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Cadmium in PDB 1wb6: S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate

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

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

Protein crystallography data

The structure of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate, PDB code: 1wb6 was solved by N.Tarbouriech, J.A.Prates, C.Fontes, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.994, 108.462, 113.026, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 14

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Cadmium atom in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate (pdb code 1wb6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 20 binding sites of Cadmium where determined in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate, PDB code: 1wb6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 20 in 1wb6

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Cadmium binding site 1 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2091

b:11.7
occ:1.00
 O A:HOH3147 2.3 11.8 1.0
SG A:CYS823 2.5 12.0 1.0
ND1 A:HIS886 2.5 12.4 1.0
SD A:MET889 2.8 12.0 1.0
CE1 A:HIS886 3.3 12.0 1.0
CG A:HIS886 3.4 9.5 1.0
CB A:CYS823 3.5 11.5 1.0
CA A:HIS886 3.7 8.6 1.0
CG A:MET889 3.8 10.8 1.0
CE A:MET889 3.8 13.6 1.0
CB A:HIS886 3.9 9.4 1.0
CB A:MET889 3.9 9.6 1.0
NE2 A:HIS886 4.2 11.2 1.0
CD2 A:HIS886 4.3 10.1 1.0
CA A:CYS823 4.3 11.8 1.0
CD A:PRO824 4.4 12.6 1.0
N A:HIS886 4.5 9.6 1.0
O A:HIS886 4.6 10.0 1.0
O A:ASP885 4.7 9.8 1.0
C A:HIS886 4.7 9.8 1.0
C A:ASP885 4.9 8.9 1.0
OD1 A:ASN890 4.9 12.9 0.5
N A:PRO824 5.0 11.9 1.0

Cadmium binding site 2 out of 20 in 1wb6

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Cadmium binding site 2 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2092

b:12.2
occ:1.00
 NE2 A:HIS1085 2.3 12.1 1.0
OE1 A:GLU1079 2.3 13.9 1.0
OE2 A:GLU894 2.3 14.2 1.0
ND1 A:HIS1083 2.3 13.1 1.0
ND1 A:HIS1076 2.4 12.9 1.0
OE2 A:GLU1079 2.4 13.6 1.0
CD A:GLU1079 2.7 12.1 1.0
CD A:GLU894 3.1 13.1 1.0
CE1 A:HIS1076 3.2 12.1 1.0
CE1 A:HIS1085 3.3 13.8 1.0
CE1 A:HIS1083 3.3 16.5 1.0
OE1 A:GLU894 3.3 14.8 1.0
CD2 A:HIS1085 3.3 13.0 1.0
CG A:HIS1083 3.4 13.5 1.0
CG A:HIS1076 3.5 10.6 1.0
CB A:HIS1083 3.7 12.8 1.0
CB A:HIS1076 3.9 10.9 1.0
O A:HOH3157 4.1 16.1 1.0
CG A:GLU1079 4.3 13.6 1.0
CA A:HIS1076 4.3 11.1 1.0
NE2 A:HIS1076 4.4 12.4 1.0
O A:HOH3160 4.4 19.5 1.0
ND1 A:HIS1085 4.4 15.2 1.0
NE2 A:HIS1083 4.4 17.4 1.0
CG A:HIS1085 4.4 14.1 1.0
CD2 A:HIS1076 4.5 11.7 1.0
CD2 A:HIS1083 4.5 15.7 1.0
CG A:GLU894 4.5 12.7 1.0
O A:HOH3303 4.7 21.2 1.0
O A:HOH3304 4.9 20.7 1.0
O A:PHE1075 5.0 12.4 1.0

Cadmium binding site 3 out of 20 in 1wb6

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Cadmium binding site 3 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2093

b:9.5
occ:0.50
 OE2 A:GLU1007 2.4 19.3 1.0
OE1 A:GLU1007 2.4 14.9 1.0
CD A:GLU1007 2.7 14.9 1.0
CG A:GLU1007 4.2 13.2 1.0
O A:HOH3078 4.5 41.6 1.0
N A:SER1004 4.5 12.7 1.0
CD2 A:LEU1003 4.7 15.0 1.0
CA A:LEU1003 4.8 12.9 1.0
O A:GLY1002 4.9 17.6 1.0

