Xenon in PDB 2z8y: Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
Enzymatic activity of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
All present enzymatic activity of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica:
1.2.7.4;
1.2.99.2;
2.3.1.169;
Protein crystallography data
The structure of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica, PDB code: 2z8y
was solved by
T.I.Doukov,
L.C.Blasiak,
C.L.Drennan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.00 /
2.51
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.540,
136.600,
141.750,
101.29,
109.22,
103.91
|
R / Rfree (%)
|
17.8 /
25
|
Other elements in 2z8y:
The structure of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica also contains other interesting chemical elements:
Xenon Binding Sites:
Xenon binding site 1 out
of 42 in 2z8y
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Xenon Binding Sites List in 2z8y
Xenon binding site 1 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 1 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1001
b:23.8
occ:0.15
|
CG2
|
A:THR602
|
3.3
|
10.1
|
1.0
|
CA
|
A:GLY592
|
3.7
|
13.5
|
1.0
|
SG
|
A:CYS468
|
3.7
|
23.4
|
1.0
|
CD1
|
A:TRP595
|
3.7
|
15.9
|
1.0
|
CB
|
A:ALA580
|
3.8
|
16.2
|
1.0
|
N
|
A:ALA580
|
3.9
|
16.1
|
1.0
|
O
|
A:HIS603
|
4.1
|
15.9
|
1.0
|
N
|
A:GLY592
|
4.1
|
14.8
|
1.0
|
CB
|
A:ALA578
|
4.2
|
14.9
|
1.0
|
C
|
A:SER579
|
4.2
|
16.3
|
1.0
|
NE1
|
A:TRP595
|
4.3
|
19.8
|
1.0
|
CG2
|
A:ILE591
|
4.4
|
11.6
|
1.0
|
N
|
A:SER579
|
4.5
|
14.4
|
1.0
|
CA
|
A:ALA580
|
4.5
|
16.4
|
1.0
|
C
|
A:ALA578
|
4.6
|
15.8
|
1.0
|
CA
|
A:SER579
|
4.6
|
14.9
|
1.0
|
CB
|
A:THR602
|
4.7
|
14.0
|
1.0
|
C
|
A:ILE591
|
4.7
|
14.4
|
1.0
|
CG
|
A:TRP595
|
4.8
|
15.9
|
1.0
|
O
|
A:SER579
|
4.8
|
15.7
|
1.0
|
CG2
|
A:VAL604
|
4.8
|
14.8
|
1.0
|
O
|
A:ILE591
|
4.8
|
16.2
|
1.0
|
C
|
A:GLY592
|
4.9
|
13.0
|
1.0
|
O
|
A:ALA588
|
4.9
|
17.3
|
1.0
|
O
|
A:ALA578
|
5.0
|
17.2
|
1.0
|
|
Xenon binding site 2 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 2 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 2 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1002
b:27.3
occ:1.00
|
CZ
|
A:PHE632
|
3.7
|
2.5
|
1.0
|
CG2
|
A:VAL102
|
3.8
|
10.4
|
1.0
|
CG
|
A:PRO608
|
3.9
|
11.5
|
1.0
|
OG1
|
A:THR593
|
4.0
|
15.8
|
1.0
|
O
|
A:ALA589
|
4.0
|
12.8
|
1.0
|
CB
|
A:PRO608
|
4.0
|
10.8
|
1.0
|
CB
|
A:ALA589
|
4.1
|
14.2
|
1.0
|
CA
|
A:ALA589
|
4.1
|
14.6
|
1.0
|
CE1
|
A:PHE632
|
4.2
|
11.9
|
1.0
|
CE2
|
A:PHE632
|
4.3
|
6.5
|
1.0
|
C
|
A:ALA589
|
4.5
|
13.7
|
1.0
|
CG1
|
A:ILE106
|
4.8
|
11.6
|
1.0
|
CD1
|
A:ILE106
|
4.8
|
2.0
|
1.0
|
CZ
|
A:PHE634
|
5.0
|
9.2
|
1.0
|
|
Xenon binding site 3 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 3 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 3 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1003
b:30.5
occ:0.60
|
XE
|
A:XE1003
|
0.0
|
30.5
|
0.6
|
XE
|
A:XE1003
|
2.8
|
14.0
|
0.2
|
CD1
|
A:ILE106
|
3.6
|
2.0
|
1.0
|
CD2
|
A:LEU620
|
