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Cadmium in PDB 4bag: Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser

Enzymatic activity of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser

All present enzymatic activity of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser:
3.2.1.8;

Protein crystallography data

The structure of Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser, PDB code: 4bag was solved by P.J.B.Pereira, D.De Sanctis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.86 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.370, 108.400, 112.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser (pdb code 4bag). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser, PDB code: 4bag:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4bag

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Cadmium binding site 1 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2086

b:14.4
occ:1.00
 O A:HOH3074 2.5 11.2 1.0
ND1 A:HIS886 2.5 12.0 1.0
SG A:CYS823 2.6 13.5 1.0
HA A:HIS886 2.8 11.9 1.0
SE A:MSE889 2.9 17.3 1.0
CE1 A:HIS886 3.2 12.6 1.0
HE1 A:HIS886 3.2 12.6 1.0
HB3 A:MSE889 3.4 11.5 1.0
HB2 A:CYS823 3.4 13.0 1.0
HD2 A:PRO824 3.4 15.8 1.0
CG A:HIS886 3.6 12.1 1.0
CB A:CYS823 3.6 13.0 1.0
CA A:HIS886 3.8 11.9 1.0
HA A:CYS823 3.9 13.5 1.0
CG A:MSE889 3.9 14.1 1.0
HE3 A:MSE889 4.0 17.9 1.0
HG2 A:MSE889 4.0 14.1 1.0
CB A:MSE889 4.0 11.5 1.0
CE A:MSE889 4.0 17.9 1.0
CB A:HIS886 4.0 11.8 1.0
HB3 A:HIS886 4.1 11.8 1.0
HB2 A:MSE889 4.1 11.5 1.0
HE2 A:MSE889 4.2 17.9 1.0
CD A:PRO824 4.3 15.8 1.0
CA A:CYS823 4.3 13.5 1.0
NE2 A:HIS886 4.3 12.1 1.0
HD3 A:PRO824 4.4 15.8 1.0
HB3 A:CYS823 4.4 13.0 1.0
CD2 A:HIS886 4.5 10.6 1.0
N A:HIS886 4.5 9.6 1.0
O A:HIS886 4.6 10.0 1.0
H A:GLN825 4.6 12.4 1.0
O A:ASP885 4.7 9.8 1.0
C A:HIS886 4.7 11.0 1.0
HG3 A:MSE889 4.8 14.1 1.0
HB2 A:GLN825 4.9 15.2 1.0
HE1 A:MSE889 4.9 17.9 1.0
C A:ASP885 4.9 9.2 1.0
OD1 A:ASN890 4.9 29.9 1.0
N A:PRO824 5.0 14.4 1.0
O A:HOH3077 5.0 24.3 1.0
HB2 A:HIS886 5.0 11.8 1.0

Cadmium binding site 2 out of 8 in 4bag

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Cadmium binding site 2 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2087

b:20.9
occ:1.00
 NE2 A:HIS947 2.4 12.9 1.0
NE2 A:HIS1080 2.5 23.9 1.0
O A:HOH3109 2.5 16.7 1.0
O A:HOH3112 2.6 24.8 1.0
CD2 A:HIS947 3.3 14.3 1.0
CE1 A:HIS947 3.4 16.1 1.0
CE1 A:HIS1080 3.4 32.2 1.0
HD2 A:HIS947 3.4 14.3 1.0
CD2 A:HIS1080 3.5 25.2 1.0
HE1 A:HIS1080 3.5 32.2 1.0
HE1 A:HIS947 3.5 16.1 1.0
HD2 A:HIS1080 3.7 25.2 1.0
O A:HOH3108 3.7 14.0 1.0
HB2 A:MSE946 4.0 11.9 1.0
O A:LEU1078 4.5 19.9 1.0
ND1 A:HIS947 4.5 12.8 1.0
CG A:HIS947 4.5 12.4 1.0
ND1 A:HIS1080 4.5 34.9 1.0
HA A:SER944 4.5 13.0 1.0
CG A:HIS1080 4.6 24.5 1.0
HD2 A:TYR932 4.6 14.4 1.0
O A:ALA943 4.7 17.1 1.0
HB3 A:TYR932 4.7 13.5 1.0
CB A:MSE946 5.0 11.9 1.0

