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

Cadmium in PDB 1gkk: Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum

Enzymatic activity of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum

All present enzymatic activity of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum:
3.2.1.8;

Protein crystallography data

The structure of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum, PDB code: 1gkk 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) 20.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.381, 108.793, 113.877, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 17.3

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 1 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3086

b:11.6
occ:1.00
 ND1 A:HIS886 2.4 9.5 1.0
O A:HOH2161 2.4 12.5 1.0
SG A:CYS823 2.5 11.0 1.0
SE A:MSE889 2.9 17.4 1.0
CE1 A:HIS886 3.0 11.1 1.0
CG A:HIS886 3.5 9.9 1.0
CB A:CYS823 3.6 11.9 1.0
CA A:HIS886 3.8 8.1 1.0
CG A:MSE889 3.9 12.8 1.0
CE A:MSE889 4.0 12.0 1.0
CB A:HIS886 4.0 8.3 1.0
CB A:MSE889 4.0 11.5 1.0
NE2 A:HIS886 4.2 10.8 1.0
CD A:PRO824 4.3 11.9 1.0
CA A:CYS823 4.3 11.7 1.0
CD2 A:HIS886 4.4 9.9 1.0
N A:HIS886 4.6 9.9 1.0
O A:HIS886 4.6 10.2 1.0
C A:HIS886 4.8 9.7 1.0
O A:ASP885 4.8 12.0 1.0
N A:PRO824 4.9 12.2 1.0
C A:CYS823 5.0 12.1 1.0

Cadmium binding site 2 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 2 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3087

b:13.2
occ:1.00
 NE2 A:HIS1085 2.3 16.2 1.0
ND1 A:HIS1076 2.3 10.0 1.0
ND1 A:HIS1083 2.3 13.2 1.0
OE1 A:GLU1079 2.3 16.8 1.0
OE2 A:GLU894 2.4 19.3 1.0
OE2 A:GLU1079 2.6 14.2 1.0
CD A:GLU1079 2.8 15.8 1.0
OE1 A:GLU894 2.8 19.1 1.0
CD A:GLU894 2.9 13.1 1.0
CE1 A:HIS1076 3.0 17.3 1.0
CE1 A:HIS1083 3.2 19.5 1.0
CE1 A:HIS1085 3.2 16.8 1.0
CD2 A:HIS1085 3.3 17.4 1.0
CG A:HIS1083 3.4 15.7 1.0
CG A:HIS1076 3.4 12.0 1.0
CB A:HIS1083 3.7 16.0 1.0
CB A:HIS1076 3.9 13.1 1.0
O A:HOH2172 4.1 27.0 1.0
NE2 A:HIS1076 4.2 13.5 1.0
CG A:GLU1079 4.3 17.1 1.0
ND1 A:HIS1085 4.4 14.9 1.0
NE2 A:HIS1083 4.4 19.8 1.0
CA A:HIS1076 4.4 13.7 1.0
CG A:HIS1085 4.4 16.1 1.0
CD2 A:HIS1076 4.4 13.9 1.0
CG A:GLU894 4.5 12.5 1.0
CD2 A:HIS1083 4.5 18.6 1.0
O A:HOH2339 4.9 21.3 1.0

Cadmium binding site 3 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 3 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3088

b:19.1
occ:1.00
 OE1 A:GLU1007 2.3 16.1 1.0
O A:HOH2267 2.3 23.6 1.0
OE2 A:GLU1007 2.4 21.0 1.0
CD A:GLU1007 2.7 18.2 1.0
CG A:GLU1007 4.2 15.8 1.0
N A:SER1004 4.5 13.6 1.0
CD2 A:LEU1003 4.7 17.8 1.0
CA A:LEU1003 4.8 14.3 1.0
CB A:SER1004 4.9 15.2 1.0
O A:GLY1002 4.9 17.8 1.0
O A:HOH2262 5.0 24.4 1.0
OG A:SER1004 5.0 16.9 1.0

