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Cadmium in PDB 2w5f: 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: 2w5f 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) 150.76 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.178, 173.178, 131.710, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 19.4

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium 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 2w5f). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium 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: 2w5f:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 1 out of 13 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 Cadmium with other atoms in the Cd 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:Cd1558

b:34.5
occ:1.00
 O A:ACT1552 2.0 32.6 1.0
OXT A:ACT1553 2.2 36.5 1.0
OD1 A:ASP169 2.3 20.3 1.0
OD2 A:ASP169 2.4 24.3 1.0
OXT A:ACT1552 2.6 34.8 1.0
O A:ACT1553 2.6 34.8 1.0
C A:ACT1552 2.7 34.9 1.0
CG A:ASP169 2.7 23.0 1.0
C A:ACT1553 2.8 36.8 1.0
O A:HOH2742 3.7 30.9 1.0
O A:HOH2287 3.9 28.6 1.0
CH3 A:ACT1552 4.2 34.1 1.0
CB A:ASP169 4.2 23.5 1.0
N A:ASN75 4.2 20.3 1.0
CH3 A:ACT1553 4.3 36.6 1.0
N A:ASP169 4.7 25.1 1.0
O A:HOH2096 4.8 39.1 1.0
CB A:ILE74 4.8 21.9 1.0
CA A:ASP169 4.9 24.5 1.0
CA A:ASN75 4.9 20.5 1.0

Cadmium binding site 2 out of 13 in 2w5f

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Cadmium binding site 2 out of 13 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 Cadmium with other atoms in the Cd 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:Cd1559

b:40.8
occ:0.70
 OE2 A:GLU42 2.1 27.5 1.0
OD2 A:ASP173 2.3 22.6 1.0
O A:ARG69 2.3 21.0 1.0
O A:HOH2014 2.4 28.6 1.0
O A:HOH2298 2.4 37.4 1.0
OD1 A:ASP173 2.5 24.7 1.0
OG1 A:THR68 2.6 20.1 1.0
CG A:ASP173 2.7 23.6 1.0
CD A:GLU42 3.3 30.2 1.0
C A:ARG69 3.5 20.9 1.0
CB A:THR68 3.6 19.4 1.0
N A:ARG69 3.8 20.4 1.0
CA A:THR40 4.0 26.0 1.0
CB A:THR40 4.1 26.1 1.0
OE1 A:GLU42 4.1 31.9 1.0
C A:THR40 4.2 28.2 1.0
CA A:ARG69 4.2 20.8 0.5
CA A:ARG69 4.2 19.7 0.5
CB A:ASP173 4.2 23.1 1.0
C A:THR68 4.2 19.7 1.0
CG A:GLU42 4.4 28.3 1.0
N A:PHE41 4.4 26.6 1.0
O A:HOH2016 4.5 55.0 1.0
N A:GLY70 4.5 21.3 1.0
CA A:THR68 4.5 19.8 1.0
OD1 A:ASP174 4.6 22.6 1.0
CG2 A:THR68 4.6 19.7 1.0
CA A:GLY70 4.7 21.7 1.0
O A:THR40 4.7 32.1 1.0
CB A:ARG69 4.8 19.0 0.5
O A:ASN65 4.8 20.6 1.0
CB A:ARG69 4.8 20.8 0.5
O A:THR68 4.8 18.7 1.0
C A:PHE41 4.9 25.1 1.0
N A:ASN65 4.9 21.7 1.0
OD2 A:ASP174 4.9 26.7 1.0
N A:GLU42 4.9 23.7 1.0
CG A:ASP174 4.9 23.9 1.0
N A:ASP174 4.9 23.3 1.0
O A:HOH2297 4.9 42.9 1.0
CA A:PHE41 5.0 25.6 1.0

Cadmium binding site 3 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 3 out of 13 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 Cadmium with other atoms in the Cd 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:Cd1560

b:47.1
occ:0.70
 O A:HOH2004 1.3 25.0 1.0
O A:ACT1554 2.0 60.5 1.0
OXT A:ACT1554 2.2 59.7 1.0
OE1 A:GLU35 2.3 28.1 1.0
C A:ACT1554 2.3 60.4 1.0
ND1 A:HIS38 2.4 19.0 1.0
OE2 A:GLU35 2.8 29.4 1.0
CD A:GLU35 2.9 29.1 1.0
CE1 A:HIS38 3.4 20.3 1.0
CG A:HIS38 3.4 20.1 1.0
CB A:HIS38 3.7 21.3 1.0
CH3 A:ACT1554 3.7 60.6 1.0
CG A:GLU35 4.4 28.5 1.0
O A:HOH2005 4.5 78.9 1.0
NE2 A:HIS38 4.5 20.5 1.0
CD2 A:HIS38 4.5 19.9 1.0

