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Cadmium in PDB 1wb5: S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate

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

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

Protein crystallography data

The structure of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate, PDB code: 1wb5 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 (°) 64.933, 108.631, 112.969, 90.00, 90.00, 90.00
R / Rfree (%) 11.8 / 13.9

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Cadmium atom in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate (pdb code 1wb5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 17 binding sites of Cadmium where determined in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate, PDB code: 1wb5:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 17 in 1wb5

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Cadmium binding site 1 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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 Syringate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2090

b:10.4
occ:1.00
 ND1 A:HIS886 2.3 9.9 1.0
O A:HOH3131 2.4 10.8 1.0
SG A:CYS823 2.5 10.4 1.0
SD A:MET889 2.8 10.6 1.0
CE1 A:HIS886 3.0 9.4 1.0
CG A:HIS886 3.5 8.1 1.0
CB A:CYS823 3.6 10.3 1.0
CA A:HIS886 3.8 7.7 1.0
CE A:MET889 3.8 12.6 1.0
CG A:MET889 3.8 10.3 1.0
CB A:HIS886 3.9 8.8 1.0
CB A:MET889 4.0 9.7 1.0
NE2 A:HIS886 4.2 9.9 1.0
CA A:CYS823 4.3 10.2 1.0
CD A:PRO824 4.4 11.1 1.0
CD2 A:HIS886 4.4 8.5 1.0
N A:HIS886 4.6 7.8 1.0
O A:HIS886 4.6 9.1 1.0
O A:ASP885 4.6 8.4 1.0
C A:HIS886 4.7 8.7 1.0
OD1 A:ASN890 4.9 12.3 0.5
C A:ASP885 4.9 7.8 1.0

Cadmium binding site 2 out of 17 in 1wb5

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Cadmium binding site 2 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:11.0
occ:1.00
 OE2 A:GLU894 2.3 12.7 1.0
NE2 A:HIS1085 2.3 10.5 1.0
OE1 A:GLU1079 2.3 12.8 1.0
ND1 A:HIS1083 2.4 11.5 1.0
ND1 A:HIS1076 2.4 11.9 1.0
OE2 A:GLU1079 2.5 13.1 1.0
CD A:GLU1079 2.8 11.0 1.0
CD A:GLU894 3.1 11.9 1.0
CE1 A:HIS1076 3.2 10.6 1.0
OE1 A:GLU894 3.3 13.6 1.0
CE1 A:HIS1083 3.3 13.3 1.0
CD2 A:HIS1085 3.3 11.9 1.0
CE1 A:HIS1085 3.3 12.1 1.0
CG A:HIS1083 3.4 11.3 1.0
CG A:HIS1076 3.5 9.8 1.0
CB A:HIS1083 3.7 11.4 1.0
CB A:HIS1076 3.9 10.1 1.0
O A:HOH3143 4.1 14.3 1.0
CG A:GLU1079 4.3 12.2 1.0
CA A:HIS1076 4.3 10.3 1.0
NE2 A:HIS1076 4.4 11.0 1.0
O A:HOH3142 4.4 17.7 1.0
ND1 A:HIS1085 4.4 13.0 1.0
CG A:HIS1085 4.4 13.1 1.0
NE2 A:HIS1083 4.4 14.3 1.0
CD2 A:HIS1083 4.5 12.9 1.0
CD2 A:HIS1076 4.5 10.9 1.0
CG A:GLU894 4.6 11.2 1.0
O A:HOH3289 4.7 19.0 1.0
O A:HOH3290 4.9 18.2 1.0
O A:PHE1075 4.9 11.2 1.0

Cadmium binding site 3 out of 17 in 1wb5

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Cadmium binding site 3 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:14.9
occ:0.90
 OE2 A:GLU1007 2.3 18.0 1.0
OE1 A:GLU1007 2.4 13.9 1.0
CD A:GLU1007 2.7 14.8 1.0
CG A:GLU1007 4.2 12.8 1.0
N A:SER1004 4.5 11.6 1.0
CD2 A:LEU1003 4.7 13.4 1.0
CA A:LEU1003 4.8 12.1 1.0
O A:HOH3231 4.8 33.0 1.0
O A:GLY1002 4.9 16.1 1.0
OG A:SER1004 5.0 14.9 1.0
CB A:SER1004 5.0 13.1 1.0

