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Cadmium in PDB 1gkl: S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid

Enzymatic activity of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid

All present enzymatic activity of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid:
3.2.1.8;

Protein crystallography data

The structure of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid, PDB code: 1gkl was solved by J.A.M.Prates, N.Tarbouriech, S.J.Charnock, C.M.G.A.Fontes, L.M.A.Ferreira, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.101, 108.233, 112.964, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16

Cadmium Binding Sites:

The binding sites of Cadmium atom in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid (pdb code 1gkl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid, PDB code: 1gkl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12;

Cadmium binding site 1 out of 12 in 1gkl

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Cadmium binding site 1 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3090

b:9.0
occ:1.00
O A:HOH2158 2.3 9.4 1.0
ND1 A:HIS886 2.4 8.6 1.0
SG A:CYS823 2.5 9.3 1.0
SD A:MET889 2.8 9.4 1.0
CE1 A:HIS886 3.0 8.4 1.0
CG A:HIS886 3.5 7.1 1.0
CB A:CYS823 3.6 10.6 1.0
CE A:MET889 3.8 10.7 1.0
CA A:HIS886 3.8 6.9 1.0
CG A:MET889 3.8 9.5 1.0
CB A:MET889 3.9 8.6 1.0
CB A:HIS886 4.1 8.0 1.0
NE2 A:HIS886 4.1 8.5 1.0
CA A:CYS823 4.3 10.1 1.0
CD A:PRO824 4.3 10.6 1.0
CD2 A:HIS886 4.4 8.0 1.0
N A:HIS886 4.6 6.8 1.0
O A:HIS886 4.6 7.9 1.0
O A:ASP885 4.7 7.2 1.0
C A:HIS886 4.7 7.0 1.0
OD1 A:ASN890 4.9 10.8 0.5
C A:ASP885 4.9 6.5 1.0
N A:PRO824 4.9 10.6 1.0

Cadmium binding site 2 out of 12 in 1gkl

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Cadmium binding site 2 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3091

b:8.9
occ:1.00
OE2 A:GLU894 2.3 11.0 1.0
NE2 A:HIS1085 2.3 9.5 1.0
OE1 A:GLU1079 2.3 9.5 1.0
ND1 A:HIS1083 2.3 10.3 1.0
ND1 A:HIS1076 2.4 8.8 1.0
OE2 A:GLU1079 2.5 10.4 1.0
CD A:GLU1079 2.7 8.5 1.0
CD A:GLU894 3.1 9.8 1.0
CE1 A:HIS1076 3.2 9.0 1.0
OE1 A:GLU894 3.3 10.7 1.0
CE1 A:HIS1083 3.3 11.1 1.0
CD2 A:HIS1085 3.3 9.6 1.0
CE1 A:HIS1085 3.3 10.1 1.0
CG A:HIS1083 3.4 10.5 1.0
CG A:HIS1076 3.5 8.0 1.0
CB A:HIS1083 3.7 10.2 1.0
CB A:HIS1076 3.9 8.4 1.0
O A:HOH2173 4.1 11.5 1.0
CG A:GLU1079 4.2 9.8 1.0
NE2 A:HIS1076 4.3 8.8 1.0
CA A:HIS1076 4.3 8.6 1.0
ND1 A:HIS1085 4.4 10.6 1.0
O A:HOH2171 4.4 16.1 1.0
NE2 A:HIS1083 4.4 12.1 1.0
CG A:HIS1085 4.4 10.6 1.0
CD2 A:HIS1076 4.5 8.7 1.0
CD2 A:HIS1083 4.5 11.8 1.0
CG A:GLU894 4.5 8.8 1.0
O A:HOH2330 4.7 16.2 1.0
O A:HOH2332 4.9 10.5 0.5
O A:PHE1075 5.0 9.7 1.0

