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Zinc 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:

Sodium (Na) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5), PDB code: 2cks:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2cks

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Zinc binding site 1 out of 8 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 Zinc with other atoms in the Zn 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:Zn1432

b:9.1
occ:1.00
 OD1 A:ASP169 1.9 11.1 0.7
OD1 A:ASP173 2.0 8.4 1.0
OD1 A:ASP169 2.0 8.9 0.3
CG A:ASP173 2.8 7.2 1.0
CG A:ASP169 2.8 9.6 0.7
OD2 A:ASP173 2.9 7.9 1.0
OD2 A:ASP169 3.0 13.2 0.7
CG A:ASP169 3.0 8.2 0.3
OD2 A:ASP169 3.2 9.1 0.3
NH2 A:ARG216 3.8 14.4 1.0
O A:HOH2041 4.0 30.7 1.0
O A:HOH2037 4.0 19.1 1.0
O A:ASP169 4.1 8.0 0.3
O A:ASP169 4.2 7.9 0.7
CB A:ASP169 4.2 8.7 0.7
CB A:ASP173 4.2 6.1 1.0
CB A:ASP169 4.4 8.2 0.3
C A:ASP169 4.5 8.0 0.3
C A:ASP169 4.6 8.1 0.7
CZ A:ARG216 4.6 12.9 1.0
NE A:ARG216 4.7 11.2 1.0
CA A:ASP169 4.7 8.4 0.7
CA A:ASP169 4.8 8.1 0.3

Zinc binding site 2 out of 8 in 2cks

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Zinc binding site 2 out of 8 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 Zinc with other atoms in the Zn 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:Zn1433

b:17.1
occ:0.40
 NA A:NA1436 1.4 12.7 0.6
OD1 A:ASP289 2.0 12.6 0.6
O A:HOH2322 2.1 27.9 1.0
O A:HOH2188 2.1 7.7 0.4
OD1 A:ASP287 2.2 14.4 1.0
O A:ALA251 2.4 11.8 1.0
O A:HOH2192 2.5 16.1 0.4
CG A:ASP289 3.0 11.6 0.6
OD2 A:ASP289 3.2 15.0 0.6
CG A:ASP287 3.4 12.6 1.0
O A:HOH2190 3.5 12.9 0.5
C A:ALA251 3.6 11.0 1.0
O A:LYS253 3.8 9.6 1.0
CB A:ASP289 3.9 8.2 0.4
OD2 A:ASP287 4.0 15.6 1.0
O A:HOH2184 4.0 15.4 1.0
OD2 A:ASP289 4.1 10.9 0.4
CA A:ALA251 4.1 10.8 1.0
CG A:ASP289 4.2 10.0 0.4
OG A:SER290 4.4 10.2 0.5
CB A:ASP289 4.4 10.0 0.6
N A:ASP289 4.4 8.6 0.4
O A:HOH2189 4.4 16.9 0.5
N A:ASP289 4.4 9.4 0.6
CA A:ASP287 4.5 9.2 1.0
CB A:ASP287 4.5 9.4 1.0
CB A:ALA251 4.6 10.9 1.0
CA A:ASP289 4.6 8.3 0.4
N A:SER252 4.7 11.3 1.0
C A:ASP287 4.7 9.2 1.0
C A:ASP289 4.7 9.4 0.6
CA A:ASP289 4.7 9.8 0.6
O A:HOH2147 4.8 43.3 1.0
N A:SER290 4.8 7.8 0.5
N A:PRO288 4.9 9.0 1.0
CA A:SER252 5.0 11.6 1.0
N A:SER290 5.0 8.9 0.5
C A:LYS253 5.0 9.2 1.0
CD A:PRO288 5.0 9.6 1.0
O A:ASP289 5.0 10.3 0.6

