Calcium in PDB 5msx: Glycoside Hydrolase BT_3662

The structure of Glycoside Hydrolase BT_3662, PDB code: 5msx was solved by A.Basle, D.Ndeh, A.Rogowski, A.Cartmell, A.S.Luis, I.Venditto, A.Labourel, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.44 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.827, 129.181, 158.080, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.5

The binding sites of Calcium atom in the Glycoside Hydrolase BT_3662 (pdb code 5msx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Glycoside Hydrolase BT_3662, PDB code: 5msx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glycoside Hydrolase BT_3662 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:14.4 occ:1.00 O A:HOH633 2.4 16.8 1.0 O A:HOH655 2.4 13.6 1.0 O A:HOH625 2.4 13.5 1.0 O A:HOH618 2.5 14.6 1.0 O A:HOH608 2.5 13.5 1.0 O A:HOH670 2.5 9.7 1.0 NE2 A:HIS261 2.6 16.8 1.0 CE1 A:HIS261 3.6 15.8 1.0 CD2 A:HIS261 3.6 16.5 1.0 OG A:SER39 4.0 17.6 1.0 O A:ALA156 4.1 17.2 1.0 O A:GLY262 4.2 16.5 1.0 O A:PRO95 4.3 17.2 1.0 O A:PRO203 4.3 16.6 1.0 O A:HOH637 4.5 28.5 1.0 O A:ASP37 4.5 15.8 1.0 OE1 A:GLU157 4.6 24.3 1.0 O A:ALA94 4.7 15.2 1.0 ND1 A:HIS261 4.7 16.6 1.0 CG A:HIS261 4.8 16.1 1.0 CB A:ALA94 4.9 16.7 1.0 O A:ASP155 4.9 17.3 1.0 CA A:GLY202 5.0 17.5 1.0

Calcium binding site 2 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glycoside Hydrolase BT_3662 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:25.6 occ:1.00 O A:PHE358 2.3 23.3 1.0 O A:SER366 2.4 17.5 1.0 OG A:SER366 2.4 16.7 1.0 O A:TRP455 2.5 18.6 1.0 O A:ALA363 2.5 21.1 1.0 OD1 A:ASP361 2.6 20.3 1.0 OE2 A:GLU456 2.6 38.3 1.0 C A:SER366 3.2 17.2 1.0 C A:PHE358 3.5 22.6 1.0 C A:ALA363 3.6 19.9 1.0 CB A:SER366 3.6 16.4 1.0 CG A:ASP361 3.6 21.8 1.0 C A:TRP455 3.6 18.9 1.0 CD A:GLU456 3.8 34.0 1.0 CA A:SER366 3.8 17.4 1.0 OD2 A:ASP361 3.9 22.5 1.0 N A:SER366 4.0 16.3 1.0 N A:ALA363 4.0 22.1 1.0 N A:ARG367 4.2 17.4 1.0 CA A:PHE358 4.2 21.9 1.0 CA A:ALA363 4.2 21.0 1.0 CG A:GLU456 4.3 30.9 1.0 CA A:TRP455 4.4 17.6 1.0 CB A:PHE358 4.5 21.6 1.0 CB A:ALA363 4.5 21.7 1.0 N A:ALA359 4.5 22.7 1.0 CA A:ARG367 4.6 18.0 1.0 N A:ASN364 4.7 18.3 1.0 N A:ASP361 4.7 22.0 1.0 N A:GLU456 4.7 20.5 1.0 CA A:ALA359 4.7 23.3 1.0 C A:ALA359 4.7 24.1 1.0 OE1 A:GLU456 4.8 38.2 1.0 CA A:GLU456 4.9 21.7 1.0 CA A:ASN364 4.9 18.1 1.0 CB A:ASP361 5.0 21.3 1.0 N A:VAL360 5.0 23.6 1.0

Calcium binding site 3 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Glycoside Hydrolase BT_3662 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:16.6 occ:1.00 O B:HOH654 2.4 17.6 1.0 O B:HOH619 2.4 18.7 1.0 O B:HOH648 2.4 15.4 1.0 O B:HOH664 2.5 16.5 1.0 O B:HOH608 2.5 13.2 1.0 NE2 B:HIS261 2.6 16.0 1.0 O B:HOH623 2.6 13.9 1.0 CE1 B:HIS261 3.5 16.6 1.0 CD2 B:HIS261 3.6 16.1 1.0 O B:ALA156 4.0 17.2 1.0 O B:GLY262 4.1 18.9 1.0 OG B:SER39 4.2 19.4 1.0 O B:PRO203 4.3 15.7 1.0 O B:PRO95 4.4 14.7 1.0 OE2 B:GLU157 4.5 25.8 1.0 O B:ASP37 4.6 19.0 1.0 ND1 B:HIS261 4.7 16.5 1.0 CG B:HIS261 4.7 16.4 1.0 O B:ALA94 4.8 16.4 1.0 O B:ASP155 4.9 16.6 1.0 CB B:ALA94 5.0 15.0 1.0 CA B:GLY202 5.0 16.2 1.0