Cadmium binding site 4 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 4 out of 13 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 Cadmium with other atoms in the Cd 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
A:Cd1561

b:57.7
occ:0.70
 O A:HOH2520 1.8 40.6 1.0
O A:HOH2747 2.2 65.7 1.0
SG A:CYS406 2.5 25.2 1.0
OXT A:ACT1557 2.5 68.3 1.0
O A:ACT1557 2.6 68.5 1.0
O A:HOH2526 2.9 70.5 1.0
C A:ACT1557 2.9 68.6 1.0
CB A:CYS406 3.3 23.0 1.0
CA A:CYS406 3.6 23.0 1.0
O A:THR346 4.0 25.9 1.0
C A:GLY350 4.0 23.1 1.0
O A:GLY350 4.2 23.2 1.0
O A:CYS406 4.3 22.6 1.0
CA A:GLY350 4.3 23.4 1.0
N A:GLY351 4.4 22.5 1.0
C A:CYS406 4.4 22.7 1.0
CH3 A:ACT1557 4.4 68.4 1.0
N A:CYS406 4.7 22.8 1.0
CD1 A:ILE410 4.8 26.0 0.5
O A:HOH2587 4.8 72.0 1.0
C A:THR346 4.9 25.3 1.0
CA A:GLY351 4.9 21.6 1.0
CB A:SER409 4.9 24.8 1.0
OG A:SER409 5.0 25.6 1.0

Cadmium binding site 5 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 5 out of 13 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 Cadmium with other atoms in the Cd binding site number 5 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:Cd1562

b:61.2
occ:0.75
 OE2 B:GLU126 2.2 39.4 1.0
OE2 A:GLU127 2.3 43.5 1.0
CD A:CD1563 2.4 68.8 0.2
OE1 A:GLU127 2.6 44.3 1.0
CD A:GLU127 2.8 41.5 1.0
CD B:GLU126 2.9 39.4 1.0
OE1 B:GLU126 3.0 39.9 1.0
O A:HOH2185 4.1 74.2 1.0
O B:HOH2187 4.2 71.8 1.0
CG A:GLU127 4.2 36.9 1.0
CG B:GLU126 4.4 39.4 1.0
O A:HOH2187 4.6 70.7 1.0
O B:GLU125 4.9 40.1 1.0

Cadmium binding site 6 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 6 out of 13 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 Cadmium with other atoms in the Cd binding site number 6 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:Cd1563

b:68.8
occ:0.25
 CD A:CD1562 2.4 61.2 0.8
OE1 B:GLU126 2.8 39.9 1.0
OE1 A:GLU127 2.8 44.3 1.0
O A:HOH2185 3.1 74.2 1.0
OE2 B:GLU126 3.2 39.4 1.0
O A:HOH2091 3.2 94.5 1.0
CD B:GLU126 3.3 39.4 1.0
O A:HOH2048 3.4 70.3 1.0
CD A:GLU127 3.7 41.5 1.0
OE2 A:GLU127 3.8 43.5 1.0
CG B:GLU126 4.6 39.4 1.0
O A:HOH2064 4.7 78.3 1.0
O A:HOH2089 4.9 69.7 1.0

Cadmium binding site 7 out of 13 in 2w5f

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Cadmium binding site 7 out of 13 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 Cadmium with other atoms in the Cd binding site number 7 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:Cd1564

b:74.7
occ:0.75
 O A:ACT1556 2.2 63.9 1.0
OE2 B:GLU127 2.2 52.1 1.0
CD B:GLU127 2.9 50.2 1.0
OE1 A:GLU126 2.9 39.1 1.0
OE2 A:GLU126 2.9 38.8 1.0
OE1 B:GLU127 3.1 52.2 1.0
C A:ACT1556 3.1 64.4 1.0
CD A:GLU126 3.1 37.2 1.0
OXT A:ACT1556 3.2 64.3 1.0
CG B:GLU127 4.1 44.2 1.0
O A:HOH2186 4.3 64.8 1.0
CG A:GLU126 4.3 35.4 1.0
CH3 A:ACT1556 4.4 64.8 1.0
O A:GLU125 4.6 35.3 1.0
O A:HOH2744 4.6 79.4 1.0