Zinc binding site 3 out of 8 in 2cks

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Zinc binding site 3 out of 8 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 Zinc with other atoms in the Zn 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
A:Zn1434

b:17.4
occ:0.40
 O A:HOH2323 1.9 14.4 0.5
O A:HOH2324 2.0 23.1 1.0
OD1 A:ASP193 2.3 19.9 1.0
CG A:ASP193 3.5 13.8 1.0
O A:HOH2068 4.1 37.5 1.0
NE1 A:TRP162 4.1 10.6 1.0
OD2 A:ASP193 4.2 19.8 1.0
CB A:ASP193 4.4 10.6 1.0
CD1 A:TRP162 4.9 9.9 1.0

Zinc binding site 4 out of 8 in 2cks

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Zinc binding site 4 out of 8 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 Zinc with other atoms in the Zn 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
A:Zn1435

b:19.1
occ:0.40
 O A:HOH2325 1.7 18.6 0.5
OE1 A:GLU355 2.0 13.5 1.0
OE1 A:GLU263 2.1 9.1 0.3
OE2 A:GLU263 2.4 8.0 0.3
CD A:GLU263 2.6 6.8 0.3
O A:HOH2326 2.7 27.7 1.0
OE2 A:GLU263 2.8 12.6 0.7
CD A:GLU355 2.8 10.3 1.0
OE2 A:GLU355 3.1 8.5 1.0
CD A:GLU263 3.1 10.7 0.7
OE1 A:GLU263 3.2 13.0 0.7
NA A:NA1437 3.2 41.1 1.0
OH A:TYR330 4.0 18.4 1.0
CG A:GLU263 4.1 6.7 0.3
CG A:GLU263 4.2 8.1 0.7
CG A:GLU355 4.2 8.2 1.0
O A:HOH2226 4.3 28.7 1.0
ND2 A:ASN262 4.4 7.1 1.0
ND1 A:HIS328 4.4 6.5 1.0
O A:HOH2159 4.5 27.3 1.0
NE2 A:HIS225 4.5 6.8 1.0
CE1 A:HIS225 4.5 6.6 1.0
OD1 A:ASN262 4.6 7.8 1.0
CE1 A:HIS328 4.9 6.6 1.0
CZ A:TYR330 5.0 16.3 1.0
CE2 A:TYR330 5.0 14.8 1.0
CG A:ASN262 5.0 7.0 1.0

Zinc binding site 5 out of 8 in 2cks

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Zinc binding site 5 out of 8 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 Zinc with other atoms in the Zn 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:Zn1432

b:8.3
occ:1.00
 OD2 B:ASP169 1.8 9.2 0.7
OD1 B:ASP173 1.9 8.1 1.0
OD1 B:ASP169 2.1 8.5 0.3
CG B:ASP169 2.8 9.6 0.7
CG B:ASP173 2.8 7.3 1.0
OD2 B:ASP173 2.8 8.2 1.0
OD1 B:ASP169 3.0 12.2 0.7
CG B:ASP169 3.0 8.4 0.3
OD2 B:ASP169 3.3 8.3 0.3
NH2 B:ARG216 3.9 14.2 1.0
O B:HOH2036 3.9 20.1 1.0
O B:ASP169 4.1 8.0 0.3
CB B:ASP173 4.2 6.0 1.0
CB B:ASP169 4.2 8.9 0.7
O B:ASP169 4.3 7.8 0.7
CB B:ASP169 4.4 8.3 0.3
C B:ASP169 4.6 8.2 0.3
C B:ASP169 4.6 8.3 0.7
CZ B:ARG216 4.6 12.7 1.0
NE B:ARG216 4.7 11.7 1.0
CA B:ASP169 4.8 8.4 0.7
CA B:ASP169 4.8 8.2 0.3

Zinc binding site 6 out of 8 in 2cks

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Zinc binding site 6 out of 8 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 Zinc with other atoms in the Zn binding site number 6 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:Zn1433

b:18.3
occ:1.00
 NE2 B:HIS146 1.9 13.7 1.0
OE2 B:GLU145 2.0 16.0 1.0
CE1 B:HIS146 2.8 14.3 1.0
CD2 B:HIS146 2.9 14.0 1.0
CD B:GLU145 3.0 14.9 1.0
CG B:GLU145 3.4 13.1 1.0
ND1 B:HIS146 4.0 13.4 1.0
CG B:HIS146 4.0 13.0 1.0
OE1 B:GLU145 4.2 14.9 1.0
O B:HOH2018 4.3 33.4 1.0
CB B:GLU145 4.8 12.3 1.0
O B:HOH2017 5.0 19.4 1.0

