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Sodium in PDB 2cks: X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)

Enzymatic activity of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)

All present enzymatic activity of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5):
3.2.1.4;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5), PDB code: 2cks was solved by G.I.Berglund, P.J.Gualfetti, C.Requadt, L.S.Gross, T.Bergfors, A.Shaw, M.Saldajeno, C.Mitchinson, M.Sandgren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.26 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.888, 70.970, 75.624, 90.00, 94.05, 90.00
R / Rfree (%) 14.2 / 16.9

Other elements in 2cks:

The structure of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) (pdb code 2cks). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5), PDB code: 2cks:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2cks

Go back to Sodium Binding Sites List in 2cks
Sodium binding site 1 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1436

b:12.7
occ:0.60
 ZN A:ZN1433 1.4 17.1 0.4
O A:HOH2192 1.8 16.1 0.4
O A:ALA251 2.4 11.8 1.0
O A:HOH2322 2.4 27.9 1.0
OD1 A:ASP287 2.5 14.4 1.0
O A:LYS253 2.6 9.6 1.0
O A:HOH2190 2.7 12.9 0.5
O A:HOH2184 2.8 15.4 1.0
OD1 A:ASP289 2.9 12.6 0.6
C A:ALA251 3.4 11.0 1.0
CG A:ASP287 3.4 12.6 1.0
O A:HOH2188 3.4 7.7 0.4
OD2 A:ASP287 3.5 15.6 1.0
OG A:SER290 3.6 10.2 0.5
O A:HOH2153 3.7 9.5 1.0
C A:LYS253 3.8 9.2 1.0
CG A:ASP289 3.8 11.6 0.6
O A:HOH2189 3.9 16.9 0.5
OD2 A:ASP289 4.0 15.0 0.6
CA A:ALA251 4.0 10.8 1.0
O A:HIS250 4.3 9.6 1.0
N A:LYS253 4.4 9.7 1.0
N A:SER252 4.4 11.3 1.0
C A:SER252 4.4 10.5 1.0
CB A:ASP289 4.5 8.2 0.4
N A:THR254 4.7 9.1 1.0
CA A:THR254 4.7 9.6 1.0
CA A:LYS253 4.7 9.0 1.0
CA A:SER252 4.7 11.6 1.0
CB A:SER290 4.8 8.6 0.5
O A:HOH2147 4.8 43.3 1.0
CB A:ASP287 4.8 9.4 1.0
O A:SER252 4.9 11.1 1.0
CB A:SER290 4.9 8.3 0.5
N A:SER290 4.9 7.8 0.5
C A:ASP289 5.0 9.4 0.6
CB A:ALA251 5.0 10.9 1.0

Sodium binding site 2 out of 5 in 2cks

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Sodium binding site 2 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1437

b:41.1
occ:1.00
 O A:HOH2326 2.2 27.7 1.0
O A:HOH2226 2.7 28.7 1.0
O A:HOH2062 3.2 30.5 1.0
ZN A:ZN1435 3.2 19.1 0.4
O A:HOH2325 4.0 18.6 0.5
NE1 A:TRP389 4.0 8.5 1.0
CZ2 A:TRP389 4.0 7.7 1.0
OE1 A:GLU355 4.1 13.5 1.0
CE2 A:TRP389 4.2 8.6 1.0
OH A:TYR189 4.2 13.1 1.0
O A:HOH2284 4.2 17.8 0.5
OH A:TYR330 4.5 18.4 1.0
CD2 A:LEU227 4.7 12.4 1.0
O A:HOH2029 4.7 14.0 0.5
OE2 A:GLU263 4.8 8.0 0.3
CD1 A:TRP389 4.9 7.8 1.0
CH2 A:TRP389 4.9 8.4 1.0
CD A:GLU355 5.0 10.3 1.0

Sodium binding site 3 out of 5 in 2cks

Go back to Sodium Binding Sites List in 2cks
Sodium binding site 3 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1436

b:14.6
occ:1.00
 OD1 B:ASP193 2.4 19.7 1.0
CG B:ASP193 3.5 14.3 1.0
NE1 B:TRP162 4.2 9.3 1.0
CB B:ASP193 4.3 11.0 1.0
OD2 B:ASP193 4.4 20.9 1.0
CD1 B:TRP162 4.9 9.2 1.0