Cadmium binding site 3 out of 12 in 1gkl

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Cadmium binding site 3 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3092

b:13.3
occ:1.00
OE1 A:GLU1007 2.3 13.7 1.0
O A:HOH2259 2.3 23.8 1.0
OE2 A:GLU1007 2.3 16.8 1.0
CD A:GLU1007 2.7 13.0 1.0
CG A:GLU1007 4.2 11.0 1.0
N A:SER1004 4.5 10.3 1.0
CD2 A:LEU1003 4.8 10.2 1.0
CA A:LEU1003 4.8 10.4 1.0
O A:HOH2260 4.9 21.9 0.5
O A:GLY1002 4.9 14.0 1.0
OG A:SER1004 5.0 12.6 1.0
CB A:SER1004 5.0 10.9 1.0

Cadmium binding site 4 out of 12 in 1gkl

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Cadmium binding site 4 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3093

b:17.4
occ:1.00
O A:HOH2337 2.2 25.2 1.0
NE2 A:HIS947 2.2 9.9 1.0
NE2 A:HIS1080 2.2 20.4 1.0
O A:HOH2219 2.3 15.8 1.0
O A:HOH2215 2.4 15.0 0.5
O A:HOH2326 2.4 28.0 1.0
CE1 A:HIS1080 3.2 21.8 1.0
CE1 A:HIS947 3.2 10.6 1.0
CD2 A:HIS947 3.2 8.8 1.0
CD2 A:HIS1080 3.3 18.5 1.0
O A:HOH2217 3.7 11.6 0.5
O A:HOH2085 4.0 42.1 1.0
ND1 A:HIS1080 4.3 21.0 1.0
ND1 A:HIS947 4.3 11.5 1.0
CG A:HIS1080 4.4 18.0 1.0
CG A:HIS947 4.4 9.3 1.0
O A:LEU1078 4.4 15.6 1.0
O A:HOH2216 4.5 29.6 1.0
O A:ALA943 4.6 13.9 1.0
O A:HOH2218 4.8 38.7 1.0
CD2 A:TYR932 4.9 10.1 1.0
CB A:MET946 5.0 8.4 1.0

Cadmium binding site 5 out of 12 in 1gkl

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Cadmium binding site 5 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3094

b:27.2
occ:0.30
ND1 A:HIS1081 1.5 21.2 1.0
O A:HOH2341 2.3 22.2 1.0
CE1 A:HIS1081 2.4 19.0 1.0
CG A:HIS1081 2.6 18.0 1.0
O A:HOH2346 2.6 25.4 1.0
CB A:HIS1081 3.2 16.8 1.0
O A:HOH2351 3.4 26.0 1.0
NE2 A:HIS1081 3.5 19.8 1.0
CD A:CD3095 3.5 16.0 0.4
CD2 A:HIS1081 3.6 19.1 1.0
CA A:HIS1081 3.8 15.9 1.0
O A:HOH2370 4.3 42.9 1.0
NE2 A:HIS1083 4.7 12.1 1.0
N A:HIS1082 4.7 13.8 1.0
C A:HIS1081 4.8 15.1 1.0
N A:HIS1081 4.9 16.0 1.0
O A:HOH2367 4.9 23.7 0.5

Cadmium binding site 6 out of 12 in 1gkl

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Cadmium binding site 6 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3095

b:16.0
occ:0.40
CE1 A:HIS1081 2.3 19.0 1.0
O A:ACT3089 2.3 24.0 1.0
O A:HOH2370 2.5 42.9 1.0
OXT A:ACT3089 2.5 24.2 1.0
C A:ACT3089 2.7 24.0 1.0
NE2 A:HIS1081 3.2 19.8 1.0
ND1 A:HIS1081 3.3 21.2 1.0
CD A:CD3094 3.5 27.2 0.3
CH3 A:ACT3089 4.2 23.9 1.0
CD2 A:HIS1081 4.4 19.1 1.0
O A:HOH2368 4.4 22.1 1.0
CG A:HIS1081 4.4 18.0 1.0
O A:HOH2367 4.5 23.7 0.5
O A:HOH2369 4.6 32.2 1.0
O A:HOH2351 4.7 26.0 1.0
O A:HOH2341 4.8 22.2 1.0
CD A:LYS855 4.8 18.1 1.0