Zinc binding site 7 out of 8 in 2cks

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Zinc binding site 7 out of 8 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 Zinc with other atoms in the Zn binding site number 7 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:Zn1434

b:25.4
occ:0.40
 NA B:NA1437 1.2 5.2 0.3
NA B:NA1437 1.2 3.7 0.3
OD1 B:ASP289 1.9 15.4 0.7
OD1 B:ASP287 2.1 15.2 1.0
O B:HOH2313 2.3 19.6 0.7
O B:HOH2312 2.5 26.1 1.0
O B:ALA251 2.8 11.2 1.0
CG B:ASP289 3.0 12.5 0.7
CG B:ASP287 3.2 13.6 1.0
OD2 B:ASP289 3.4 15.7 0.7
O B:LYS253 3.5 10.3 1.0
OD2 B:ASP287 3.6 16.7 1.0
O B:HOH2187 3.6 19.2 1.0
C B:ALA251 3.9 10.5 1.0
CB B:ASP289 4.1 9.2 0.3
CB B:ASP289 4.3 10.9 0.7
O B:HOH2155 4.3 9.0 1.0
N B:SER290 4.4 8.2 0.2
CB B:SER290 4.4 7.9 0.2
N B:SER290 4.4 9.9 0.8
N B:ASP289 4.4 9.9 0.7
C B:ASP289 4.4 10.2 0.7
CB B:ASP287 4.4 10.4 1.0
CA B:ALA251 4.5 10.0 1.0
N B:ASP289 4.5 9.2 0.3
CG B:ASP289 4.5 9.7 0.3
OD2 B:ASP289 4.5 10.1 0.3
CA B:ASP289 4.6 10.4 0.7
CA B:ASP287 4.6 9.9 1.0
C B:LYS253 4.7 9.6 1.0
CA B:ASP289 4.7 9.0 0.3
C B:ASP287 4.8 9.9 1.0
CA B:SER290 4.8 8.0 0.2
C B:ASP289 4.8 8.7 0.3
O B:ASP289 4.9 11.2 0.7
O B:HOH2147 4.9 34.5 1.0

Zinc binding site 8 out of 8 in 2cks

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Zinc binding site 8 out of 8 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 Zinc with other atoms in the Zn binding site number 8 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:Zn1435

b:14.9
occ:0.30
 O B:HOH2314 1.7 16.9 0.5
OE1 B:GLU355 1.9 16.0 1.0
OE2 B:GLU263 2.1 9.5 0.3
OE1 B:GLU263 2.6 9.2 0.3
CD B:GLU263 2.7 7.9 0.3
CD B:GLU355 2.8 10.6 1.0
OE1 B:GLU263 2.8 12.3 0.7
O B:HOH2103 2.9 24.5 1.0
OE2 B:GLU355 3.1 9.2 1.0
CD B:GLU263 3.1 11.8 0.7
OE2 B:GLU263 3.2 11.9 0.7
OH B:TYR330 4.0 19.0 1.0
CG B:GLU355 4.2 8.9 1.0
CG B:GLU263 4.2 7.4 0.3
CG B:GLU263 4.2 8.9 0.7
NE2 B:HIS225 4.4 7.3 0.5
ND1 B:HIS328 4.5 7.3 1.0
ND2 B:ASN262 4.5 8.1 1.0
CE1 B:HIS225 4.5 4.2 0.5
NE2 B:HIS225 4.6 4.4 0.5
O B:HOH2226 4.6 28.6 1.0
O B:HOH2161 4.7 30.0 1.0
CE1 B:HIS225 4.7 6.3 0.5
OD1 B:ASN262 4.7 8.4 1.0
CZ B:TYR330 4.9 15.6 1.0
CE2 B:TYR330 4.9 14.6 1.0
CE1 B:HIS328 4.9 7.5 1.0
CB B:GLU355 5.0 6.8 1.0

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: Wed Oct 16 22:25:17 2024

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