Calcium in PDB 1i8a: Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose

All present enzymatic activity of Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose:
3.2.1.8;

The structure of Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose, PDB code: 1i8a was solved by V.Notenboom, A.B.Boraston, R.A.J.Warren, D.G.Kilburn, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.760, 56.760, 123.100, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 21.7

The binding sites of Calcium atom in the Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose (pdb code 1i8a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose, PDB code: 1i8a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca190 b:2.0 occ:1.00 OE1 A:GLU91 2.4 5.0 1.0 OD1 A:ASP94 2.4 6.9 1.0 OD2 A:ASP93 2.4 5.2 1.0 OD1 A:ASP93 2.6 6.0 1.0 OD1 A:ASN83 2.6 7.1 1.0 OD1 A:ASP81 2.6 5.4 1.0 OD2 A:ASP94 2.7 5.0 1.0 O A:HOH200 2.8 12.0 1.0 CG A:ASP93 2.8 5.1 1.0 CG A:ASP94 2.9 5.8 1.0 CG A:ASN83 3.4 6.4 1.0 CG A:ASP81 3.4 6.6 1.0 CD A:GLU91 3.5 5.6 1.0 ND2 A:ASN83 3.6 6.4 1.0 OD2 A:ASP81 3.8 7.3 1.0 CG A:GLU91 3.9 7.4 1.0 CB A:GLU91 3.9 7.3 1.0 CB A:ASP94 4.3 4.7 1.0 CB A:ASP93 4.3 5.7 1.0 N A:ASP94 4.4 6.4 1.0 CA A:ASP81 4.4 6.5 1.0 N A:HIS85 4.4 8.0 1.0 CB A:ASP81 4.4 7.3 1.0 N A:ASN83 4.4 7.3 1.0 CB A:HIS85 4.5 7.9 1.0 OE2 A:GLU91 4.6 6.8 1.0 C A:ASP81 4.7 7.6 1.0 N A:GLU82 4.7 8.3 1.0 N A:ASN84 4.7 6.7 1.0 C A:ASP93 4.7 7.7 1.0 CB A:ASN83 4.7 6.4 1.0 OG1 A:THR87 4.7 5.8 1.0 CA A:ASP94 4.7 5.9 1.0 O A:HOH224 4.7 7.9 1.0 CG A:HIS85 4.8 7.0 1.0 N A:GLU91 4.9 8.0 1.0 CA A:ASP93 4.9 7.2 1.0 CA A:GLU91 5.0 8.2 1.0 CA A:ASN83 5.0 7.5 1.0

Calcium binding site 2 out of 3 in the Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca191 b:2.0 occ:1.00 O A:VAL10 2.3 9.5 1.0 OD1 A:ASP16 2.3 7.9 1.0 O A:GLU14 2.4 11.3 1.0 OE2 A:GLU130 2.5 6.8 1.0 OE1 A:GLU130 2.5 8.2 1.0 OD1 A:ASP12 2.5 9.6 1.0 O A:HOH230 2.6 9.1 1.0 CD A:GLU130 2.8 8.1 1.0 CG A:ASP16 3.3 9.9 1.0 CG A:ASP12 3.5 10.8 1.0 C A:GLU14 3.5 10.6 1.0 C A:VAL10 3.5 9.2 1.0 OD2 A:ASP16 3.7 9.2 1.0 N A:GLU14 3.9 12.2 1.0 OD2 A:ASP12 3.9 11.6 1.0 N A:ASP12 4.0 10.1 1.0 CA A:GLU14 4.1 13.0 1.0 N A:VAL10 4.2 9.1 1.0 N A:ASP16 4.2 9.1 1.0 CA A:VAL10 4.3 9.2 1.0 N A:GLY13 4.3 9.8 1.0 CG A:GLU130 4.3 8.8 1.0 CB A:GLU14 4.4 15.6 1.0 NE1 A:TRP19 4.4 9.8 1.0 N A:ILE11 4.5 8.0 1.0 CB A:VAL10 4.5 8.0 1.0 N A:ILE15 4.5 10.4 1.0 CA A:ILE11 4.6 9.7 1.0 CB A:ASP16 4.6 8.7 1.0 CB A:ASP12 4.7 11.0 1.0 C A:ILE11 4.7 9.0 1.0 CA A:ASP12 4.7 10.4 1.0 CA A:ILE15 4.8 10.1 1.0 C A:GLY13 4.8 11.4 1.0 C A:ASP12 4.9 12.3 1.0 C A:ILE15 4.9 10.1 1.0 CA A:ASP16 4.9 9.4 1.0 CB A:PRO9 5.0 9.4 1.0

Calcium binding site 3 out of 3 in the Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca192 b:2.0 occ:1.00 O A:VAL62 2.3 12.1 1.0 OD1 A:ASP154 2.4 7.0 1.0 OD1 A:ASP60 2.4 8.9 1.0 OD1 A:ASP74 2.5 7.1 1.0 O A:ALA155 2.5 7.5 1.0 OD2 A:ASP60 2.6 9.3 1.0 OD2 A:ASP74 2.7 8.6 1.0 CG A:ASP60 2.9 7.2 1.0 O A:HOH215 2.9 19.8 1.0 CG A:ASP74 2.9 7.9 1.0 C A:VAL62 3.5 11.9 1.0 CG A:ASP154 3.6 6.6 1.0 C A:ALA155 3.7 9.8 1.0 N A:ALA155 3.7 8.4 1.0 O A:HOH232 4.0 17.3 1.0 CA A:ALA155 4.3 8.4 1.0 OD2 A:ASP154 4.3 8.5 1.0 CB A:ASP74 4.3 7.2 1.0 CA A:VAL62 4.4 11.4 1.0 CB A:ASP60 4.4 9.4 1.0 C A:ASP154 4.4 7.8 1.0 N A:LEU63 4.4 11.7 1.0 CA A:ASP154 4.5 8.2 1.0 CB A:VAL62 4.5 11.0 1.0 CA A:LEU63 4.5 12.2 1.0 N A:VAL62 4.5 10.5 1.0 CB A:ASP154 4.6 7.3 1.0 N A:ASN156 4.7 10.2 1.0 O A:HOH209 4.8 12.0 1.0 N A:ASN64 4.9 11.1 1.0 CG1 A:VAL62 4.9 9.0 1.0 CA A:ASN156 5.0 11.5 1.0

V.Notenboom, A.B.Boraston, D.G.Kilburn, D.R.Rose. Crystal Structures of the Family 9 Carbohydrate-Binding Module From Thermotoga Maritima Xylanase 10A in Native and Ligand-Bound Forms. Biochemistry V. 40 6248 2001.
ISSN: ISSN 0006-2960
PubMed: 11371186
DOI: 10.1021/BI0101704