Mercury in PDB 1is9: Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Enzymatic activity of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
All present enzymatic activity of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution:
3.2.1.4;
Protein crystallography data
The structure of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution, PDB code: 1is9
was solved by
A.Schmidt,
A.Gonzalez,
R.J.Morris,
M.Costabel,
P.M.Alzari,
V.S.Lamzin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
1.03
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.441,
62.829,
103.891,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.1 /
14.9
|
Other elements in 1is9:
The structure of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution also contains other interesting chemical elements:
Mercury Binding Sites:
The binding sites of Mercury atom in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
(pdb code 1is9). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the
Endoglucanase A From Clostridium Thermocellum at Atomic Resolution, PDB code: 1is9:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
Mercury binding site 1 out
of 6 in 1is9
Go back to
Mercury Binding Sites List in 1is9
Mercury binding site 1 out
of 6 in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1001
b:6.0
occ:1.00
|
SG
|
A:CYS270
|
2.3
|
4.9
|
1.0
|
CL
|
A:CL1007
|
2.3
|
6.1
|
1.0
|
OG1
|
A:THR254
|
2.6
|
5.5
|
1.0
|
O
|
A:HOH1194
|
3.0
|
8.3
|
1.0
|
O
|
A:ALA266
|
3.2
|
3.9
|
1.0
|
CB
|
A:CYS270
|
3.3
|
4.5
|
1.0
|
CB
|
A:THR254
|
3.4
|
5.5
|
1.0
|
N
|
A:CYS270
|
3.4
|
4.2
|
1.0
|
CA
|
A:CYS270
|
3.7
|
4.4
|
1.0
|
CB
|
A:ASN269
|
3.9
|
5.5
|
1.0
|
OH
|
A:TYR250
|
3.9
|
7.3
|
1.0
|
C
|
A:THR254
|
3.9
|
5.2
|
1.0
|
C
|
A:ALA266
|
4.0
|
3.8
|
1.0
|
O
|
A:THR254
|
4.0
|
7.4
|
1.0
|
CA
|
A:ALA266
|
4.1
|
4.2
|
1.0
|
CZ
|
A:TYR250
|
4.1
|
5.6
|
1.0
|
C
|
A:ASN269
|
4.1
|
4.7
|
1.0
|
N
|
A:ALA255
|
4.2
|
4.3
|
1.0
|
CA
|
A:THR254
|
4.3
|
5.2
|
1.0
|
CB
|
A:ALA266
|
4.5
|
4.5
|
1.0
|
CE2
|
A:TYR250
|
4.5
|
5.9
|
1.0
|
CE1
|
A:TYR250
|
4.6
|
5.7
|
1.0
|
CA
|
A:ASN269
|
4.6
|
4.7
|
1.0
|
CG2
|
A:THR254
|
4.6
|
5.8
|
1.0
|
CA
|
A:ALA255
|
4.7
|
4.5
|
1.0
|
O
|
A:ASN269
|
4.9
|
5.0
|
1.0
|
|
Mercury binding site 2 out
of 6 in 1is9
Go back to
Mercury Binding Sites List in 1is9
Mercury binding site 2 out
of 6 in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1002
b:6.1
occ:1.00
|
SG
|
A:CYS229
|
2.3
|
4.7
|
1.0
|
CL
|
A:CL1012
|
2.3
|
5.2
|
0.8
|
O
|
A:THR230
|
2.6
|
6.0
|
1.0
|
O
|
A:CYS229
|
2.9
|
4.5
|
1.0
|
C
|
A:CYS229
|
3.2
|
4.3
|
1.0
|
CB
|
A:CYS229
|
3.3
|
4.8
|
1.0
|
C
|
A:THR230
|
3.4
|
6.0
|
1.0
|
CG2
|
A:ILE211
|
3.6
|
6.4
|
1.0
|
CA
|
A:CYS229
|
3.7
|
4.5
|
1.0
|
N
|
A:THR230
|
3.8
|
4.9
|
1.0
|
N
|
A:CYS229
|
4.1
|
3.9
|
1.0
|
CA
|
A:THR230
|
4.1
|
5.3
|
1.0
|
CG2
|
A:THR179
|
4.2
|
6.3
|
1.0
|
N
|
A:ALA231
|
4.2
|
6.5
|
1.0
|
CA
|
A:ALA231
|
4.4
|
7.4
|
1.0
|
O
|
A:THR179
|
4.5
|
4.4
|
1.0
|
CG
|
A:PRO181
|
4.5
|
4.5
|
1.0
|
CZ
|
A:PHE184
|
4.6
|
5.8
|
1.0
|
CD
|
A:PRO181
|
4.7
|
3.9
|
1.0
|
N
|
A:GLY233
|
4.8
|
6.3
|
1.0
|
CA
|
A:GLY233
|
4.8
|
6.3
|
1.0
|
C
|
A:THR179
|
4.8
|
4.0
|
1.0
|
CB
|
A:ILE211
|
4.9
|
6.2
|
1.0
|
CD1
|
A:ILE211
|
4.9
|
9.0
|
1.0
|
CG1
|
A:ILE211
|
5.0
|
7.5
|
1.0
|
N
|
A:THR179
|
5.0
|
4.9
|
1.0
|
|
Mercury binding site 3 out
of 6 in 1is9
Go back to
Mercury Binding Sites List in 1is9
Mercury binding site 3 out
of 6 in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1003
b:7.1
occ:1.00
|
SG
|
A:CYS208
|
2.3
|
4.6
|
1.0
|
CL
|
A:CL1013
|
2.3
|
6.0
|
0.8
|
CL
|
A:CL1011
|
2.6
|
9.1
|
0.5
|
CA
|
A:CYS208
|
3.2
|
4.6
|
1.0
|
CB
|
A:CYS208
|
3.3
|
4.9
|
1.0
|
CE1
|
A:PHE184
|
3.3
|
5.9
|
1.0
|
CD1
|
A:PHE184
|
3.5
|
5.3
|
1.0
|
N
|
A:CYS208
|
3.5
|
3.7
|
1.0
|
CZ
|
A:PHE184
|
3.5
|
5.8
|
1.0
|
CG
|
A:PHE184
|
3.8
|
4.7
|
1.0
|
CE2
|
A:PHE184
|
3.9
|
5.8
|
1.0
|
CB
|
A:LEU167
|
3.9
|
6.0
|
1.0
|
CD2
|
A:PHE184
|
4.0
|
5.0
|
1.0
|
C
|
A:LYS207
|
4.1
|
4.1
|
1.0
|
N
|
A:LEU167
|
4.2
|
5.2
|
1.0
|
O
|
A:VAL204
|
4.3
|
4.8
|
1.0
|
O
|
A:LYS207
|
4.5
|
4.1
|
1.0
|
C
|
A:CYS208
|
4.6
|
3.8
|
1.0
|
CB
|
A:PHE184
|
4.7
|
4.4
|
1.0
|
CG
|
A:LYS207
|
4.7
|
6.1
|
1.0
|
CA
|
A:LEU167
|
4.7
|
5.4
|
1.0
|
CG1
|
A:ILE211
|
4.8
|
7.5
|
1.0
|
CB
|
A:LYS207
|
4.8
|
5.2
|
1.0
|
|
Mercury binding site 4 out
of 6 in 1is9
Go back to
Mercury Binding Sites List in 1is9
Mercury binding site 4 out
of 6 in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1004
b:8.7
occ:0.60
|
SG
|
A:CYS74
|
1.5
|
6.5
|
0.5
|
SG
|
A:CYS74
|
2.2
|
5.7
|
0.5
|
HG
|
A:HG1005
|
2.2
|
8.9
|
0.4
|
CL
|
A:CL1009
|
2.3
|
8.7
|
0.5
|
O
|
A:LEU70
|
3.0
|
6.0
|
1.0
|
CB
|
A:CYS74
|
3.1
|
6.7
|
1.0
|
CD1
|
A:PHE356
|
3.4
|
9.8
|
1.0
|
CD1
|
A:LEU350
|
3.5
|
8.9
|
1.0
|
CE1
|
A:PHE356
|
3.7
|
10.6
|
1.0
|
C
|
A:LEU70
|
3.8
|
4.7
|
1.0
|
CL
|
A:CL1010
|
4.0
|
9.4
|
0.5
|
O
|
A:HOH1742
|
4.3
|
27.6
|
1.0
|
CB
|
A:LEU70
|
4.3
|
5.0
|
1.0
|
CA
|
A:CYS74
|
4.4
|
6.7
|
1.0
|
CG
|
A:PHE356
|
4.4
|
6.5
|
1.0
|
CA
|
A:LEU70
|
4.5
|
4.9
|
1.0
|
N
|
A:CYS74
|
4.6
|
6.1
|
1.0
|
N
|
A:LEU71
|
4.6
|
4.5
|
1.0
|
O
|
A:ASN355
|
4.7
|
5.5
|
1.0
|
CG
|
A:LEU350
|
4.7
|
7.2
|
1.0
|
CA
|
A:LEU71
|
4.8
|
5.1
|
1.0
|
CB
|
A:LEU350
|
4.8
|
5.6
|
1.0
|
CZ
|
A:PHE356
|
4.8
|
10.4
|
1.0
|
CB
|
A:PHE356
|
4.9
|
5.5
|
1.0
|
|
Mercury binding site 5 out
