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Calcium in PDB 4xur: Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose

Enzymatic activity of Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose

All present enzymatic activity of Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose:
3.2.1.8;

Protein crystallography data

The structure of Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose, PDB code: 4xur 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) 33.55 / 1.67
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 92.769, 92.769, 48.571, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 19.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose (pdb code 4xur). 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 From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose, PDB code: 4xur:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4xur

Go back to Calcium Binding Sites List in 4xur
Calcium binding site 1 out of 3 in the Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose


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 From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:16.4
occ:1.00
 O A:HOH1133 2.2 16.8 1.0
O A:ARG206 2.3 17.6 1.0
OE2 A:GLU179 2.4 17.9 1.0
O A:ASP177 2.4 17.1 1.0
OD1 A:ASP325 2.5 10.1 1.0
OD2 A:ASP325 2.5 10.5 1.0
OG A:SER204 2.6 20.5 1.0
CG A:ASP325 2.8 11.7 1.0
CD A:GLU179 3.5 21.3 1.0
C A:ARG206 3.5 17.8 1.0
C A:ASP177 3.5 16.1 1.0
CB A:SER204 3.6 21.3 1.0
CG A:GLU179 4.0 19.8 1.0
CA A:ASP177 4.1 16.9 1.0
N A:ARG206 4.2 20.0 1.0
CB A:ASP177 4.3 18.3 1.0
CA A:ARG206 4.3 20.2 1.0
CB A:ASP325 4.3 11.3 1.0
OD1 A:ASP326 4.4 14.1 1.0
N A:SER207 4.5 16.1 1.0
OE1 A:GLU179 4.5 21.2 1.0
N A:PHE178 4.6 16.1 1.0
CA A:SER207 4.6 15.6 1.0
CB A:PHE178 4.7 16.6 1.0
CB A:ARG206 4.8 22.1 1.0
N A:HIS202 4.8 17.1 1.0
O A:HIS202 4.8 20.3 1.0
N A:GLU179 4.9 17.5 1.0
CB A:SER207 4.9 15.7 1.0
C A:PHE178 4.9 17.0 1.0
CA A:SER204 4.9 20.2 1.0
CA A:PHE178 5.0 16.9 1.0
CA A:GLY201 5.0 18.0 1.0

Calcium binding site 2 out of 3 in 4xur

Go back to Calcium Binding Sites List in 4xur
Calcium binding site 2 out of 3 in the Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose


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 From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:14.7
occ:1.00
 OE2 B:GLU179 2.3 17.5 1.0
O B:HOH1119 2.3 14.0 1.0
O B:ASP177 2.3 12.6 1.0
O B:ARG206 2.4 13.8 1.0
OD1 B:ASP325 2.5 11.5 1.0
OG B:SER204 2.6 18.1 1.0
OD2 B:ASP325 2.7 13.1 1.0
CG B:ASP325 3.0 11.9 1.0
CD B:GLU179 3.4 18.0 1.0
C B:ASP177 3.5 13.9 1.0
CB B:SER204 3.5 19.4 1.0
C B:ARG206 3.6 15.0 1.0
CG B:GLU179 4.1 18.2 1.0
CA B:ASP177 4.1 12.8 1.0
N B:ARG206 4.1 17.1 1.0
CB B:ASP177 4.2 13.6 1.0
OD1 B:ASP326 4.3 15.6 1.0
CA B:ARG206 4.4 16.8 1.0
CB B:ASP325 4.5 11.6 1.0
OE1 B:GLU179 4.5 21.4 1.0
N B:SER207 4.6 14.2 1.0
N B:PHE178 4.6 13.7 1.0
CA B:SER207 4.8 13.7 1.0
N B:HIS202 4.8 15.2 1.0
N B:GLU179 4.8 18.8 1.0
CA B:SER204 4.8 17.9 1.0
O B:HIS202 4.8 17.0 1.0
CB B:PHE178 4.9 14.0 1.0
CB B:ARG206 4.9 19.6 1.0
C B:PHE178 4.9 16.3 1.0
N B:ASN205 4.9 17.9 1.0
C B:SER204 4.9 16.3 1.0
CA B:GLY201 5.0 16.0 1.0
CA B:PHE178 5.0 15.7 1.0
CG B:ASP177 5.0 14.9 1.0
CD2 B:PHE178 5.0 13.8 1.0

Calcium binding site 3 out of 3 in 4xur

Go back to Calcium Binding Sites List in 4xur
Calcium binding site 3 out of 3 in the Structure of the CBM22-2 Xylan-Binding Domain From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose


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 From Paenibacillus Barcinonensis XYN10C in Complex with Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1005

b:24.1
occ:1.00
 O C:ARG206 2.3 21.5 1.0
O C:HOH1131 2.4 19.7 1.0
OD2 C:ASP325 2.4 16.9 1.0
OE2 C:GLU179 2.4 27.0 1.0
O C:ASP177 2.5 20.3 1.0
OG C:SER204 2.5 29.1 1.0
OD1 C:ASP325 2.6 15.5 1.0
CG C:ASP325 2.8 16.8 1.0
C C:ARG206 3.4 23.0 1.0
CB C:SER204 3.6 29.3 1.0
C C:ASP177 3.6 20.7 1.0
CD C:GLU179 3.6 28.3 1.0
N C:ARG206 4.1 27.6 1.0
CA C:ASP177 4.2 20.2 1.0
CA C:ARG206 4.2 23.2 1.0
CB C:ASP177 4.3 22.4 1.0
OD1 C:ASP326 4.3 24.9 1.0
CB C:ASP325 4.4 15.1 1.0
CG C:GLU179 4.4 25.6 1.0
N C:SER207 4.4 20.3 1.0
OE1 C:GLU179 4.6 28.8 1.0
N C:HIS202 4.7 23.5 1.0
CA C:SER207 4.7 19.7 1.0
CB C:ARG206 4.7 25.9 1.0
N C:PHE178 4.7 23.2 1.0
CB C:PHE178 4.7 23.0 1.0
O C:HIS202 4.8 28.2 1.0
CA C:SER204 4.8 29.5 1.0
CA C:GLY201 4.9 22.0 1.0
CB C:SER207 4.9 17.9 1.0
C C:PHE178 4.9 25.3 1.0
C C:SER204 4.9 30.7 1.0
N C:GLU179 5.0 26.4 1.0
CA C:PHE178 5.0 22.5 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: Wed Jul 9 02:57:04 2025

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