Cadmium binding site 4 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 4 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3089

b:21.0
occ:1.00
 NE2 A:HIS1080 2.0 26.6 1.0
O A:HOH2341 2.1 19.0 1.0
O A:HOH2226 2.1 37.3 1.0
NE2 A:HIS947 2.2 12.0 1.0
O A:HOH2227 2.3 30.6 1.0
O A:HOH2337 2.3 19.2 1.0
CE1 A:HIS1080 3.0 30.5 1.0
CD2 A:HIS1080 3.1 23.9 1.0
CE1 A:HIS947 3.1 22.9 1.0
CD2 A:HIS947 3.3 19.8 1.0
ND1 A:HIS1080 4.1 28.9 1.0
CG A:HIS1080 4.2 24.7 1.0
ND1 A:HIS947 4.3 20.8 1.0
O A:HOH2224 4.3 21.0 1.0
CG A:HIS947 4.4 16.9 1.0
O A:LEU1078 4.6 20.5 1.0
CD2 A:TYR932 4.9 14.8 1.0

Cadmium binding site 5 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 5 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3090

b:22.6
occ:0.30
 ND1 A:HIS1081 1.9 35.5 1.0
O A:HOH2342 2.0 29.0 1.0
CG A:HIS1081 2.8 28.8 1.0
O A:HOH2345 2.9 37.4 1.0
CE1 A:HIS1081 2.9 35.4 1.0
O A:HOH2349 3.1 29.8 1.0
CB A:HIS1081 3.2 24.1 1.0
O A:HOH2344 3.5 20.5 1.0
CA A:HIS1081 3.8 22.2 1.0
CD2 A:HIS1081 4.0 33.3 1.0
NE2 A:HIS1081 4.0 34.8 1.0
NE2 A:HIS1083 4.5 19.8 1.0
O A:HIS1080 4.6 22.1 0.5
N A:HIS1082 4.7 18.6 1.0
N A:HIS1081 4.8 21.9 0.5
C A:HIS1081 4.8 21.2 1.0
N A:HIS1081 4.8 21.8 0.5

Cadmium binding site 6 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 6 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3086

b:12.1
occ:1.00
 ND1 B:HIS886 2.4 10.2 1.0
O B:HOH2192 2.4 13.5 1.0
SG B:CYS823 2.5 11.4 1.0
SE B:MSE889 2.9 17.1 1.0
CE1 B:HIS886 3.1 10.3 1.0
CG B:HIS886 3.5 8.8 1.0
CB B:CYS823 3.6 11.8 1.0
CA B:HIS886 3.8 8.7 1.0
CB B:HIS886 3.9 8.4 1.0
CE B:MSE889 4.0 9.6 1.0
CG B:MSE889 4.0 13.2 1.0
CB B:MSE889 4.1 12.1 1.0
NE2 B:HIS886 4.2 11.1 1.0
CA B:CYS823 4.3 11.8 1.0
CD2 B:HIS886 4.4 9.2 1.0
CD B:PRO824 4.5 12.0 1.0
O B:HIS886 4.6 11.4 1.0
N B:HIS886 4.6 10.6 1.0
C B:HIS886 4.7 10.4 1.0
O B:ASP885 4.8 9.9 1.0
ND2 B:ASN890 4.9 14.6 0.5
O B:HOH2058 4.9 34.4 1.0

Cadmium binding site 7 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 7 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3087

