Atomistry » Cadmium » PDB 1vqp-1yjw » 1wb4
Atomistry »
  Cadmium »
    PDB 1vqp-1yjw »
      1wb4 »

Cadmium in PDB 1wb4: S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate

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

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

Protein crystallography data

The structure of S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate, PDB code: 1wb4 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) 79.06 / 1.4
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.066, 108.405, 113.180, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 13.4

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cadmium atom in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate (pdb code 1wb4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate, PDB code: 1wb4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 1 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:10.9
occ:1.00
 ND1 A:HIS886 2.4 11.3 1.0
O A:HOH3157 2.4 11.4 1.0
SG A:CYS823 2.5 10.8 1.0
SD A:MET889 2.8 11.3 1.0
CE1 A:HIS886 3.1 10.2 1.0
CG A:HIS886 3.4 8.5 1.0
CB A:CYS823 3.6 11.5 1.0
CA A:HIS886 3.8 7.9 1.0
CE A:MET889 3.8 13.8 1.0
CG A:MET889 3.8 11.1 1.0
CB A:HIS886 3.9 9.0 1.0
CB A:MET889 4.0 9.7 1.0
NE2 A:HIS886 4.2 9.6 1.0
CA A:CYS823 4.3 10.7 1.0
CD2 A:HIS886 4.4 8.7 1.0
CD A:PRO824 4.4 11.0 1.0
N A:HIS886 4.6 8.6 1.0
O A:HIS886 4.6 9.7 1.0
O A:ASP885 4.7 8.9 1.0
C A:HIS886 4.7 9.5 1.0
OD1 A:ASN890 4.9 13.6 0.5
C A:ASP885 4.9 8.2 1.0
N A:PRO824 5.0 10.4 1.0

Cadmium binding site 2 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 2 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:11.5
occ:1.00
 OE1 A:GLU1079 2.3 13.0 1.0
NE2 A:HIS1085 2.3 12.0 1.0
OE2 A:GLU894 2.3 13.3 1.0
ND1 A:HIS1076 2.3 12.0 1.0
ND1 A:HIS1083 2.4 12.9 1.0
OE2 A:GLU1079 2.5 13.8 1.0
CD A:GLU1079 2.7 11.5 1.0
CE1 A:HIS1076 3.1 11.4 1.0
CD A:GLU894 3.2 13.1 1.0
CD2 A:HIS1085 3.3 13.1 1.0
OE1 A:GLU894 3.3 15.3 1.0
CE1 A:HIS1083 3.3 14.0 1.0
CE1 A:HIS1085 3.4 13.4 1.0
CG A:HIS1083 3.4 12.6 1.0
CG A:HIS1076 3.4 9.8 1.0
CB A:HIS1083 3.7 12.4 1.0
CB A:HIS1076 3.9 10.4 1.0
O A:HOH3165 4.1 15.2 1.0
CG A:GLU1079 4.2 12.8 1.0
NE2 A:HIS1076 4.3 12.1 1.0
CA A:HIS1076 4.3 10.6 1.0
O A:HOH3163 4.4 17.9 1.0
CG A:HIS1085 4.4 14.1 1.0
ND1 A:HIS1085 4.5 14.2 1.0
NE2 A:HIS1083 4.5 15.4 1.0
CD2 A:HIS1076 4.5 11.4 1.0
CD2 A:HIS1083 4.5 14.3 1.0
CG A:GLU894 4.5 11.7 1.0
O A:HOH3333 4.7 21.0 1.0
O A:HOH3336 4.9 19.2 1.0
O A:PHE1075 5.0 12.5 1.0

Cadmium binding site 3 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 3 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:13.1
occ:0.70
 O A:HOH3259 2.3 13.2 0.5
OE2 A:GLU1007 2.4 19.6 1.0
OE1 A:GLU1007 2.4 15.3 1.0
CD A:GLU1007 2.7 16.1 1.0
CG A:GLU1007 4.2 13.6 1.0
N A:SER1004 4.5 12.5 1.0
CD2 A:LEU1003 4.7 15.2 1.0
CA A:LEU1003 4.8 12.3 1.0
O A:HOH3258 4.8 28.2 0.5
O A:GLY1002 4.9 17.8 1.0
OG A:SER1004 5.0 16.1 1.0
CB A:SER1004 5.0 14.5 1.0