Cadmium binding site 4 out of 17 in 1wb5

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Cadmium binding site 4 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:18.0
occ:1.00
 NE2 A:HIS1080 2.2 20.2 1.0
NE2 A:HIS947 2.3 11.5 1.0
O A:HOH3182 2.3 35.1 1.0
O A:HOH3286 2.4 20.1 1.0
O A:HOH3185 2.4 13.7 1.0
CE1 A:HIS1080 3.1 23.8 1.0
CD2 A:HIS1080 3.2 18.9 1.0
O A:HOH3183 3.2 17.1 1.0
CE1 A:HIS947 3.2 11.9 1.0
CD2 A:HIS947 3.2 10.6 1.0
ND1 A:HIS1080 4.2 21.8 1.0
CG A:HIS1080 4.3 18.0 1.0
O A:LEU1078 4.3 16.7 1.0
O A:HOH3184 4.3 29.7 1.0
ND1 A:HIS947 4.4 12.7 1.0
CG A:HIS947 4.4 10.3 1.0
O A:ALA943 4.4 16.5 1.0
CB A:MET946 4.8 10.1 1.0

Cadmium binding site 5 out of 17 in 1wb5

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Cadmium binding site 5 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:35.0
occ:0.30
 ND1 A:HIS1081 1.5 23.9 1.0
O A:HOH3298 2.0 26.1 1.0
CE1 A:HIS1081 2.4 20.6 1.0
O A:HOH3300 2.6 26.4 1.0
CG A:HIS1081 2.6 19.8 1.0
CB A:HIS1081 3.2 18.5 1.0
O A:HOH3301 3.4 27.7 1.0
NE2 A:HIS1081 3.5 23.1 1.0
CD A:CD2095 3.6 16.5 0.4
CD2 A:HIS1081 3.6 20.0 1.0
CA A:HIS1081 3.8 17.3 1.0
N A:HIS1082 4.7 15.4 1.0
NE2 A:HIS1083 4.8 14.3 1.0
C A:HIS1081 4.9 16.8 1.0
O A:HOH3317 4.9 33.2 1.0
N A:HIS1081 4.9 17.2 1.0

Cadmium binding site 6 out of 17 in 1wb5

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Cadmium binding site 6 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:16.5
occ:0.40
 CE1 A:HIS1081 2.3 20.6 1.0
O A:ACT2089 2.4 25.7 1.0
OXT A:ACT2089 2.5 25.6 1.0
C A:ACT2089 2.8 25.5 1.0
NE2 A:HIS1081 3.1 23.1 1.0
ND1 A:HIS1081 3.3 23.9 1.0
CD A:CD2094 3.6 35.0 0.3
O A:HOH3317 4.1 33.2 1.0
CH3 A:ACT2089 4.3 25.5 1.0
CD2 A:HIS1081 4.3 20.0 1.0
CG A:HIS1081 4.4 19.8 1.0
O A:HOH3319 4.5 25.0 1.0
O A:HOH3298 4.6 26.1 1.0
O A:HOH3318 4.6 38.2 1.0
O A:HOH3301 4.7 27.7 1.0
CD A:LYS855 4.8 20.1 1.0

Cadmium binding site 7 out of 17 in 1wb5

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Cadmium binding site 7 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:23.6
occ:0.20
 O A:HOH3132 2.3 33.1 1.0
O A:HIS1076 2.4 13.7 1.0
O A:HOH3290 2.4 18.2 1.0
O A:HOH3283 2.4 23.6 1.0
O A:HOH3288 2.4 28.6 1.0
O A:HOH3284 2.6 28.6 1.0
C A:HIS1076 3.5 11.0 1.0
O A:HOH3311 3.9 25.1 1.0
CA A:GLU1077 3.9 12.8 1.0
N A:LEU1078 4.0 15.4 1.0
OE2 A:GLU1077 4.1 14.2 1.0
O A:HOH3299 4.1 24.3 1.0
N A:GLU1077 4.1 11.9 1.0
OE1 A:GLU1077 4.2 16.5 1.0
CG A:GLU1079 4.2 12.2 1.0
CD A:GLU1077 4.3 15.2 1.0
OE2 A:GLU1079 4.3 13.1 1.0
C A:GLU1077 4.4 14.3 1.0
N A:GLU1079 4.5 14.9 1.0
CA A:HIS1076 4.6 10.3 1.0
CB A:HIS1076 4.6 10.1 1.0
CD A:GLU1079 4.7 11.0 1.0
CA A:LEU1078 4.9 15.8 1.0

