Calcium in PDB 6r3m: Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide

All present enzymatic activity of Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide:
3.2.1.4;

The structure of Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide, PDB code: 6r3m was solved by D.O.Ribeiro, A.L.Carvalho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.62 / 1.45
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	103.249, 103.249, 39.580, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.8

The binding sites of Calcium atom in the Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide (pdb code 6r3m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide, PDB code: 6r3m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:9.8 occ:1.00 OD2 A:ASP141 2.3 10.9 1.0 OE1 A:GLU101 2.4 8.1 1.0 O A:THR139 2.4 9.6 1.0 OG A:SER137 2.5 10.6 1.0 OE1 A:GLU91 2.5 7.8 1.0 OE2 A:GLU91 2.5 7.9 1.0 OD2 A:ASP135 2.5 8.9 1.0 OD1 A:ASP135 2.6 8.8 1.0 CD A:GLU91 2.8 7.7 1.0 CG A:ASP135 2.9 9.0 1.0 CD A:GLU101 3.4 8.0 1.0 CG A:ASP141 3.4 11.6 1.0 CB A:SER137 3.5 10.6 1.0 C A:THR139 3.6 9.9 1.0 O A:HOH301 4.1 25.9 1.0 CB A:GLU101 4.1 7.6 1.0 OE2 A:GLU101 4.2 9.0 1.0 O A:HOH393 4.2 13.6 1.0 N A:ASP141 4.2 8.7 1.0 OG1 A:THR139 4.2 19.6 1.0 N A:THR139 4.3 9.7 1.0 CB A:ASP141 4.3 10.0 1.0 OD1 A:ASP141 4.3 15.7 1.0 CG A:GLU91 4.3 7.5 1.0 CB A:ASP135 4.4 9.5 1.0 CG A:GLU101 4.4 8.0 1.0 N A:SER137 4.4 10.9 1.0 CA A:SER137 4.4 10.7 1.0 O A:HOH363 4.4 10.6 1.0 O A:HOH338 4.5 19.8 1.0 NE1 A:TRP103 4.5 7.3 1.0 CA A:THR139 4.5 10.4 1.0 N A:LEU140 4.6 9.4 1.0 CA A:LEU140 4.6 9.3 1.0 N A:GLY138 4.7 9.9 1.0 C A:LEU140 4.8 9.2 1.0 C A:SER137 4.9 10.8 1.0 CA A:ASP141 4.9 8.9 1.0

Calcium binding site 2 out of 2 in the Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum in Complex with Beta-1,3-1,4-Mixed-Linked Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:11.4 occ:1.00 O A:ASN40 2.3 6.7 1.0 OE2 A:GLU14 2.3 9.2 1.0 O A:THR38 2.4 8.2 1.0 O A:HOH330 2.4 13.5 1.0 OD1 A:ASP163 2.4 7.2 1.0 O A:ASP12 2.4 7.8 1.0 OD2 A:ASP163 2.7 7.5 1.0 CG A:ASP163 2.9 7.7 1.0 CD A:GLU14 3.4 9.9 1.0 C A:ASN40 3.5 6.8 1.0 C A:ASP12 3.6 8.0 1.0 C A:THR38 3.6 8.7 1.0 N A:ASN40 3.7 6.9 1.0 C A:GLY39 4.1 7.2 1.0 CG A:GLU14 4.1 9.1 1.0 OG1 A:THR38 4.2 14.3 1.0 CA A:ASN40 4.2 6.8 1.0 OE1 A:GLU14 4.2 13.7 1.0 OD1 A:ASN164 4.3 9.2 1.0 CA A:GLY39 4.3 7.5 1.0 CA A:ASP12 4.3 8.8 1.0 CB A:ASP163 4.4 7.6 1.0 CB A:ASP12 4.4 9.5 1.0 N A:GLY39 4.4 8.0 1.0 CB A:PHE13 4.5 7.9 1.0 N A:THR38 4.5 9.9 1.0 N A:GLY41 4.5 7.0 1.0 CA A:THR38 4.6 10.1 1.0 N A:PHE13 4.6 8.0 1.0 CA A:PHE13 4.8 8.0 1.0 C A:PHE13 4.8 8.3 1.0 CG A:ASN164 4.8 8.8 1.0 O A:GLY39 4.8 7.9 1.0 CA A:GLY41 4.9 7.1 1.0 ND2 A:ASN164 4.9 10.6 1.0 CB A:THR38 4.9 11.9 1.0 N A:GLU14 4.9 8.2 1.0

D.O.Ribeiro, A.Viegas, V.M.R.Pires, J.Medeiros-Silva, P.Bule, W.Chai, F.Marcelo, C.M.G.A.Fontes, E.J.Cabrita, A.S.Palma, A.L.Carvalho. Molecular Basis For the Preferential Recognition of Beta 1,3-1,4-Glucans By the Family 11 Carbohydrate-Binding Module From Clostridium Thermocellum. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31794092
DOI: 10.1111/FEBS.15162