Cadmium binding site 4 out of 20 in 1wb6

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Cadmium binding site 4 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2094

b:12.3
occ:0.50
 NE2 A:HIS1080 2.2 20.9 1.0
NE2 A:HIS947 2.3 13.1 1.0
O A:HOH3299 2.5 23.2 1.0
O A:HOH3205 2.5 14.7 1.0
O A:HOH3309 2.5 30.4 1.0
CE1 A:HIS1080 3.1 25.8 1.0
O A:HOH3207 3.2 19.0 1.0
CE1 A:HIS947 3.2 12.8 1.0
CD2 A:HIS947 3.2 13.3 1.0
CD2 A:HIS1080 3.3 19.6 1.0
ND1 A:HIS1080 4.3 23.8 1.0
O A:HOH3206 4.4 31.7 1.0
ND1 A:HIS947 4.4 13.9 1.0
CG A:HIS1080 4.4 20.0 1.0
CG A:HIS947 4.4 11.1 1.0
O A:ALA943 4.4 19.0 1.0
O A:LEU1078 4.4 16.5 1.0
CB A:MET946 4.8 11.3 1.0

Cadmium binding site 5 out of 20 in 1wb6

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Cadmium binding site 5 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2095

b:30.5
occ:0.30
 ND1 A:HIS1081 1.3 28.4 1.0
O A:HOH3315 1.9 21.4 1.0
CE1 A:HIS1081 2.3 25.0 1.0
CG A:HIS1081 2.4 23.0 1.0
O A:HOH3318 2.7 28.7 1.0
CB A:HIS1081 3.0 20.4 1.0
O A:HOH3324 3.1 30.9 1.0
NE2 A:HIS1081 3.4 27.6 1.0
CD2 A:HIS1081 3.5 24.4 1.0
CD A:CD2096 3.6 20.6 0.4
CA A:HIS1081 3.7 19.2 1.0
O A:HOH3316 4.3 45.4 1.0
NE2 A:HIS1083 4.6 17.4 1.0
N A:HIS1082 4.7 15.9 1.0
N A:HIS1081 4.7 18.4 1.0
C A:HIS1081 4.7 18.7 1.0
O A:HOH3341 4.8 41.2 1.0

Cadmium binding site 6 out of 20 in 1wb6

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Cadmium binding site 6 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2096

b:20.6
occ:0.40
 CE1 A:HIS1081 2.3 25.0 1.0
O A:ACT2090 2.4 31.7 1.0
OXT A:ACT2090 2.5 32.5 1.0
C A:ACT2090 2.8 31.4 1.0
NE2 A:HIS1081 3.2 27.6 1.0
ND1 A:HIS1081 3.3 28.4 1.0
CD A:CD2095 3.6 30.5 0.3
CH3 A:ACT2090 4.2 30.4 1.0
O A:HOH3341 4.3 41.2 1.0
CD2 A:HIS1081 4.4 24.4 1.0
CG A:HIS1081 4.5 23.0 1.0
O A:HOH3345 4.5 25.6 1.0
O A:HOH3315 4.5 21.4 1.0
O A:HOH3324 4.5 30.9 1.0
O A:HOH3344 4.6 35.8 1.0
CD A:LYS855 4.8 22.1 1.0

Cadmium binding site 7 out of 20 in 1wb6

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Cadmium binding site 7 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2097

b:17.3
occ:0.30
 O A:HOH3191 2.2 11.9 1.0
O A:GLU926 2.2 10.9 1.0
O A:HOH3182 2.3 14.7 1.0
O A:TYR929 2.4 11.2 1.0
O A:HOH3185 2.4 15.7 1.0
O A:HOH3192 2.5 16.4 1.0
C A:GLU926 3.4 10.9 1.0
C A:TYR929 3.4 10.2 1.0
CA A:SER930 4.0 10.2 1.0
O A:ALA933 4.1 14.1 1.0
N A:SER930 4.1 9.8 1.0
N A:THR931 4.1 10.2 1.0
C A:SER927 4.1 11.3 1.0
CA A:SER927 4.2 12.1 1.0
O A:SER927 4.2 12.2 1.0
N A:SER927 4.2 11.4 1.0
CA A:GLU926 4.3 10.0 1.0
N A:TYR929 4.3 9.5 1.0
CA A:TYR929 4.5 9.3 1.0
O A:HOH3187 4.5 21.9 1.0
C A:SER930 4.7 9.7 1.0
N A:LYS928 4.7 10.7 1.0
OG1 A:THR931 4.7 10.1 1.0
OG A:SER930 4.8 12.1 0.5
CB A:GLU926 4.8 10.5 1.0
C A:LYS928 4.8 10.1 1.0