Cadmium binding site 3 out of 8 in 4bag

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Cadmium binding site 3 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2088

b:13.1
occ:1.00
 OE2 A:GLU894 2.4 12.8 1.0
NE2 A:HIS1085 2.5 14.3 1.0
OE1 A:GLU1079 2.5 14.7 1.0
ND1 A:HIS1083 2.5 11.7 1.0
OE2 A:GLU1079 2.5 12.8 1.0
ND1 A:HIS1076 2.5 10.1 1.0
CD A:GLU1079 2.8 16.5 1.0
CD A:GLU894 3.1 13.1 1.0
OE1 A:GLU894 3.1 16.7 1.0
CE1 A:HIS1076 3.3 13.3 1.0
HB2 A:HIS1083 3.3 12.9 1.0
CD2 A:HIS1085 3.3 13.4 1.0
HE1 A:HIS1076 3.3 13.3 1.0
HD2 A:HIS1085 3.4 13.4 1.0
CG A:HIS1083 3.4 14.4 1.0
CE1 A:HIS1083 3.4 17.9 1.0
CE1 A:HIS1085 3.5 14.0 1.0
HB3 A:HIS1076 3.6 11.9 1.0
HE1 A:HIS1083 3.6 17.9 1.0
CG A:HIS1076 3.6 10.5 1.0
HB3 A:HIS1083 3.6 12.9 1.0
CB A:HIS1083 3.7 12.9 1.0
HE1 A:HIS1085 3.7 14.0 1.0
HA A:HIS1076 3.7 12.2 1.0
CB A:HIS1076 4.0 11.9 1.0
O A:HOH3058 4.1 15.7 1.0
O A:HOH3082 4.3 18.6 1.0
CG A:GLU1079 4.3 15.1 1.0
CA A:HIS1076 4.4 12.2 1.0
NE2 A:HIS1076 4.4 11.5 1.0
CG A:HIS1085 4.5 13.2 1.0
ND1 A:HIS1085 4.5 14.3 1.0
NE2 A:HIS1083 4.6 15.6 1.0
CG A:GLU894 4.6 11.5 1.0
CD2 A:HIS1076 4.6 9.8 1.0
CD2 A:HIS1083 4.6 14.6 1.0
O A:HOH3165 4.6 23.1 1.0
HG3 A:GLU1079 4.7 15.1 1.0
HG2 A:GLU1079 4.7 15.1 1.0
HB2 A:HIS1081 4.7 21.5 1.0
HG3 A:GLU894 4.8 11.5 1.0
HB2 A:HIS1076 4.9 11.9 1.0
HG2 A:GLU894 4.9 11.5 1.0
O A:HOH3163 4.9 15.2 1.0
HB3 A:GLU1079 5.0 15.2 1.0
O A:PHE1075 5.0 13.5 1.0
HB2 A:GLU1079 5.0 15.2 1.0

Cadmium binding site 4 out of 8 in 4bag

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Cadmium binding site 4 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2089

b:15.9
occ:1.00
 NE2 A:HIS1084 2.4 14.2 1.0
NE2 A:HIS1082 2.4 23.5 1.0
O A:HOH3173 2.5 17.6 1.0
CE1 A:HIS1084 3.3 15.6 1.0
CE1 A:HIS1082 3.3 27.9 1.0
HE1 A:HIS1082 3.3 27.9 1.0
HE1 A:HIS1084 3.3 15.6 1.0
CD2 A:HIS1084 3.4 17.1 1.0
CD2 A:HIS1082 3.5 20.2 1.0
HD2 A:HIS1084 3.6 17.1 1.0
HD2 A:HIS1082 3.7 20.2 1.0
ND1 A:HIS1084 4.4 14.1 1.0
ND1 A:HIS1082 4.4 29.8 1.0
CG A:HIS1084 4.5 13.5 1.0
CG A:HIS1082 4.6 22.9 1.0

