.6 37.4 1.0 OE1 D:GLU457 2.6 32.1 1.0 O D:HOH1027 2.9 31.9 1.0 CD D:GLU457 2.9 31.2 1.0 O D:HOH1048 3.3 31.6 1.0 CD D:GLU463 3.6 33.3 1.0 O D:HOH909 3.7 27.9 1.0 CD D:GLU179 3.7 35.0 1.0 OE1 D:GLU463 4.0 35.6 1.0 OE1 D:GLU179 4.1 38.3 1.0 O D:HOH948 4.2 27.6 1.0 O D:HOH956 4.3 26.6 1.0 ND1 D:HIS438 4.4 29.0 1.0 N D:GLY439 4.4 27.6 1.0 O D:HOH1036 4.4 30.6 1.0 CG D:GLU457 4.4 26.2 1.0 O D:HOH927 4.7 17.7 1.0 CA D:GLY439 4.7 28.0 1.0 OD1 D:ASP408 4.7 28.0 1.0 OD2 D:ASP408 4.8 26.5 1.0 CG D:GLU179 4.9 26.4 1.0 CG D:GLU463 4.9 32.5 1.0 CB D:HIS438 5.0 28.6 1.0

A.Kikuchi, M.Okuyama, K.Kato, S.Osaki, M.Ma, Y.Kumagai, K.Matsunaga, P.Klahan, T.Tagami, M.Yao, A.Kimura. A Novel Glycoside Hydrolase Family 97 Enzyme: Bifunctional Beta-L-Arabinopyranosidase/ Alpha-Galactosidase From Bacteroides Thetaiotaomicron. Biochimie V. 142 41 2017.
ISSN: ISSN 1638-6183
PubMed: 28804002
DOI: 10.1016/J.BIOCHI.2017.08.003