Cadmium binding site 4 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 4 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:17.3
occ:0.80
 NE2 A:HIS1080 2.2 21.1 1.0
NE2 A:HIS947 2.2 13.0 1.0
O A:HOH3341 2.3 28.8 1.0
O A:HOH3331 2.4 24.6 1.0
O A:HOH3218 2.4 15.1 1.0
CE1 A:HIS1080 3.1 25.6 1.0
CE1 A:HIS947 3.2 13.3 1.0
CD2 A:HIS947 3.2 11.5 1.0
CD2 A:HIS1080 3.3 19.3 1.0
O A:HOH3216 3.3 18.0 1.0
O A:HOH3104 4.2 48.2 1.0
ND1 A:HIS1080 4.3 22.8 1.0
CG A:HIS1080 4.4 19.5 1.0
ND1 A:HIS947 4.4 13.6 1.0
CG A:HIS947 4.4 11.0 1.0
O A:LEU1078 4.4 17.7 1.0
O A:HOH3215 4.4 30.2 1.0
O A:ALA943 4.5 18.4 1.0
CB A:MET946 4.8 10.9 1.0

Cadmium binding site 5 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 5 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:27.0
occ:0.30
 ND1 A:HIS1081 1.4 27.3 1.0
O A:HOH3347 2.0 22.1 1.0
CE1 A:HIS1081 2.4 23.2 1.0
CG A:HIS1081 2.5 21.6 1.0
O A:HOH3353 2.8 30.5 1.0
CB A:HIS1081 3.1 19.3 1.0
O A:HOH3356 3.1 28.8 1.0
NE2 A:HIS1081 3.4 25.4 1.0
CD2 A:HIS1081 3.5 22.6 1.0
CD A:CD2095 3.5 19.4 0.4
O A:HOH3369 3.6 48.3 1.0
CA A:HIS1081 3.8 18.1 1.0
NE2 A:HIS1083 4.5 15.4 1.0
O A:HOH3368 4.7 26.9 0.5
N A:HIS1082 4.7 15.7 1.0
N A:HIS1081 4.8 17.5 1.0
C A:HIS1081 4.9 17.7 1.0

Cadmium binding site 6 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 6 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:19.4
occ:0.40
 CE1 A:HIS1081 2.4 23.2 1.0
O A:ACY2089 2.4 29.9 1.0
OXT A:ACY2089 2.5 29.8 1.0
O A:HOH3369 2.6 48.3 1.0
C A:ACY2089 2.8 29.3 1.0
NE2 A:HIS1081 3.2 25.4 1.0
ND1 A:HIS1081 3.4 27.3 1.0
CD A:CD2094 3.5 27.0 0.3
CH3 A:ACY2089 4.3 29.1 1.0
CD2 A:HIS1081 4.3 22.6 1.0
O A:HOH3368 4.4 26.9 0.5
O A:HOH3347 4.4 22.1 1.0
CG A:HIS1081 4.4 21.6 1.0
O A:HOH3370 4.5 25.2 1.0
O A:HOH3371 4.6 37.0 1.0
O A:HOH3356 4.6 28.8 1.0
CD A:LYS855 4.8 21.3 1.0

