Calcium in PDB 5b6t: Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb

All present enzymatic activity of Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb:
3.2.1.55;

The structure of Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb, PDB code: 5b6t was solved by T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.63 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.854, 77.765, 74.458, 90.00, 93.01, 90.00
R / Rfree (%)	15 / 17.4

The structure of Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb also contains other interesting chemical elements:

Lead

(Pb)

1 atom

The binding sites of Calcium atom in the Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb (pdb code 5b6t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb, PDB code: 5b6t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:9.6 occ:1.00 O A:HOH876 2.1 7.5 1.0 O A:HOH799 2.1 6.4 1.0 O A:HOH673 2.1 6.3 1.0 O A:HOH847 2.1 7.1 1.0 NE2 A:HIS346 2.2 6.7 1.0 O A:HOH619 2.2 6.3 1.0 CD2 A:HIS346 3.1 6.6 1.0 CE1 A:HIS346 3.2 6.6 1.0 O A:HOH646 3.8 7.0 1.0 O A:PRO165 3.9 6.0 1.0 O A:HOH672 4.1 7.2 1.0 ND1 A:HIS346 4.3 6.7 1.0 CG A:HIS346 4.3 6.3 1.0 O A:ASP109 4.3 6.4 1.0 O A:GLY347 4.3 7.0 1.0 OE2 A:GLU348 4.4 6.0 1.0 O A:PRO110 4.5 6.7 1.0 O A:HOH737 4.5 7.0 1.0 C A:ASP109 4.7 6.3 1.0 ND2 A:ASN279 4.8 6.5 1.0 CE3 A:TRP226 4.8 5.9 1.0 CZ3 A:TRP226 4.8 5.9 1.0 O A:ALA278 4.9 6.9 1.0 CG A:GLU348 4.9 6.0 1.0 C A:PRO165 4.9 5.9 1.0 CB A:ASP109 5.0 6.6 1.0

Calcium binding site 2 out of 2 in the Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Coprinopsis Cinerea GH62 Alpha-L- Arabinofuranosidase Complexed with Pb within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:10.1 occ:1.00 O B:HOH836 2.0 8.2 1.0 O B:HOH769 2.1 7.4 1.0 O B:HOH639 2.1 6.8 1.0 O B:HOH833 2.1 7.0 1.0 O B:HOH634 2.2 7.4 1.0 NE2 B:HIS346 2.2 7.2 1.0 CD2 B:HIS346 3.1 7.0 1.0 CE1 B:HIS346 3.2 7.2 1.0 O B:HOH619 3.7 8.5 1.0 O B:PRO165 4.0 6.9 1.0 O B:HOH724 4.1 7.9 1.0 CG B:HIS346 4.3 7.3 1.0 ND1 B:HIS346 4.3 7.2 1.0 O B:ASP109 4.3 7.1 1.0 O B:GLY347 4.3 6.5 1.0 OE1 B:GLU348 4.5 6.9 1.0 O B:HOH671 4.5 7.4 1.0 O B:PRO110 4.5 7.6 1.0 CE3 B:TRP226 4.7 7.1 1.0 ND2 B:ASN279 4.8 8.4 1.0 C B:ASP109 4.8 6.7 1.0 CZ3 B:TRP226 4.8 7.1 1.0 O B:ALA278 4.9 7.6 1.0 CG B:GLU348 4.9 6.3 1.0 O B:ALA164 5.0 6.8 1.0 C B:ALA164 5.0 6.6 1.0

T.Tonozuka, Y.Tanaka, S.Okuyama, T.Miyazaki, A.Nishikawa, M.Yoshida. Structure of the Catalytic Domain of Alpha-L-Arabinofuranosidase From Coprinopsis Cinerea, CCABF62A, Provides Insights Into Structure-Function Relationships in Glycoside Hydrolase Family 62 Appl. Biochem. Biotechnol. V. 181 511 2017.
ISSN: ISSN 1559-0291
PubMed: 27589854
DOI: 10.1007/S12010-016-2227-0