Cadmium binding site 8 out of 17 in 1wb5

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Cadmium binding site 8 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:18.0
occ:0.30
 O A:HOH3173 2.2 10.7 1.0
O A:GLU926 2.3 10.0 1.0
O A:HOH3162 2.3 14.0 1.0
O A:HOH3167 2.4 16.1 1.0
O A:TYR929 2.4 10.6 1.0
O A:HOH3172 2.4 16.3 1.0
C A:GLU926 3.4 9.5 1.0
C A:TYR929 3.5 9.4 1.0
CA A:SER930 4.0 9.5 1.0
O A:ALA933 4.1 12.9 1.0
N A:SER930 4.1 9.4 1.0
C A:SER927 4.1 11.1 1.0
N A:THR931 4.2 9.5 1.0
CA A:SER927 4.2 10.2 1.0
O A:SER927 4.2 12.2 1.0
N A:SER927 4.2 10.0 1.0
CA A:GLU926 4.3 9.2 1.0
N A:TYR929 4.3 9.6 1.0
CA A:TYR929 4.5 9.2 1.0
O A:HOH3168 4.5 20.4 1.0
C A:SER930 4.7 9.3 1.0
N A:LYS928 4.7 10.0 1.0
OG1 A:THR931 4.7 9.1 1.0
OG A:SER930 4.8 10.5 0.5
CB A:GLU926 4.9 8.8 1.0
C A:LYS928 4.9 9.9 1.0

Cadmium binding site 9 out of 17 in 1wb5

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Cadmium binding site 9 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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

b:19.2
occ:0.20
 O B:HOH3168 2.3 21.8 1.0
O B:HOH3337 2.3 19.3 1.0
O B:HOH3183 4.0 29.9 1.0
CA B:SER935 4.2 12.8 1.0
O B:HOH3181 4.3 16.9 1.0
N B:THR936 4.3 11.7 1.0
O B:HOH3169 4.4 18.4 1.0
OG1 B:THR936 4.4 15.5 1.0
O3 B:GOL2088 4.4 12.9 1.0
O B:GLU934 4.7 16.8 1.0
CB B:SER935 4.7 13.8 1.0
C B:SER935 4.7 11.5 1.0
C3 B:GOL2088 4.8 12.1 1.0
O B:HOH3167 4.9 29.4 1.0

Cadmium binding site 10 out of 17 in 1wb5

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Cadmium binding site 10 out of 17 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Syringate


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 Syringate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2090

b:10.0
occ:1.00
 ND1 B:HIS886 2.3 8.9 1.0
O B:HOH3134 2.3 10.6 1.0
SG B:CYS823 2.5 9.5 1.0
SD B:MET889 2.8 10.2 1.0
CE1 B:HIS886 3.1 8.9 1.0
CG B:HIS886 3.4 8.1 1.0
CB B:CYS823 3.6 9.9 1.0
CA B:HIS886 3.8 8.0 1.0
CE B:MET889 3.8 10.2 1.0
CG B:MET889 3.8 9.7 1.0
CB B:HIS886 3.9 8.4 1.0
CB B:MET889 4.0 9.6 1.0
NE2 B:HIS886 4.2 9.7 1.0
CA B:CYS823 4.3 9.6 1.0
CD2 B:HIS886 4.4 8.2 1.0
CD B:PRO824 4.6 10.0 1.0
N B:HIS886 4.6 8.4 1.0
O B:HIS886 4.6 9.5 1.0
O B:ASP885 4.7 8.3 1.0
C B:HIS886 4.7 8.4 1.0
O B:HOH3038 4.8 42.5 1.0
ND2 B:ASN890 4.9 8.4 0.5
C B:ASP885 4.9 8.1 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: Sat Dec 12 08:15:21 2020

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