Cadmium binding site 8 out of 20 in 1wb6

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Cadmium binding site 8 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2098

b:29.3
occ:0.30
 O A:LEU1034 2.3 16.2 1.0
O A:PHE1037 2.3 14.8 1.0
O A:HOH3264 2.4 37.3 1.0
O A:HOH3267 2.5 27.9 1.0
O A:LYS1032 2.5 19.8 1.0
C A:LEU1034 3.4 16.2 1.0
C A:PHE1037 3.5 12.9 1.0
C A:LYS1032 3.7 17.4 1.0
O A:HOH3271 3.8 23.5 1.0
N A:LEU1034 4.1 16.1 1.0
CA A:PRO1035 4.2 16.6 1.0
C A:ALA1033 4.2 18.4 1.0
N A:PRO1035 4.2 16.6 1.0
N A:PHE1037 4.2 12.6 1.0
CA A:PHE1037 4.3 12.4 1.0
CA A:LEU1034 4.3 15.9 1.0
C A:PRO1035 4.4 16.4 1.0
O A:ALA1033 4.5 21.1 1.0
N A:ASP1038 4.5 12.6 1.0
CA A:LYS1032 4.6 16.6 1.0
OD1 A:ASP1038 4.6 19.1 1.0
N A:ALA1033 4.6 17.8 1.0
CB A:PHE1037 4.6 12.5 1.0
CA A:ALA1033 4.6 18.1 1.0
O A:MET1031 4.6 14.2 1.0
O A:PRO1035 4.6 18.0 1.0
CA A:ASP1038 4.8 12.1 1.0
N A:HIS1036 4.9 14.8 1.0

Cadmium binding site 9 out of 20 in 1wb6

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Cadmium binding site 9 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2099

b:28.6
occ:0.20
 O A:HIS1076 2.4 15.4 1.0
O A:HOH3304 2.4 20.7 1.0
O A:HOH3305 2.4 33.3 1.0
O A:HOH3300 2.5 25.1 1.0
O A:HOH3296 2.6 31.4 1.0
C A:HIS1076 3.5 11.3 1.0
CA A:GLU1077 3.9 13.3 1.0
N A:LEU1078 3.9 16.7 1.0
O A:HOH3334 4.0 29.3 1.0
O A:HOH3297 4.0 20.5 0.5
OE2 A:GLU1077 4.1 15.9 1.0
O A:HOH3313 4.1 28.9 1.0
N A:GLU1077 4.1 12.6 1.0
OE1 A:GLU1077 4.2 16.8 1.0
CG A:GLU1079 4.2 13.6 1.0
OE2 A:GLU1079 4.3 13.6 1.0
CD A:GLU1077 4.3 15.4 1.0
C A:GLU1077 4.3 15.4 1.0
N A:GLU1079 4.4 16.2 1.0
CA A:HIS1076 4.6 11.1 1.0
CB A:HIS1076 4.6 10.9 1.0
CD A:GLU1079 4.7 12.1 1.0
CA A:LEU1078 4.9 17.2 1.0

Cadmium binding site 10 out of 20 in 1wb6

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Cadmium binding site 10 out of 20 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Vanillate


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 Vanillate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2100

b:28.0
occ:0.40
 O B:HOH3175 2.2 20.5 1.0
O B:HOH3340 2.3 18.2 1.0
O B:HOH3190 4.1 29.2 1.0
CA B:SER935 4.3 13.2 1.0
O B:HOH3186 4.3 17.1 1.0
N B:THR936 4.4 12.2 1.0
OG1 B:THR936 4.4 16.1 1.0
O3 B:GOL2088 4.4 12.5 1.0
O B:HOH3174 4.4 17.6 1.0
O B:GLU934 4.7 16.4 1.0
CB B:SER935 4.8 13.8 1.0
C3 B:GOL2088 4.8 11.5 1.0
C B:SER935 4.8 11.6 1.0
O B:HOH3176 4.9 31.0 1.0

Reference:

N.Tarbouriech, J.A.Prates, C.Fontes, G.J.Davies. Molecular Determinants of Substrate Specificity in the Feruloyl Esterase Module of Xylanase 10B From Clostridium Thermocellum Acta Crystallogr.,Sect.D V. 61 194 2005.
ISSN: ISSN 0907-4449
PubMed: 15681871
DOI: 10.1107/S0907444904029695
Page generated: Sun Jan 24 09:43:09 2021

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