Calcium in PDB 6dms: Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107

The structure of Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107, PDB code: 6dms was solved by C.Vickers, K.Abe, O.Salama-Alber, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.58 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.527, 156.527, 84.409, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 29.3

The binding sites of Calcium atom in the Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107 (pdb code 6dms). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107, PDB code: 6dms:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:62.1 occ:1.00 OD1 A:ASP336 2.4 53.3 1.0 OD1 A:ASP330 2.4 65.3 1.0 O A:PHE327 2.4 55.3 1.0 O A:ARG332 2.5 64.1 1.0 OD1 A:ASN335 2.7 54.3 1.0 C A:PHE327 3.5 53.8 1.0 CG A:ASP330 3.6 64.4 1.0 CG A:ASP336 3.6 54.2 1.0 C A:ARG332 3.6 62.4 1.0 CG A:ASN335 3.8 54.9 1.0 O A:ASP330 3.9 66.0 1.0 CA A:ARG328 3.9 55.1 1.0 OD2 A:ASP330 4.2 64.1 1.0 N A:ARG328 4.2 54.2 1.0 N A:ARG332 4.2 63.4 1.0 OD2 A:ASP336 4.3 55.1 1.0 C A:ARG328 4.3 57.1 1.0 CA A:ARG332 4.3 62.5 1.0 C A:ASP330 4.4 65.8 1.0 N A:ASP330 4.4 63.8 1.0 ND2 A:ASN335 4.5 55.0 1.0 N A:ASP336 4.5 55.4 1.0 CA A:ASP336 4.6 54.2 1.0 CB A:ARG332 4.6 61.5 1.0 N A:ASP329 4.6 60.2 1.0 CB A:PHE327 4.6 52.8 1.0 N A:THR333 4.7 61.7 1.0 C A:ASN335 4.7 56.3 1.0 CB A:ASP336 4.7 54.3 1.0 CA A:PHE327 4.7 53.1 1.0 CA A:ASP330 4.7 64.8 1.0 CB A:ASP330 4.7 64.5 1.0 O A:ARG328 4.9 58.0 1.0 CA A:THR333 4.9 60.3 1.0 O A:ASN335 5.0 58.4 1.0

Calcium binding site 2 out of 2 in the Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Endo-Fucoidan Hydrolase MFFCNA4_H294Q From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.3 occ:1.00 O A:GLY528 2.5 69.5 1.0 OE1 A:GLU562 2.7 76.2 1.0 OD2 A:ASP564 2.9 65.8 1.0 OD2 A:ASP609 2.9 59.6 1.0 OD2 A:ASP560 3.0 68.6 1.0 OD1 A:ASP560 3.4 67.7 1.0 C A:GLY528 3.6 69.0 1.0 CG A:ASP560 3.6 67.8 1.0 CG A:ASP609 3.6 59.5 1.0 O A:HOH945 3.7 34.1 1.0 CD A:GLU562 3.9 74.9 1.0 CG A:ASP564 4.0 65.2 1.0 CA A:GLY528 4.2 69.0 1.0 CB A:ASP609 4.2 59.0 1.0 CB A:GLU562 4.3 71.2 1.0 OD1 A:ASP609 4.4 59.5 1.0 CB A:ASP564 4.5 65.0 1.0 CD A:PRO530 4.5 65.4 1.0 CG A:GLU562 4.7 72.9 1.0 N A:THR529 4.7 68.4 1.0 OE2 A:GLU562 4.8 76.2 1.0 N A:PRO530 5.0 65.3 1.0

C.Vickers, F.Liu, K.Abe, O.Salama-Alber, M.Jenkins, C.M.K.Springate, J.E.Burke, S.G.Withers, A.B.Boraston. Endo-Fucoidan Hydrolases From Glycoside Hydrolase Family 107 (GH107) Display Structural and Mechanistic Similarities to Alpha-L-Fucosidases From GH29. J. Biol. Chem. V. 293 18296 2018.
ISSN: ESSN 1083-351X
PubMed: 30282808
DOI: 10.1074/JBC.RA118.005134