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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

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Cadmium binding site 1 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


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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

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Cadmium binding site 2 out of 10 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum


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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

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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

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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

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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

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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

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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

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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

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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

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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 Aug 28 11:52:34 2020
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