Cadmium binding site 7 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 7 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:25.2
occ:0.15
 O A:HOH3335 2.3 34.2 1.0
O A:HIS1076 2.4 14.9 1.0
O A:HOH3336 2.4 19.2 1.0
O A:HOH3332 2.5 27.8 1.0
O A:HOH3326 2.6 32.5 1.0
C A:HIS1076 3.5 11.3 1.0
CA A:GLU1077 3.9 13.4 1.0
O A:HOH3362 3.9 31.3 1.0
N A:LEU1078 3.9 16.4 1.0
O A:HOH3327 3.9 18.4 0.5
OE2 A:GLU1077 4.0 15.3 1.0
N A:GLU1077 4.1 12.1 1.0
O A:HOH3348 4.1 27.0 1.0
OE1 A:GLU1077 4.2 17.8 1.0
CD A:GLU1077 4.2 16.2 1.0
CG A:GLU1079 4.2 12.8 1.0
OE2 A:GLU1079 4.3 13.8 1.0
C A:GLU1077 4.4 15.2 1.0
N A:GLU1079 4.4 16.1 1.0
CA A:HIS1076 4.6 10.6 1.0
CB A:HIS1076 4.6 10.4 1.0
CD A:GLU1079 4.7 11.5 1.0
O A:HOH3148 4.8 46.6 1.0
CA A:LEU1078 4.9 17.0 1.0

Cadmium binding site 8 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 8 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:11.2
occ:0.15
 O A:HOH3203 2.2 11.5 1.0
O A:GLU926 2.2 10.8 1.0
O A:HOH3193 2.3 15.9 1.0
O A:TYR929 2.4 11.3 1.0
O A:HOH3197 2.4 16.6 1.0
O A:HOH3202 2.5 18.5 1.0
C A:GLU926 3.4 9.9 1.0
C A:TYR929 3.4 9.9 1.0
CA A:SER930 3.9 9.7 1.0
N A:SER930 4.1 9.9 1.0
C A:SER927 4.1 12.1 1.0
O A:ALA933 4.1 14.0 1.0
CA A:SER927 4.2 10.9 1.0
N A:THR931 4.2 10.0 1.0
O A:SER927 4.2 13.3 1.0
N A:SER927 4.2 10.9 1.0
CA A:GLU926 4.3 9.7 1.0
N A:TYR929 4.3 9.7 1.0
O A:HOH3196 4.3 20.3 1.0
CA A:TYR929 4.5 9.4 1.0
O A:HOH3199 4.5 20.6 1.0
C A:SER930 4.6 10.2 1.0
N A:LYS928 4.7 10.1 1.0
OG1 A:THR931 4.7 9.9 1.0
CB A:GLU926 4.8 9.8 1.0
OG A:SER930 4.8 10.3 0.5
C A:LYS928 4.8 10.9 1.0

Cadmium binding site 9 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 9 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:28.3
occ:0.15
 O B:HOH3096 2.1 36.1 1.0
O A:HOH3229 2.3 36.3 1.0
O A:ASN985 2.3 17.7 1.0
O B:HOH3234 2.4 20.0 1.0
C A:ASN985 3.5 14.6 1.0
O B:HOH3230 4.0 37.7 1.0
O A:HOH3230 4.1 25.4 1.0
O A:HOH3227 4.3 36.2 1.0
N A:SER986 4.4 14.4 1.0
CA A:ASN985 4.4 14.7 1.0
O B:HOH3233 4.4 39.0 1.0
O B:HOH3231 4.4 15.9 1.0
CA A:SER986 4.5 13.6 1.0
O B:HOH3229 4.7 16.0 1.0
CB A:ASN985 4.7 13.7 1.0
O B:ASN985 4.8 18.4 1.0

Cadmium binding site 10 out of 18 in 1wb4

Go back to Cadmium Binding Sites List in 1wb4
Cadmium binding site 10 out of 18 in the S954A Mutant of the Feruloyl Esterase Module From Clostridium Thermocellum Complexed with Sinapinate


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

b:18.3
occ:0.15
 O B:HOH3209 2.3 24.2 1.0
O B:HOH3376 2.3 21.1 1.0
O B:HOH3208 4.1 29.5 1.0
CA B:SER935 4.2 13.0 1.0
O B:HOH3203 4.3 18.0 1.0
N B:THR936 4.4 11.7 1.0
O3 B:GOL2088 4.4 13.9 1.0
OG1 B:THR936 4.5 17.4 1.0
O B:GLU934 4.6 17.4 1.0
CB B:SER935 4.7 14.3 1.0
C B:SER935 4.8 12.2 1.0
C3 B:GOL2088 4.8 13.6 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: Fri Jul 19 14:25:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy