Atomistry » Cadmium » PDB 1dpe-1gwg » 1gkl
Atomistry »
  Cadmium »
    PDB 1dpe-1gwg »
      1gkl »

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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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;

Cadmium binding site 1 out of 12 in 1gkl

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

Go back to Cadmium Binding Sites List in 1gkl
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

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: Fri Jul 19 13:24:42 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