b:14.1
occ:1.00
 ND1 B:HIS1083 2.3 13.3 1.0
ND1 B:HIS1076 2.3 12.3 1.0
NE2 B:HIS1085 2.3 15.7 1.0
OE2 B:GLU894 2.4 20.7 1.0
OE1 B:GLU1079 2.4 18.9 1.0
OE2 B:GLU1079 2.5 15.2 1.0
CD B:GLU1079 2.8 17.1 1.0
OE1 B:GLU894 2.9 21.8 1.0
CD B:GLU894 3.0 16.4 1.0
CE1 B:HIS1076 3.1 17.8 1.0
CE1 B:HIS1083 3.1 18.4 1.0
CD2 B:HIS1085 3.3 17.7 1.0
CE1 B:HIS1085 3.3 19.1 1.0
CG B:HIS1083 3.4 18.1 1.0
CG B:HIS1076 3.4 14.3 1.0
CB B:HIS1083 3.7 15.8 1.0
CB B:HIS1076 3.9 14.4 1.0
O B:HOH2202 4.1 27.8 1.0
NE2 B:HIS1076 4.3 13.9 1.0
CG B:GLU1079 4.3 20.0 1.0
NE2 B:HIS1083 4.3 20.6 1.0
CA B:HIS1076 4.4 14.3 1.0
ND1 B:HIS1085 4.4 19.3 1.0
CD2 B:HIS1076 4.4 13.9 1.0
CG B:HIS1085 4.4 17.3 1.0
CD2 B:HIS1083 4.4 19.0 1.0
CG B:GLU894 4.5 14.1 1.0
O B:HOH2359 4.9 13.9 0.5

Cadmium binding site 8 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 8 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3088

b:17.6
occ:1.00
 O B:HOH2293 2.3 22.3 1.0
OE2 B:GLU1007 2.3 18.0 1.0
OE1 B:GLU1007 2.4 14.4 1.0
CD B:GLU1007 2.7 13.0 1.0
CG B:GLU1007 4.2 14.0 1.0
O B:HOH2153 4.5 29.0 1.0
N B:SER1004 4.6 13.1 1.0
CD2 B:LEU1003 4.7 17.2 1.0
O B:HOH2063 4.8 36.0 1.0
CA B:LEU1003 4.8 15.6 1.0
O B:HOH2249 4.9 19.9 1.0

Cadmium binding site 9 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 9 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3089

b:23.3
occ:1.00
 O B:HOH2251 2.0 44.5 1.0
O B:HOH2358 2.1 9.0 1.0
NE2 B:HIS1080 2.2 32.1 1.0
NE2 B:HIS947 2.2 13.8 1.0
O B:HOH2361 2.3 24.9 1.0
O B:HOH2250 2.4 28.4 1.0
CE1 B:HIS1080 2.9 34.8 1.0
CD2 B:HIS947 3.2 19.6 1.0
CE1 B:HIS947 3.2 21.1 1.0
CD2 B:HIS1080 3.4 32.3 1.0
O B:HOH2248 4.1 23.7 1.0
O B:HOH2117 4.1 39.3 1.0
ND1 B:HIS1080 4.1 34.6 1.0
O B:HOH2247 4.3 28.9 1.0
ND1 B:HIS947 4.3 17.6 1.0
CG B:HIS1080 4.4 30.8 1.0
CG B:HIS947 4.4 14.6 1.0
O B:LEU1078 4.6 22.2 1.0
O B:ALA943 4.8 22.8 1.0
CD2 B:TYR932 4.9 18.7 1.0

Cadmium binding site 10 out of 10 in 1gkk

Go back to Cadmium Binding Sites List in 1gkk
Cadmium binding site 10 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3090

b:21.6
occ:0.30
 O B:HOH2366 1.9 37.1 1.0
ND1 B:HIS1081 2.2 30.3 1.0
O B:HOH2368 2.6 39.3 1.0
O B:HOH2374 3.0 35.3 1.0
CG B:HIS1081 3.1 28.8 1.0
CE1 B:HIS1081 3.2 31.1 1.0
CB B:HIS1081 3.3 26.5 1.0
O B:HOH2367 3.6 21.9 1.0
CA B:HIS1081 3.8 25.6 1.0
CD2 B:HIS1081 4.3 30.1 1.0
NE2 B:HIS1081 4.3 32.2 1.0
NE2 B:HIS1083 4.6 20.6 1.0
N B:HIS1081 4.7 26.3 1.0
N B:HIS1082 4.7 22.3 1.0
C B:HIS1081 4.8 24.2 1.0

Reference:

J.A.M.Prates, N.Tarbouriech, S.J.Charnock, C.M.G.A.Fontes, L.M.A.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 13:24:01 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy