Calcium in PDB 6dns: Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107

The structure of Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107, PDB code: 6dns 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)	20.00 / 2.24
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.914, 61.914, 324.395, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 27.1

The binding sites of Calcium atom in the Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107 (pdb code 6dns). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107, PDB code: 6dns:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA9 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 MFFCNA9 From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:53.9 occ:1.00 OD1 A:ASP330 2.3 34.0 1.0 OD1 A:ASP336 2.3 27.9 1.0 O A:PHE327 2.4 34.0 1.0 O A:ARG332 2.5 32.3 1.0 OD1 A:ASN335 3.1 28.2 1.0 CG A:ASP330 3.5 34.4 1.0 O A:ASP330 3.5 33.7 1.0 C A:ARG332 3.5 32.5 1.0 C A:PHE327 3.5 33.2 1.0 CG A:ASP336 3.5 28.1 1.0 O A:ARG328 3.6 34.8 1.0 C A:ARG328 3.7 34.9 1.0 CA A:ARG328 3.8 34.4 1.0 N A:ASP330 3.8 35.0 1.0 C A:ASP330 4.0 34.3 1.0 N A:ARG332 4.0 33.2 1.0 OD2 A:ASP336 4.1 28.3 1.0 N A:ARG328 4.1 34.0 1.0 OD2 A:ASP330 4.2 34.5 1.0 CA A:ASP330 4.3 34.5 1.0 CG A:ASN335 4.3 28.1 1.0 CA A:ARG332 4.3 32.8 1.0 N A:ASP329 4.3 35.3 1.0 N A:THR333 4.4 32.5 1.0 CB A:ASP330 4.5 34.4 1.0 CA A:THR333 4.5 32.2 1.0 C A:ASP329 4.6 35.4 1.0 N A:ASP336 4.7 27.9 1.0 CA A:ASP336 4.7 27.8 1.0 CB A:ASP336 4.7 28.0 1.0 CA A:PHE327 4.7 32.5 1.0 CB A:ARG332 4.7 32.5 1.0 CB A:PHE327 4.8 32.1 1.0 ND2 A:ASN335 4.8 27.8 1.0 N A:THR331 4.9 34.0 1.0 C A:ASN335 5.0 28.3 1.0

Calcium binding site 2 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA9 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 MFFCNA9 From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:33.2 occ:1.00 O A:HOH838 2.3 27.1 1.0 O A:THR77 2.5 26.3 1.0 OD2 A:ASP79 2.7 24.4 1.0 OD1 A:ASP79 3.0 24.2 1.0 CG A:ASP79 3.2 24.3 1.0 C A:THR77 3.5 26.1 1.0 OE1 A:GLN416 3.8 31.8 1.0 CA A:THR77 3.9 26.5 1.0 O A:GLY44 4.1 28.8 1.0 CB A:THR77 4.1 26.5 1.0 CD A:GLN416 4.4 31.9 1.0 NE2 A:GLN416 4.5 31.6 1.0 CB A:ASP79 4.7 24.2 1.0 N A:VAL78 4.7 25.6 1.0 O A:ARG425 4.9 25.4 1.0 CG2 A:THR77 4.9 26.5 1.0 C A:VAL78 4.9 24.8 1.0 N A:ASP79 5.0 24.4 1.0

Calcium binding site 3 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA9 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 3 of Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:38.8 occ:1.00 O A:GLY419 2.3 32.2 1.0 OD1 A:ASP451 2.3 32.5 1.0 OE2 A:GLU453 2.4 37.0 1.0 OD1 A:ASP504 2.4 38.4 1.0 OD2 A:ASP502 2.8 39.8 1.0 CG A:ASP451 3.4 33.0 1.0 C A:GLY419 3.5 32.3 1.0 CG A:ASP504 3.5 38.9 1.0 CG A:ASP502 3.5 40.0 1.0 CD A:GLU453 3.6 37.1 1.0 OD1 A:ASP502 3.8 40.2 1.0 OD2 A:ASP451 3.8 33.2 1.0 CB A:ASP504 3.9 38.9 1.0 CA A:GLY419 4.1 32.5 1.0 CD A:PRO452 4.2 34.2 1.0 CB A:GLU453 4.3 36.8 1.0 N A:GLU453 4.3 36.0 1.0 CG A:GLU453 4.4 37.0 1.0 N A:GLY419 4.5 32.5 1.0 OE1 A:GLU453 4.5 37.4 1.0 N A:LYS420 4.5 32.5 1.0 N A:PRO452 4.6 34.2 1.0 OD2 A:ASP504 4.6 39.1 1.0 OG A:SER503 4.6 39.9 1.0 CB A:ASP451 4.6 33.3 1.0 CB A:ASP502 4.6 40.1 1.0 N A:ASP504 4.6 39.1 1.0 CA A:LYS420 4.8 32.6 1.0 CA A:ASP451 4.9 33.1 1.0 C A:LYS420 4.9 32.3 1.0 CA A:ASP504 4.9 39.0 1.0 CG A:PRO452 4.9 34.4 1.0 CA A:GLU453 5.0 36.6 1.0

Calcium binding site 4 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA9 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 4 of Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:51.5 occ:1.00 O A:HOH850 2.4 40.7 1.0 OE2 A:GLU390 3.4 32.9 1.0 CD A:GLU390 4.3 32.6 1.0 OD1 A:ASN59 4.8 26.3 1.0 OD2 A:ASP115 4.8 38.8 1.0 CG A:GLU390 4.9 32.5 1.0

Calcium binding site 5 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA9 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 5 of Endo-Fucoidan Hydrolase MFFCNA9 From Glycoside Hydrolase Family 107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:40.9 occ:1.00 O A:GLY528 2.4 47.3 1.0 OD2 A:ASP564 2.4 36.2 1.0 OD2 A:ASP609 2.6 37.5 1.0 OD2 A:ASP560 2.7 37.1 1.0 OE1 A:GLU562 3.0 37.5 1.0 OD1 A:ASP560 3.3 36.6 1.0 CG A:ASP560 3.4 36.9 1.0 C A:GLY528 3.4 47.0 1.0 CG A:ASP564 3.5 36.8 1.0 CG A:ASP609 3.7 37.5 1.0 CA A:GLY528 3.9 47.9 1.0 CD A:GLU562 3.9 37.8 1.0 CB A:GLU562 4.1 37.8 1.0 CB A:ASP564 4.1 36.6 1.0 CG A:GLU562 4.2 37.7 1.0 CB A:ASP609 4.3 37.1 1.0 OD1 A:ASP564 4.5 37.4 1.0 N A:THR529 4.6 45.5 1.0 CD A:PRO530 4.7 42.5 1.0 OD1 A:ASP609 4.7 38.3 1.0 N A:PRO530 4.8 42.8 1.0 CB A:ASP560 4.9 36.8 1.0 C A:THR529 4.9 43.6 1.0 OE2 A:GLU562 5.0 38.1 1.0 N A:GLU562 5.0 37.6 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