Cadmium binding site 7 out of 12 in 1gkl

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Cadmium binding site 7 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3090

b:8.9
occ:1.00
O B:HOH2155 2.3 10.0 1.0
ND1 B:HIS886 2.4 8.5 1.0
SG B:CYS823 2.5 8.5 1.0
SD B:MET889 2.8 9.1 1.0
CE1 B:HIS886 3.0 7.2 1.0
CG B:HIS886 3.4 7.7 1.0
CB B:CYS823 3.5 9.2 1.0
CA B:HIS886 3.8 7.0 1.0
CE B:MET889 3.8 9.2 1.0
CG B:MET889 3.9 8.9 1.0
CB B:HIS886 3.9 7.6 1.0
CB B:MET889 4.0 8.5 1.0
NE2 B:HIS886 4.2 8.4 1.0
CA B:CYS823 4.3 8.9 1.0
CD2 B:HIS886 4.4 7.4 1.0
CD B:PRO824 4.5 9.3 1.0
N B:HIS886 4.6 6.8 1.0
O B:HIS886 4.6 7.8 1.0
O B:ASP885 4.7 6.8 1.0
C B:HIS886 4.7 7.1 1.0
C B:ASP885 5.0 6.9 1.0

Cadmium binding site 8 out of 12 in 1gkl

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Cadmium binding site 8 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3091

b:9.4
occ:1.00
OE2 B:GLU894 2.3 12.4 1.0
NE2 B:HIS1085 2.3 9.8 1.0
OE1 B:GLU1079 2.3 11.4 1.0
ND1 B:HIS1083 2.3 10.3 1.0
ND1 B:HIS1076 2.4 8.9 1.0
OE2 B:GLU1079 2.5 12.1 1.0
CD B:GLU1079 2.7 11.7 1.0
CD B:GLU894 3.1 11.7 1.0
CE1 B:HIS1076 3.2 8.8 1.0
OE1 B:GLU894 3.2 13.8 1.0
CE1 B:HIS1083 3.3 11.3 1.0
CD2 B:HIS1085 3.3 10.6 1.0
CE1 B:HIS1085 3.3 10.9 1.0
CG B:HIS1083 3.4 10.5 1.0
CG B:HIS1076 3.5 8.9 1.0
CB B:HIS1083 3.7 10.7 1.0
CB B:HIS1076 3.9 8.8 1.0
O B:HOH2168 4.1 13.8 1.0
CG B:GLU1079 4.2 11.9 1.0
NE2 B:HIS1076 4.3 9.2 1.0
CA B:HIS1076 4.4 9.1 1.0
ND1 B:HIS1085 4.4 12.2 1.0
NE2 B:HIS1083 4.4 12.9 1.0
CG B:HIS1085 4.4 11.8 1.0
O B:HOH2166 4.5 11.6 0.5
CD2 B:HIS1076 4.5 9.6 1.0
CD2 B:HIS1083 4.5 11.9 1.0
CG B:GLU894 4.5 10.0 1.0
O B:HOH2343 4.7 19.8 1.0
O B:HOH2342 4.9 11.2 0.5
O B:PHE1075 4.9 10.0 1.0
CB B:GLU1079 5.0 13.1 1.0

Cadmium binding site 9 out of 12 in 1gkl

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Cadmium binding site 9 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3092

b:12.1
occ:1.00
OE2 B:GLU1007 2.3 14.5 1.0
OE1 B:GLU1007 2.4 12.1 1.0
CD B:GLU1007 2.7 12.5 1.0
CG B:GLU1007 4.2 10.6 1.0
O B:HOH2119 4.6 24.3 1.0
N B:SER1004 4.6 11.1 1.0
O B:HOH2087 4.7 22.2 0.5
CD2 B:LEU1003 4.7 10.7 1.0
O B:HOH2226 4.8 19.1 1.0
O B:HOH2264 4.8 36.0 1.0
CA B:LEU1003 4.9 11.1 1.0

Cadmium binding site 10 out of 12 in 1gkl

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Cadmium binding site 10 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3093

b:18.0
occ:1.00
O B:HOH2348 2.2 21.9 1.0
O B:HOH2335 2.2 32.5 1.0
NE2 B:HIS947 2.2 11.4 1.0
NE2 B:HIS1080 2.2 21.7 1.0
O B:HOH2223 2.3 16.6 1.0
O B:HOH2222 2.5 16.4 0.5
CE1 B:HIS1080 3.1 22.9 1.0
CE1 B:HIS947 3.2 11.5 1.0
CD2 B:HIS947 3.2 9.5 1.0
CD2 B:HIS1080 3.3 20.8 1.0
O B:HOH2225 3.7 17.6 0.5
O B:HOH2088 4.1 34.8 1.0
ND1 B:HIS1080 4.3 22.1 1.0
ND1 B:HIS947 4.3 12.8 1.0
O B:HOH2224 4.4 29.1 1.0
CG B:HIS1080 4.4 19.6 1.0
CG B:HIS947 4.4 10.1 1.0
O B:LEU1078 4.4 16.6 1.0
O B:ALA943 4.5 14.8 1.0
CD2 B:TYR932 4.9 11.3 1.0

Cadmium binding site 11 out of 12 in 1gkl

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Cadmium binding site 11 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3094

b:30.4
occ:0.30
ND1 B:HIS1081 1.7 21.5 1.0
O B:HOH2354 2.0 23.9 1.0
O B:HOH2353 2.4 33.9 1.0
O B:HOH2355 2.5 26.9 1.0
CE1 B:HIS1081 2.6 19.7 1.0
CG B:HIS1081 2.8 18.5 1.0
CB B:HIS1081 3.4 17.4 1.0
O B:HOH2361 3.5 27.9 1.0
CD B:CD3095 3.6 17.4 0.4
NE2 B:HIS1081 3.7 20.1 1.0
CD2 B:HIS1081 3.9 19.5 1.0
CA B:HIS1081 3.9 16.6 1.0
N B:HIS1082 4.7 14.6 1.0
C B:HIS1081 4.9 15.6 1.0
N B:HIS1081 4.9 16.9 1.0
NE2 B:HIS1083 5.0 12.9 1.0

Cadmium binding site 12 out of 12 in 1gkl

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Cadmium binding site 12 out of 12 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3095

b:17.4
occ:0.40
O B:HOH2381 2.1 36.0 1.0
CE1 B:HIS1081 2.3 19.7 1.0
O B:ACT3089 2.3 28.2 1.0
O B:HOH2353 2.3 33.9 1.0
OXT B:ACT3089 2.4 28.3 1.0
C B:ACT3089 2.7 28.1 1.0
NE2 B:HIS1081 3.2 20.1 1.0
ND1 B:HIS1081 3.3 21.5 1.0
CD B:CD3094 3.6 30.4 0.3
CH3 B:ACT3089 4.2 27.9 1.0
O B:HOH2380 4.3 35.3 1.0
CD2 B:HIS1081 4.3 19.5 1.0
CG B:HIS1081 4.4 18.5 1.0
O B:HOH2361 4.6 27.9 1.0
CD B:LYS855 4.6 19.5 1.0
O B:HOH2112 4.7 16.8 0.5
CE B:LYS855 4.7 23.5 1.0
O B:HOH2354 4.8 23.9 1.0

Reference:

J.A.Prates, N.Tarbouriech, S.J.Charnock, C.M.Fontes, L.M.Ferreira, G.J.Davies. The Structure of the Feruloyl Esterase Module of Xylanase 10B From Clostridium Thermocellum Provides Insights Into Substrate Recognition. Structure V. 9 1183 2001.
ISSN: ISSN 0969-2126
PubMed: 11738044
DOI: 10.1016/S0969-2126(01)00684-0
Page generated: Wed Oct 28 09:53:17 2020
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