Cadmium binding site 5 out of 8 in 4bag

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Cadmium binding site 5 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2086

b:15.0
occ:1.00
 O B:HOH3071 2.5 13.2 1.0
ND1 B:HIS886 2.5 13.9 1.0
SG B:CYS823 2.6 13.7 1.0
HA B:HIS886 2.9 12.4 1.0
SE B:MSE889 2.9 17.7 1.0
CE1 B:HIS886 3.2 13.5 1.0
HE1 B:HIS886 3.3 13.5 1.0
HD2 B:PRO824 3.4 13.7 1.0
HB2 B:CYS823 3.4 12.4 1.0
HB3 B:MSE889 3.4 11.1 1.0
CG B:HIS886 3.6 13.3 1.0
CB B:CYS823 3.6 12.4 1.0
CA B:HIS886 3.8 12.4 1.0
CG B:MSE889 4.0 13.6 1.0
HA B:CYS823 4.0 13.4 1.0
HE1 B:MSE889 4.0 16.2 1.0
CB B:HIS886 4.0 12.9 1.0
HB3 B:HIS886 4.0 12.9 1.0
CE B:MSE889 4.0 16.2 1.0
HG2 B:MSE889 4.1 13.6 1.0
CB B:MSE889 4.1 11.1 1.0
HE3 B:MSE889 4.2 16.2 1.0
HB2 B:MSE889 4.2 11.1 1.0
CD B:PRO824 4.3 13.7 1.0
CA B:CYS823 4.4 13.4 1.0
NE2 B:HIS886 4.4 13.5 1.0
HB3 B:CYS823 4.4 12.4 1.0
CD2 B:HIS886 4.5 12.9 1.0
N B:HIS886 4.6 10.6 1.0
O B:HIS886 4.6 10.8 1.0
H B:GLN825 4.6 12.9 1.0
C B:HIS886 4.7 11.8 1.0
HG2 B:PRO824 4.7 12.8 1.0
O B:ASP885 4.8 10.6 1.0
HD3 B:PRO824 4.8 13.7 1.0
HB2 B:GLN825 4.8 14.4 1.0
HG3 B:MSE889 4.8 13.6 1.0
HE2 B:MSE889 4.9 16.2 1.0
HB2 B:HIS886 5.0 12.9 1.0
C B:ASP885 5.0 10.7 1.0

Cadmium binding site 6 out of 8 in 4bag

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Cadmium binding site 6 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2087

b:13.8
occ:1.00
 OE2 B:GLU894 2.4 16.0 1.0
OE1 B:GLU1079 2.4 13.5 1.0
NE2 B:HIS1085 2.5 13.2 1.0
ND1 B:HIS1076 2.5 10.2 1.0
OE2 B:GLU1079 2.5 13.5 1.0
ND1 B:HIS1083 2.5 20.4 1.0
CD B:GLU1079 2.8 15.3 1.0
OE1 B:GLU894 3.0 19.0 1.0
CD B:GLU894 3.1 15.7 1.0
CE1 B:HIS1076 3.3 14.3 1.0
HB2 B:HIS1083 3.3 13.5 1.0
CD2 B:HIS1085 3.3 14.6 1.0
HE1 B:HIS1076 3.3 14.3 1.0
CG B:HIS1083 3.4 18.2 1.0
HD2 B:HIS1085 3.4 14.6 1.0
CE1 B:HIS1085 3.5 14.7 1.0
HB3 B:HIS1076 3.5 10.9 1.0
HB3 B:HIS1083 3.5 13.5 1.0
CG B:HIS1076 3.6 12.4 1.0
CB B:HIS1083 3.6 13.5 1.0
HE1 B:HIS1085 3.6 14.7 1.0
CE1 B:HIS1083 3.7 16.6 1.0
HA B:HIS1076 3.7 11.5 1.0
HE1 B:HIS1083 3.9 16.6 1.0
CB B:HIS1076 3.9 10.9 1.0
O B:HOH3053 4.1 19.5 1.0
O B:HOH3077 4.3 21.1 1.0
CG B:GLU1079 4.3 15.7 1.0
CA B:HIS1076 4.4 11.5 1.0
NE2 B:HIS1076 4.4 11.1 1.0
CG B:HIS1085 4.5 13.5 1.0
ND1 B:HIS1085 4.5 16.2 1.0
CG B:GLU894 4.5 12.7 1.0
CD2 B:HIS1076 4.6 11.7 1.0
CD2 B:HIS1083 4.6 12.7 1.0
HG3 B:GLU1079 4.7 15.7 1.0
NE2 B:HIS1083 4.7 20.9 1.0
O B:HOH3139 4.7 24.1 1.0
HG2 B:GLU1079 4.8 15.7 1.0
HG3 B:GLU894 4.8 12.7 1.0
HB2 B:HIS1076 4.8 10.9 1.0
HB2 B:HIS1081 4.8 22.5 1.0
HG2 B:GLU894 4.9 12.7 1.0
O B:HOH3135 4.9 17.7 1.0
HB3 B:GLU1079 5.0 14.7 1.0
HB2 B:GLU1079 5.0 14.7 1.0