Cadmium binding site 8 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 8 out of 13 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 Cadmium with other atoms in the Cd binding site number 8 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:Cd1565

b:58.4
occ:0.50
 O A:HOH2621 2.3 75.1 1.0
O A:HOH2583 2.4 66.0 1.0
O A:HOH2624 2.4 68.6 1.0
OD2 A:ASP401 2.5 32.0 1.0
OD1 A:ASP401 2.8 32.3 1.0
CG A:ASP401 2.9 27.9 1.0
NH1 A:ARG404 4.2 26.6 1.0
OD1 A:ASN441 4.2 27.8 1.0
CB A:ASP401 4.5 24.0 1.0
O A:HOH2580 4.6 46.8 1.0
NH2 A:ARG404 4.6 25.0 1.0
CZ A:ARG404 4.8 24.4 1.0
O A:HOH2294 4.9 91.3 1.0

Cadmium binding site 9 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 9 out of 13 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 Cadmium with other atoms in the Cd binding site number 9 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:Cd1555

b:36.0
occ:0.70
 OXT B:ACT1553 1.8 43.1 1.0
O B:HOH2852 1.9 44.9 1.0
C B:ACT1553 2.3 45.5 1.0
SG B:CYS406 2.4 21.2 1.0
O B:ACT1553 2.4 45.6 1.0
OXT B:ACT1552 2.4 45.7 1.0
O B:ACT1552 3.0 46.1 1.0
C B:ACT1552 3.1 46.3 1.0
CB B:CYS406 3.3 21.1 1.0
CA B:CYS406 3.5 20.7 1.0
CH3 B:ACT1553 3.6 46.6 1.0
O B:GLY350 4.0 19.0 1.0
C B:GLY350 4.1 19.2 1.0
O B:HOH2575 4.1 60.4 1.0
O B:CYS406 4.2 20.5 1.0
O B:THR346 4.2 19.6 1.0
C B:CYS406 4.3 20.4 1.0
CA B:GLY350 4.4 18.1 1.0
O B:HOH2657 4.5 60.4 1.0
N B:GLY351 4.5 18.2 1.0
O B:HOH2851 4.6 54.6 1.0
O B:HOH2853 4.6 68.4 1.0
CH3 B:ACT1552 4.6 45.8 1.0
CG2 B:ILE410 4.7 22.4 0.5
N B:CYS406 4.7 20.6 1.0
CA B:GLY351 4.9 18.1 1.0
CB B:SER409 4.9 22.5 1.0
CG1 B:ILE410 5.0 22.4 0.5
OG B:SER409 5.0 24.8 1.0

Cadmium binding site 10 out of 13 in 2w5f

Go back to Cadmium Binding Sites List in 2w5f
Cadmium binding site 10 out of 13 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 Cadmium with other atoms in the Cd binding site number 10 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:Cd1556

b:39.0
occ:0.70
 OE2 B:GLU42 2.0 11.4 0.7
OD2 B:ASP173 2.1 18.1 1.0
O B:HOH2305 2.3 33.9 1.0
O B:ARG69 2.4 19.0 1.0
O B:THR40 2.4 19.5 1.0
OD1 B:ASP173 2.5 25.9 1.0
OG1 B:THR68 2.6 15.7 1.0
CG B:ASP173 2.7 23.5 1.0
CD B:GLU42 3.2 16.0 0.7
C B:THR40 3.4 18.2 1.0
CB B:THR68 3.5 16.9 1.0
C B:ARG69 3.5 19.1 1.0
N B:ARG69 3.8 18.5 1.0
CA B:THR40 3.9 18.0 1.0
OE1 B:GLU42 4.1 14.3 0.7
CB B:THR40 4.1 18.4 1.0
C B:THR68 4.2 18.0 1.0
CG B:GLU42 4.2 16.0 0.7
CA B:ARG69 4.2 18.3 1.0
CB B:ASP173 4.2 24.3 1.0
O B:HOH2014 4.3 58.4 1.0
CA B:THR68 4.5 17.1 1.0
N B:GLY70 4.5 19.0 1.0
CG2 B:THR68 4.6 15.3 1.0
N B:PHE41 4.6 17.8 1.0
OD1 B:ASP174 4.6 27.4 1.0
CA B:GLY70 4.7 19.1 1.0
O B:ASN65 4.7 16.0 1.0
CB B:ARG69 4.7 18.7 1.0
O B:THR68 4.8 18.3 1.0
CB B:PHE41 4.9 17.8 1.0
C B:PHE41 4.9 17.2 1.0
OD2 B:ASP174 4.9 26.5 1.0
N B:ASN65 4.9 17.8 1.0
O B:HOH2307 5.0 50.4 1.0
N B:GLU42 5.0 16.3 1.0
CG B:ASP174 5.0 26.3 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 19 15:19:24 2024

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