Calcium binding site 4 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Glycoside Hydrolase BT_3662 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:33.2 occ:1.00 O B:ALA363 2.3 21.3 1.0 O B:PHE358 2.4 29.9 1.0 O B:TRP455 2.4 29.2 1.0 OG B:SER366 2.5 22.4 1.0 O B:SER366 2.5 23.8 1.0 OD1 B:ASP361 2.5 31.0 1.0 OE2 B:GLU456 2.6 45.6 1.0 C B:SER366 3.3 22.3 1.0 C B:ALA363 3.5 22.6 1.0 CG B:ASP361 3.5 31.2 1.0 C B:PHE358 3.6 31.0 1.0 C B:TRP455 3.6 29.2 1.0 CB B:SER366 3.7 22.0 1.0 CD B:GLU456 3.7 41.9 1.0 CA B:SER366 3.8 21.8 1.0 OD2 B:ASP361 3.8 29.9 1.0 N B:ALA363 3.9 24.8 1.0 N B:SER366 4.0 20.7 1.0 CA B:ALA363 4.1 24.1 1.0 CG B:GLU456 4.2 39.4 1.0 N B:ARG367 4.3 22.6 1.0 CA B:PHE358 4.3 30.9 1.0 CB B:ALA363 4.4 23.7 1.0 CA B:TRP455 4.4 26.7 1.0 N B:ASN364 4.5 21.3 1.0 N B:ASP361 4.6 30.9 1.0 N B:ALA359 4.6 32.0 1.0 CB B:PHE358 4.6 30.1 1.0 N B:GLU456 4.6 29.9 1.0 CA B:ARG367 4.7 24.0 1.0 OE1 B:GLU456 4.7 44.5 1.0 C B:ALA359 4.8 31.8 1.0 CA B:ALA359 4.8 32.4 1.0 CA B:ASN364 4.8 21.1 1.0 CA B:GLU456 4.8 31.6 1.0 CB B:ASP361 4.9 30.8 1.0 N B:GLY362 4.9 27.9 1.0

Calcium binding site 5 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Glycoside Hydrolase BT_3662 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:14.0 occ:1.00 O C:HOH691 2.3 11.7 1.0 O C:HOH670 2.3 15.7 1.0 O C:HOH673 2.3 15.9 1.0 O C:HOH638 2.4 11.4 1.0 O C:HOH649 2.5 13.1 1.0 O C:HOH647 2.6 13.6 1.0 NE2 C:HIS261 2.7 15.9 1.0 CD2 C:HIS261 3.6 15.7 1.0 CE1 C:HIS261 3.7 15.7 1.0 O C:ALA156 4.1 16.6 1.0 OG C:SER39 4.2 16.7 1.0 O C:GLY262 4.2 15.4 1.0 O C:PRO203 4.3 12.4 1.0 O C:PRO95 4.4 16.6 1.0 OE1 C:GLU157 4.6 17.0 1.0 O C:ASP37 4.6 17.5 1.0 O C:ALA94 4.7 17.7 1.0 ND1 C:HIS261 4.8 15.6 1.0 CG C:HIS261 4.8 15.6 1.0 O C:ASP155 4.9 16.1 1.0 CA C:GLY202 4.9 15.8 1.0 C C:ASP155 5.0 17.2 1.0

Calcium binding site 6 out of 6 in the Glycoside Hydrolase BT_3662


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Glycoside Hydrolase BT_3662 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:34.8 occ:1.00 O C:PHE358 2.3 21.1 1.0 O C:TRP455 2.4 21.7 1.0 O C:SER366 2.4 19.5 1.0 OD1 C:ASP361 2.4 25.8 1.0 O C:ALA363 2.4 22.1 1.0 OE2 C:GLU456 2.6 41.6 1.0 OG C:SER366 2.6 21.1 1.0 C C:SER366 3.2 20.9 1.0 CG C:ASP361 3.5 26.6 1.0 C C:PHE358 3.5 24.9 1.0 C C:ALA363 3.6 21.2 1.0 C C:TRP455 3.6 23.6 1.0 CB C:SER366 3.7 20.8 1.0 CD C:GLU456 3.7 41.3 1.0 OD2 C:ASP361 3.8 28.8 1.0 CA C:SER366 3.8 19.9 1.0 N C:SER366 4.0 18.6 1.0 N C:ALA363 4.1 23.7 1.0 N C:ARG367 4.2 20.5 1.0 CG C:GLU456 4.2 36.4 1.0 CA C:PHE358 4.3 26.3 1.0 CA C:ALA363 4.3 22.1 1.0 CA C:TRP455 4.4 22.6 1.0 N C:ALA359 4.5 24.9 1.0 CB C:ALA363 4.5 22.7 1.0 CB C:PHE358 4.5 24.2 1.0 CA C:ARG367 4.6 21.4 1.0 N C:GLU456 4.6 26.3 1.0 N C:ASN364 4.6 19.9 1.0 C C:ALA359 4.7 24.0 1.0 N C:ASP361 4.7 25.6 1.0 CA C:ALA359 4.7 24.1 1.0 OE1 C:GLU456 4.7 45.2 1.0 CA C:GLU456 4.8 28.4 1.0 CB C:ASP361 4.8 24.2 1.0 CA C:ASN364 4.9 18.9 1.0 N C:GLY362 4.9 24.7 1.0 O C:ALA359 4.9 24.4 1.0 N C:VAL360 5.0 24.9 1.0

D.Ndeh, A.Rogowski, A.Cartmell, A.S.Luis, A.Basle, J.Gray, I.Venditto, J.Briggs, X.Zhang, A.Labourel, N.Terrapon, F.Buffetto, S.Nepogodiev, Y.Xiao, R.A.Field, Y.Zhu, M.A.O'neill, B.R.Urbanowicz, W.S.York, G.J.Davies, D.W.Abbott, M.C.Ralet, E.C.Martens, B.Henrissat, H.J.Gilbert. Complex Pectin Metabolism By Gut Bacteria Reveals Novel Catalytic Functions. Nature V. 544 65 2017.
ISSN: ISSN 0028-0836
PubMed: 28329766
DOI: 10.1038/NATURE21725