Cadmium binding site 7 out of 8 in 4bag

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Cadmium binding site 7 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2088

b:15.6
occ:1.00
 NE2 B:HIS1084 2.4 15.6 1.0
NE2 B:HIS1082 2.5 18.5 1.0
O B:HOH3144 2.6 17.5 1.0
CE1 B:HIS1084 3.3 15.7 1.0
HE1 B:HIS1084 3.4 15.7 1.0
CD2 B:HIS1084 3.4 15.8 1.0
CE1 B:HIS1082 3.4 23.7 1.0
CD2 B:HIS1082 3.4 15.4 1.0
HE1 B:HIS1082 3.5 23.7 1.0
HD2 B:HIS1082 3.6 15.4 1.0
HD2 B:HIS1084 3.6 15.8 1.0
ND1 B:HIS1084 4.4 16.4 1.0
CG B:HIS1084 4.5 15.2 1.0
ND1 B:HIS1082 4.5 22.9 1.0
CG B:HIS1082 4.6 21.3 1.0

Cadmium binding site 8 out of 8 in 4bag

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Cadmium binding site 8 out of 8 in the Feruloyl Esterase Domain of Xyny From Clostridium Thermocellum After Exposure to 266NM Uv Laser


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 After Exposure to 266NM Uv Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2089

b:21.8
occ:1.00
 NE2 B:HIS947 2.4 13.6 1.0
NE2 B:HIS1080 2.4 26.6 1.0
O B:HOH3095 2.6 18.3 1.0
O B:HOH3140 2.6 20.6 1.0
O B:HOH3098 2.6 23.5 1.0
CE1 B:HIS1080 3.1 30.2 1.0
HE1 B:HIS1080 3.1 30.2 1.0
CD2 B:HIS947 3.3 14.6 1.0
HD2 B:HIS947 3.4 14.6 1.0
CE1 B:HIS947 3.4 18.0 1.0
CD2 B:HIS1080 3.5 24.1 1.0
HE1 B:HIS947 3.6 18.0 1.0
HD2 B:HIS1080 3.8 24.1 1.0
HB2 B:MSE946 3.9 12.7 1.0
ND1 B:HIS1080 4.3 30.4 1.0
HA B:SER944 4.4 13.6 1.0
O B:LEU1078 4.4 19.8 1.0
CG B:HIS947 4.5 12.1 1.0
CG B:HIS1080 4.5 22.1 1.0
ND1 B:HIS947 4.5 14.9 1.0
HD2 B:TYR932 4.6 15.1 1.0
O B:ALA943 4.6 17.3 1.0
HB3 B:TYR932 4.8 12.7 1.0
CB B:MSE946 4.9 12.7 1.0

Reference:

P.J.B.Pereira, A.Royant, S.Panjikar, D.De Sanctis. In-House Uv Radiation-Damage-Induced Phasing of Selenomethionine-Labeled Protein Structures. J.Struct.Biol. V. 181 89 2013.
ISSN: ISSN 1047-8477
PubMed: 23178456
DOI: 10.1016/J.JSB.2012.11.003
Page generated: Fri Jul 19 16:57:23 2024

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