of 6 in 1is9
Go back to
Mercury Binding Sites List in 1is9
Mercury binding site 5 out
of 6 in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1005
b:8.9
occ:0.40
|
SG
|
A:CYS74
|
1.8
|
6.5
|
0.5
|
SG
|
A:CYS74
|
2.1
|
5.7
|
0.5
|
HG
|
A:HG1004
|
2.2
|
8.7
|
0.6
|
CL
|
A:CL1010
|
2.3
|
9.4
|
0.5
|
O
|
A:LEU70
|
2.9
|
6.0
|
1.0
|
O
|
A:HOH1742
|
3.4
|
27.6
|
1.0
|
CB
|
A:CYS74
|
3.4
|
6.7
|
1.0
|
CG1
|
A:VAL73
|
3.5
|
6.6
|
1.0
|
N
|
A:CYS74
|
3.8
|
6.1
|
1.0
|
CD1
|
A:PHE131
|
3.8
|
8.1
|
1.0
|
C
|
A:LEU70
|
3.8
|
4.7
|
1.0
|
CG
|
A:PHE131
|
3.9
|
7.5
|
1.0
|
CE1
|
A:PHE131
|
3.9
|
8.3
|
1.0
|
CD2
|
A:PHE131
|
3.9
|
8.4
|
1.0
|
CE1
|
A:PHE356
|
4.0
|
10.6
|
1.0
|
CZ
|
A:PHE131
|
4.0
|
9.0
|
1.0
|
CA
|
A:CYS74
|
4.0
|
6.7
|
1.0
|
CE2
|
A:PHE131
|
4.0
|
8.4
|
1.0
|
CD1
|
A:PHE356
|
4.1
|
9.8
|
1.0
|
CL
|
A:CL1009
|
4.1
|
8.7
|
0.5
|
CA
|
A:LEU70
|
4.2
|
4.9
|
1.0
|
O
|
A:HOH1722
|
4.4
|
39.1
|
1.0
|
CD2
|
A:LEU70
|
4.4
|
7.7
|
1.0
|
CB
|
A:LEU70
|
4.5
|
5.0
|
1.0
|
CB
|
A:PHE131
|
4.6
|
6.7
|
1.0
|
C
|
A:VAL73
|
4.7
|
5.7
|
1.0
|
CB
|
A:VAL73
|
4.8
|
6.5
|
1.0
|
|
Mercury binding site 6 out
of 6 in 1is9
Go back to
Mercury Binding Sites List in 1is9
Mercury binding site 6 out
of 6 in the Endoglucanase A From Clostridium Thermocellum at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Endoglucanase A From Clostridium Thermocellum at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1006
b:9.6
occ:0.75
|
SG
|
A:CYS159
|
2.1
|
12.6
|
1.0
|
CL
|
A:CL1014
|
2.3
|
9.5
|
0.5
|
O
|
A:HOH1738
|
2.4
|
9.8
|
1.0
|
O
|
A:HOH1424
|
2.5
|
6.8
|
1.0
|
OG1
|
A:THR119
|
2.7
|
6.0
|
1.0
|
CB
|
A:CYS159
|
3.2
|
9.2
|
1.0
|
N
|
A:ASP171
|
3.7
|
6.8
|
1.0
|
CB
|
A:THR119
|
3.7
|
5.3
|
1.0
|
CA
|
A:THR119
|
3.8
|
4.5
|
1.0
|
CD1
|
A:LEU97
|
3.8
|
8.4
|
1.0
|
C
|
A:GLY170
|
3.8
|
6.7
|
1.0
|
CA
|
A:ASP171
|
4.0
|
6.9
|
1.0
|
N
|
A:THR119
|
4.1
|
4.4
|
1.0
|
CB
|
A:ASP171
|
4.1
|
7.0
|
1.0
|
CG2
|
A:THR119
|
4.2
|
6.2
|
1.0
|
O
|
A:GLY170
|
4.3
|
7.4
|
1.0
|
CA
|
A:CYS159
|
4.3
|
7.5
|
1.0
|
CA
|
A:GLY170
|
4.3
|
7.7
|
1.0
|
CD2
|
A:LEU155
|
4.5
|
9.4
|
1.0
|
C
|
A:ALA118
|
4.7
|
4.7
|
1.0
|
CD2
|
A:LEU97
|
4.7
|
7.7
|
1.0
|
CB
|
A:ALA117
|
4.8
|
6.6
|
1.0
|
CG
|
A:LEU97
|
4.8
|
7.0
|
1.0
|
N
|
A:CYS159
|
4.8
|
7.3
|
1.0
|
N
|
A:GLY170
|
4.8
|
6.4
|
1.0
|
O
|
A:LYS168
|
4.8
|
5.9
|
1.0
|
CG
|
A:ASP171
|
5.0
|
6.7
|
1.0
|
|
Reference:
A.Schmidt,
A.Gonzalez,
R.J.Morris,
M.Costabel,
P.M.Alzari,
V.S.Lamzin.
Advantages of High-Resolution Phasing: Mad to Atomic Resolution. Acta Crystallogr.,Sect.D V. 58 1433 2002.
ISSN: ISSN 0907-4449
PubMed: 12198299
DOI: 10.1107/S0907444902011368
Page generated: Sun Aug 11 00:17:41 2024
|