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Calcium in PDB 4xut: Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C

Enzymatic activity of Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C

All present enzymatic activity of Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C:
3.2.1.8;

Protein crystallography data

The structure of Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C, PDB code: 4xut was solved by M.A.Sainz-Polo, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 1.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 92.478, 92.478, 48.382, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C (pdb code 4xut). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C, PDB code: 4xut:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4xut

Go back to Calcium Binding Sites List in 4xut
Calcium binding site 1 out of 3 in the Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:21.6
occ:1.00
 O A:ARG206 2.2 17.5 1.0
O A:HOH546 2.3 23.0 1.0
O A:ASP177 2.3 22.0 1.0
OE2 A:GLU179 2.4 26.6 1.0
OD2 A:ASP325 2.5 18.3 1.0
OD1 A:ASP325 2.5 15.3 1.0
OG A:SER204 2.5 26.1 1.0
CG A:ASP325 2.8 15.5 1.0
C A:ARG206 3.4 19.7 1.0
CB A:SER204 3.4 28.3 1.0
C A:ASP177 3.5 18.9 1.0
CD A:GLU179 3.5 30.2 1.0
CG A:GLU179 4.0 28.4 1.0
CA A:ASP177 4.1 20.4 1.0
N A:ARG206 4.1 23.9 1.0
CA A:ARG206 4.2 22.3 1.0
CB A:ASP177 4.3 21.7 1.0
CB A:ASP325 4.3 15.2 1.0
OD1 A:ASP326 4.4 19.2 1.0
N A:SER207 4.4 18.8 1.0
OE1 A:GLU179 4.6 28.4 1.0
N A:PHE178 4.6 18.7 1.0
CB A:ARG206 4.7 25.8 1.0
CA A:SER207 4.7 19.3 1.0
CB A:PHE178 4.7 19.8 1.0
O A:HIS202 4.8 22.1 1.0
N A:HIS202 4.8 20.8 1.0
CA A:SER204 4.8 26.3 1.0
N A:GLU179 4.8 22.7 1.0
CA A:GLY201 4.9 22.5 1.0
N A:ASN205 4.9 26.1 1.0
C A:PHE178 4.9 22.4 1.0
C A:SER204 4.9 27.6 1.0
CB A:SER207 4.9 19.4 1.0
CA A:PHE178 5.0 20.1 1.0

Calcium binding site 2 out of 3 in 4xut

Go back to Calcium Binding Sites List in 4xut
Calcium binding site 2 out of 3 in the Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:17.9
occ:1.00
 O B:ARG206 2.3 18.0 1.0
O B:HOH1120 2.3 18.8 1.0
O B:ASP177 2.3 18.3 1.0
OE2 B:GLU179 2.4 22.8 1.0
OD1 B:ASP325 2.5 14.2 1.0
OD2 B:ASP325 2.5 14.9 1.0
OG B:SER204 2.5 18.3 1.0
CG B:ASP325 2.8 14.5 1.0
CB B:SER204 3.4 22.1 1.0
C B:ARG206 3.4 18.2 1.0
C B:ASP177 3.5 17.6 1.0
CD B:GLU179 3.5 26.8 1.0
CG B:GLU179 4.0 24.9 1.0
CA B:ASP177 4.1 19.0 1.0
N B:ARG206 4.1 22.9 1.0
CB B:ASP177 4.2 21.3 1.0
CA B:ARG206 4.3 22.0 1.0
OD1 B:ASP326 4.3 19.2 1.0
CB B:ASP325 4.3 14.2 1.0
N B:SER207 4.4 16.0 1.0
OE1 B:GLU179 4.6 29.1 1.0
O B:HOH1129 4.6 25.6 1.0
N B:PHE178 4.6 16.0 1.0
CA B:SER207 4.7 16.3 1.0
CB B:ARG206 4.7 25.1 1.0
CA B:SER204 4.7 21.5 1.0
O B:HIS202 4.8 18.7 1.0
N B:HIS202 4.8 18.9 1.0
CB B:PHE178 4.8 16.2 1.0
N B:GLU179 4.8 21.8 1.0
CA B:GLY201 4.9 21.0 1.0
C B:SER204 4.9 22.8 1.0
N B:ASN205 4.9 23.3 1.0
C B:PHE178 5.0 17.5 1.0
CA B:PHE178 5.0 16.9 1.0
CB B:SER207 5.0 16.1 1.0

Calcium binding site 3 out of 3 in 4xut

Go back to Calcium Binding Sites List in 4xut
Calcium binding site 3 out of 3 in the Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the CBM22-2 Xylan-Binding Domain in Complex with 1,3:1,4 Beta-Glucotetraose B From Paenibacillus Barcinonensis XYN10C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:31.1
occ:1.00
 O C:ARG206 2.2 27.4 1.0
OE2 C:GLU179 2.4 40.8 1.0
O C:ASP177 2.4 28.9 1.0
OG C:SER204 2.4 36.4 1.0
OD2 C:ASP325 2.4 22.1 1.0
OD1 C:ASP325 2.5 25.0 1.0
CG C:ASP325 2.8 23.9 1.0
C C:ARG206 3.4 24.7 1.0
CB C:SER204 3.4 37.1 1.0
CD C:GLU179 3.5 40.6 1.0
C C:ASP177 3.6 25.8 1.0
N C:ARG206 4.0 31.4 1.0
CG C:GLU179 4.1 35.9 1.0
CA C:ARG206 4.2 30.1 1.0
CA C:ASP177 4.2 26.0 1.0
CB C:ASP177 4.3 27.5 1.0
CB C:ASP325 4.4 22.1 1.0
N C:SER207 4.4 25.5 1.0
OD1 C:ASP326 4.4 33.3 1.0
OE1 C:GLU179 4.6 43.8 1.0
CB C:ARG206 4.6 31.6 1.0
CA C:SER207 4.6 23.2 1.0
N C:PHE178 4.7 25.0 1.0
CA C:SER204 4.7 37.6 1.0
N C:HIS202 4.7 31.6 1.0
O C:HIS202 4.7 31.4 1.0
CB C:PHE178 4.8 26.3 1.0
CA C:GLY201 4.8 31.3 1.0
C C:SER204 4.8 39.6 1.0
N C:ASN205 4.8 42.2 1.0
N C:GLU179 4.8 28.7 1.0
CB C:SER207 4.9 22.7 1.0
C C:PHE178 5.0 28.8 1.0

Reference:

M.A.Sainz-Polo, B.Gonzalez, M.Menendez, F.I.Pastor, J.Sanz-Aparicio. Exploring Multimodularity in Plant Cell Wall Deconstruction: Structural and Functional Analysis of XYN10C Containing the CBM22-1-CBM22-2 Tandem. J.Biol.Chem. V. 290 17116 2015.
ISSN: ESSN 1083-351X
PubMed: 26001782
DOI: 10.1074/JBC.M115.659300
Page generated: Sun Jul 14 14:44:16 2024

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