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Calcium in PDB 2wze: 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: 2wze 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) 101.02 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.037, 173.037, 136.159, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 18.9

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 2wze). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 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: 2wze:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2wze

Go back to Calcium Binding Sites List in 2wze
Calcium binding site 1 out of 2 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:76.7
occ:1.00
 OD2 A:ASP173 2.0 69.1 1.0
OE2 A:GLU42 2.1 88.9 1.0
O A:ARG69 2.4 68.0 1.0
OD1 A:ASP173 2.6 74.2 1.0
CG A:ASP173 2.7 70.5 1.0
OG1 A:THR68 2.7 77.3 1.0
O A:HOH2008 3.2 31.6 1.0
CD A:GLU42 3.4 88.7 1.0
CB A:THR68 3.4 75.7 1.0
C A:ARG69 3.6 68.8 1.0
O A:THR40 3.7 85.4 1.0
C A:THR40 3.7 81.7 1.0
OD1 A:ASP174 3.8 84.8 1.0
N A:ARG69 3.9 71.3 1.0
CA A:THR40 4.1 80.4 1.0
CB A:ASP173 4.1 72.8 1.0
OE1 A:GLU42 4.2 90.0 1.0
CB A:THR40 4.2 81.1 1.0
N A:PHE41 4.2 81.8 1.0
CG2 A:THR68 4.3 75.8 1.0
CA A:ARG69 4.4 68.9 1.0
C A:THR68 4.4 74.6 1.0
CG A:GLU42 4.4 81.2 1.0
CA A:THR68 4.6 76.5 1.0
N A:GLY70 4.7 69.2 1.0
CG A:ASP174 4.7 84.2 1.0
C A:PHE41 4.8 79.5 1.0
O A:HOH2109 4.8 38.0 1.0
N A:ASP174 4.9 74.0 1.0
CA A:PHE41 4.9 79.3 1.0
N A:GLU42 4.9 78.0 1.0
O A:ASN65 4.9 82.2 1.0
CA A:GLY70 4.9 69.6 1.0
CB A:ARG69 4.9 67.0 1.0
CA A:GLY64 5.0 80.0 1.0
OG1 A:THR40 5.0 78.4 1.0

Calcium binding site 2 out of 2 in 2wze

Go back to Calcium Binding Sites List in 2wze
Calcium binding site 2 out of 2 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
B:Ca1552

b:61.2
occ:1.00
 O B:ARG69 2.1 49.3 1.0
O B:HOH2136 2.2 28.4 1.0
OE2 B:GLU42 2.2 58.9 1.0
O B:THR40 2.4 55.8 1.0
OD2 B:ASP173 2.4 66.7 1.0
OD1 B:ASP173 2.4 61.3 1.0
OG1 B:THR68 2.6 61.2 1.0
CG B:ASP173 2.8 62.6 1.0
C B:ARG69 3.4 52.5 1.0
CD B:GLU42 3.5 59.3 1.0
C B:THR40 3.5 53.3 1.0
CB B:THR68 3.6 60.9 1.0
N B:ARG69 3.9 56.1 1.0
CA B:THR40 4.1 54.7 1.0
CA B:ARG69 4.2 53.3 1.0
C B:THR68 4.3 59.2 1.0
CB B:ASP173 4.3 60.9 1.0
OE1 B:GLU42 4.3 58.6 1.0
CB B:THR40 4.3 56.0 1.0
N B:GLY70 4.4 52.5 1.0
CG B:GLU42 4.5 59.4 1.0
CG2 B:THR68 4.5 61.3 1.0
CA B:THR68 4.6 61.8 1.0
OD2 B:ASP174 4.6 78.8 1.0
CA B:GLY70 4.6 54.8 1.0
N B:PHE41 4.6 51.2 1.0
CB B:PHE41 4.8 50.0 1.0
O B:HOH2028 4.8 51.7 1.0
O B:ASN65 4.8 67.8 1.0
N B:ASP174 4.9 62.5 1.0
CB B:ARG69 4.9 51.6 1.0
C B:PHE41 4.9 50.4 1.0
O B:THR68 4.9 59.6 1.0
CG B:ASP174 4.9 73.7 1.0
N B:GLU42 4.9 51.0 1.0
CA B:PHE41 4.9 49.8 1.0
OD1 B:ASP174 5.0 75.1 1.0
N B:ASN65 5.0 67.4 1.0
OG1 B:THR40 5.0 57.7 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: Fri Jul 12 18:58:06 2024

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