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Calcium in PDB 2wys: High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose

Enzymatic activity of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose

All present enzymatic activity of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose:
3.2.1.8;

Protein crystallography data

The structure of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose, PDB code: 2wys was solved by S.Najmudin, B.A.Pinheiro, M.J.Romao, J.A.M.Prates, C.M.G.A.Fontes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.85 / 2.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.700, 173.700, 135.325, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose (pdb code 2wys). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose, PDB code: 2wys:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2wys

Go back to Calcium Binding Sites List in 2wys
Calcium binding site 1 out of 4 in the High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1552

b:81.5
occ:1.00
 OD1 A:ASP46 3.1 72.2 1.0
N A:VAL43 3.5 68.3 1.0
OD2 A:ASP46 3.7 74.5 1.0
N A:GLU42 3.8 67.8 1.0
CG A:ASP46 3.8 68.4 1.0
N A:ASN44 4.0 64.0 1.0
OG1 A:THR40 4.2 71.0 1.0
CG2 A:VAL43 4.2 67.1 1.0
O A:ASN44 4.2 60.6 1.0
N A:PHE41 4.2 69.9 1.0
CB A:VAL43 4.3 67.3 1.0
CA A:VAL43 4.3 66.9 1.0
C A:PHE41 4.3 68.1 1.0
CA A:GLU42 4.4 68.7 1.0
CA A:PHE41 4.4 68.8 1.0
C A:GLU42 4.4 68.6 1.0
CB A:GLU42 4.6 69.0 1.0
C A:VAL43 4.7 65.5 1.0
CB A:ASN44 4.8 61.7 1.0
ND2 A:ASN44 4.9 60.0 1.0
CA A:ASN44 4.9 62.1 1.0
C A:ASN44 5.0 61.0 1.0

Calcium binding site 2 out of 4 in 2wys

Go back to Calcium Binding Sites List in 2wys
Calcium binding site 2 out of 4 in the High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1553

b:95.0
occ:1.00
 OD2 A:ASP295 3.2 80.3 1.0
O A:HOH2076 3.6 59.5 1.0
OD1 A:ASP295 3.8 80.1 1.0
CG A:ASP295 3.9 80.2 1.0
CD1 A:TRP287 4.3 58.5 1.0
CB A:PRO285 4.4 61.3 1.0
NE1 A:TRP287 4.6 57.7 1.0

Calcium binding site 3 out of 4 in 2wys

Go back to Calcium Binding Sites List in 2wys
Calcium binding site 3 out of 4 in the High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1554

b:62.9
occ:1.00
 OD2 A:ASP173 2.3 66.5 1.0
OE2 A:GLU42 2.3 71.5 1.0
O A:ARG69 2.4 72.1 1.0
O A:THR40 2.6 72.2 1.0
O A:HOH2037 2.8 41.1 1.0
OD1 A:ASP173 2.8 65.8 1.0
CG A:ASP173 2.9 68.0 1.0
OG1 A:THR68 3.0 75.6 1.0
CB A:THR68 3.4 76.6 1.0
C A:ARG69 3.5 73.0 1.0
N A:ARG69 3.5 74.7 1.0
CD A:GLU42 3.6 74.7 1.0
C A:THR40 3.7 71.7 1.0
O A:HOH2003 3.7 60.8 1.0
CA A:ARG69 4.0 73.5 1.0
C A:THR68 4.0 75.8 1.0
OE1 A:GLU42 4.2 74.7 1.0
CB A:ASP173 4.4 68.2 1.0
CA A:THR68 4.4 76.3 1.0
CA A:THR40 4.4 72.8 1.0
CB A:THR40 4.5 72.8 1.0
O A:HOH2014 4.5 73.9 1.0
CG2 A:THR68 4.5 76.5 1.0
CB A:ARG69 4.5 73.0 1.0
N A:GLY70 4.6 73.0 1.0
O A:THR68 4.7 75.7 1.0
N A:PHE41 4.7 69.9 1.0
CG A:GLU42 4.8 71.9 1.0
O A:ASN65 4.8 81.2 1.0
CA A:GLY64 4.8 82.6 1.0
CB A:PHE41 4.8 68.4 1.0
N A:GLU42 4.9 67.8 1.0
C A:PHE41 4.9 68.1 1.0
OG1 A:THR40 4.9 71.0 1.0
CA A:PHE41 5.0 68.8 1.0

Calcium binding site 4 out of 4 in 2wys

Go back to Calcium Binding Sites List in 2wys
Calcium binding site 4 out of 4 in the High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Crystallographic Structure of the Clostridium Thermocellum N-Terminal Endo-1,4-Beta-D-Xylanase 10B (XYN10B) CBM22- 1- GH10 Modules Complexed with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1552

b:58.3
occ:1.00
 O B:ARG69 2.2 62.5 1.0
OD2 B:ASP173 2.2 62.7 1.0
OE2 B:GLU42 2.3 60.2 1.0
O B:HOH2047 2.3 37.4 1.0
O B:THR40 2.3 60.9 1.0
OG1 B:THR68 2.7 66.3 1.0
OD1 B:ASP173 2.8 63.8 1.0
CG B:ASP173 2.8 62.4 1.0
C B:ARG69 3.3 63.4 1.0
CD B:GLU42 3.5 63.4 1.0
C B:THR40 3.5 60.3 1.0
CB B:THR68 3.5 67.3 1.0
N B:ARG69 3.8 65.3 1.0
CA B:ARG69 4.1 63.8 1.0
CA B:THR40 4.3 61.6 1.0
OE1 B:GLU42 4.3 63.1 1.0
CB B:ASP173 4.3 61.8 1.0
N B:GLY70 4.4 63.3 1.0
CB B:THR40 4.4 61.7 1.0
C B:THR68 4.4 66.5 1.0
CG2 B:THR68 4.4 65.3 1.0
CG B:GLU42 4.5 59.3 1.0
CB B:ARG69 4.5 63.5 1.0
N B:PHE41 4.5 58.1 1.0
CA B:GLY70 4.6 64.2 1.0
CB B:PHE41 4.6 57.2 1.0
OG1 B:THR40 4.6 62.5 1.0
C B:PHE41 4.7 55.7 1.0
CA B:THR68 4.7 67.4 1.0
N B:GLU42 4.7 55.4 1.0
CA B:PHE41 4.8 56.6 1.0
OD2 B:ASP174 4.8 73.5 1.0
O B:ASN65 4.8 73.5 1.0

Reference:

S.Najmudin, B.A.Pinheiro, J.A.M.Prates, H.J.Gilbert, M.J.Romao, C.M.G.A.Fontes. Putting An N-Terminal End to the Clostridium Thermocellum Xylanase XYN10B Story: Crystal Structure of the CBM22-1-GH10 Modules Complexed with Xylohexaose. J.Struct.Biol. V. 172 353 2010.
ISSN: ISSN 1047-8477
PubMed: 20682344
DOI: 10.1016/J.JSB.2010.07.009
Page generated: Tue Jul 8 09:16:21 2025

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