Sodium binding site 4 out of 5 in 2cks

Go back to Sodium Binding Sites List in 2cks
Sodium binding site 4 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1437

b:5.2
occ:0.30
 NA B:NA1437 0.0 5.2 0.3
ZN B:ZN1434 1.2 25.4 0.4
NA B:NA1437 1.8 3.7 0.3
O B:ALA251 2.3 11.2 1.0
O B:LYS253 2.3 10.3 1.0
O B:HOH2313 2.4 19.6 0.7
O B:HOH2312 2.5 26.1 1.0
OD1 B:ASP287 2.7 15.2 1.0
O B:HOH2187 2.9 19.2 1.0
OD1 B:ASP289 3.0 15.4 0.7
C B:ALA251 3.4 10.5 1.0
CG B:ASP287 3.5 13.6 1.0
C B:LYS253 3.6 9.6 1.0
OD2 B:ASP287 3.6 16.7 1.0
O B:HOH2155 3.7 9.0 1.0
CG B:ASP289 4.0 12.5 0.7
CA B:ALA251 4.0 10.0 1.0
N B:LYS253 4.2 10.2 1.0
O B:HIS250 4.2 9.1 1.0
OD2 B:ASP289 4.2 15.7 0.7
C B:SER252 4.3 10.6 0.6
C B:SER252 4.3 10.5 0.4
N B:SER252 4.3 10.5 0.4
N B:SER252 4.3 10.6 0.6
N B:THR254 4.5 9.3 1.0
CA B:LYS253 4.5 9.7 1.0
CA B:THR254 4.5 9.1 1.0
O B:HOH2147 4.5 34.5 1.0
CA B:SER252 4.6 10.6 0.4
O B:SER252 4.6 10.9 0.6
CA B:SER252 4.6 10.8 0.6
CB B:SER290 4.8 7.9 0.2
O B:SER252 4.8 10.6 0.4
CG2 B:THR254 4.9 9.8 0.5
CB B:ASP287 4.9 10.4 1.0

Sodium binding site 5 out of 5 in 2cks

Go back to Sodium Binding Sites List in 2cks
Sodium binding site 5 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1437

b:3.7
occ:0.30
 NA B:NA1437 0.0 3.7 0.3
ZN B:ZN1434 1.2 25.4 0.4
NA B:NA1437 1.8 5.2 0.3
O B:HOH2313 2.1 19.6 0.7
OD1 B:ASP289 2.2 15.4 0.7
O B:ALA251 2.4 11.2 1.0
OD1 B:ASP287 2.4 15.2 1.0
CG B:ASP289 3.1 12.5 0.7
OD2 B:ASP289 3.2 15.7 0.7
C B:ALA251 3.5 10.5 1.0
O B:HOH2312 3.6 26.1 1.0
CG B:ASP287 3.6 13.6 1.0
O B:LYS253 4.0 10.3 1.0
OD2 B:ASP289 4.1 10.1 0.3
CA B:ALA251 4.1 10.0 1.0
OD2 B:ASP287 4.2 16.7 1.0
O B:HOH2190 4.3 34.3 1.0
CG B:ASP289 4.3 9.7 0.3
CB B:ASP289 4.4 9.2 0.3
O B:HOH2187 4.4 19.2 1.0
O B:HOH2147 4.4 34.5 1.0
CA B:ASP287 4.5 9.9 1.0
CB B:ASP289 4.5 10.9 0.7
N B:SER252 4.6 10.5 0.4
N B:SER252 4.6 10.6 0.6
N B:ASP289 4.6 9.9 0.7
CB B:ALA251 4.6 10.1 1.0
CB B:ASP287 4.6 10.4 1.0
N B:ASP289 4.6 9.2 0.3
C B:ASP287 4.8 9.9 1.0
CA B:SER252 4.8 10.6 0.4
CA B:SER252 4.9 10.8 0.6
CD B:PRO288 4.9 10.2 1.0
CA B:ASP289 4.9 10.4 0.7
N B:PRO288 5.0 9.3 1.0
C B:SER252 5.0 10.6 0.6
OD1 B:ASP289 5.0 10.6 0.3

Reference:

G.I.Berglund, P.J.Gualfetti, C.Requadt, L.S.Gross, T.Bergfors, A.Shaw, M.Saldajeno, C.Mitchinson, M.Sandgren. The Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A in Complex with Cellotetraose To Be Published.
Page generated: Sun Aug 17 10:17:24 2025

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