3.6
|
15.3
|
1.0
|
CB
|
A:ALA234
|
4.0
|
7.6
|
1.0
|
CG1
|
A:VAL102
|
4.1
|
9.1
|
1.0
|
CG1
|
A:VAL231
|
4.2
|
13.7
|
1.0
|
OG1
|
A:THR593
|
4.3
|
15.8
|
1.0
|
CD1
|
A:LEU620
|
4.4
|
18.7
|
1.0
|
CG2
|
A:THR593
|
4.4
|
11.7
|
1.0
|
XE
|
A:XE1004
|
4.4
|
30.1
|
0.8
|
CG
|
A:LEU620
|
4.6
|
17.6
|
1.0
|
CG2
|
A:VAL102
|
4.9
|
10.4
|
1.0
|
|
Xenon binding site 4 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 4 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 4 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1003
b:14.0
occ:0.19
|
XE
|
A:XE1003
|
0.0
|
14.0
|
0.2
|
XE
|
A:XE1003
|
2.8
|
30.5
|
0.6
|
CG1
|
A:VAL102
|
3.2
|
9.1
|
1.0
|
CB
|
A:ALA234
|
3.6
|
7.6
|
1.0
|
O
|
A:ALA99
|
4.0
|
14.4
|
1.0
|
CA
|
A:ALA99
|
4.1
|
10.3
|
1.0
|
CG2
|
A:VAL231
|
4.2
|
13.9
|
1.0
|
CA
|
A:VAL231
|
4.2
|
13.4
|
1.0
|
CB
|
A:ALA99
|
4.3
|
9.0
|
1.0
|
N
|
A:GLY103
|
4.4
|
11.1
|
1.0
|
CB
|
A:VAL102
|
4.6
|
12.8
|
1.0
|
C
|
A:ALA99
|
4.6
|
11.7
|
1.0
|
CB
|
A:VAL231
|
4.6
|
13.5
|
1.0
|
CD1
|
A:ILE106
|
4.6
|
2.0
|
1.0
|
CG1
|
A:VAL231
|
4.6
|
13.7
|
1.0
|
CA
|
A:GLY103
|
4.7
|
11.0
|
1.0
|
O
|
A:LEU230
|
4.8
|
12.7
|
1.0
|
N
|
A:VAL231
|
4.8
|
11.7
|
1.0
|
C
|
A:VAL102
|
5.0
|
11.3
|
1.0
|
|
Xenon binding site 5 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 5 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 5 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1004
b:30.1
occ:0.84
|
CD2
|
A:LEU620
|
3.3
|
15.3
|
1.0
|
CD1
|
A:ILE235
|
3.9
|
3.9
|
1.0
|
CG1
|
A:VAL231
|
3.9
|
13.7
|
1.0
|
CG1
|
A:VAL596
|
3.9
|
7.9
|
1.0
|
CG1
|
A:ILE235
|
4.2
|
14.3
|
1.0
|
CE2
|
A:PHE632
|
4.3
|
6.5
|
1.0
|
XE
|
A:XE1003
|
4.4
|
30.5
|
0.6
|
CB
|
A:VAL596
|
4.5
|
12.4
|
1.0
|
CG2
|
A:THR593
|
4.6
|
11.7
|
1.0
|
CA
|
A:LEU620
|
4.6
|
15.6
|
1.0
|
CB
|
A:ALA624
|
4.6
|
16.0
|
1.0
|
CG
|
A:LEU620
|
4.7
|
17.6
|
1.0
|
CD2
|
A:PHE632
|
4.8
|
5.9
|
1.0
|
CB
|
A:LEU620
|
5.0
|
16.3
|
1.0
|
|
Xenon binding site 6 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 6 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 6 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1005
b:24.5
occ:1.00
|
CG2
|
M:THR31
|
3.8
|
8.9
|
1.0
|
CG2
|
A:ILE623
|
3.8
|
11.5
|
1.0
|
CG1
|
A:VAL228
|
4.0
|
10.5
|
1.0
|
CG2
|
A:VAL627
|
4.0
|
13.4
|
1.0
|
CE1
|
A:PHE232
|
4.1
|
14.0
|
1.0
|
CZ
|
A:PHE232
|
4.4
|
8.0
|
1.0
|
CG2
|
A:VAL228
|
4.4
|
12.4
|
1.0
|
CG
|
M:TYR35
|
4.5
|
15.4
|
1.0
|
CD1
|
A:ILE619
|
4.5
|
9.4
|
1.0
|
CD1
|
M:TYR35
|
4.5
|
10.6
|
1.0
|
CB
|
A:ILE623
|
4.6
|
14.4
|
1.0
|
CG2
|
A:ILE619
|
4.6
|
11.6
|
1.0
|
CB
|
M:TYR35
|
4.6
|
15.0
|
1.0
|
CG1
|
A:ILE619
|
4.7
|
10.0
|
1.0
|
CB
|
A:VAL627
|
4.8
|
13.4
|
1.0
|
CB
|
A:VAL228
|
4.8
|
13.2
|
1.0
|
CG1
|
A:VAL627
|
4.9
|
12.4
|
1.0
|
CD2
|
M:TYR35
|
4.9
|
17.2
|
1.0
|
|
Xenon binding site 7 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 7 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 7 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Xe1010
b:32.0
occ:0.41
|
O
|
A:SER396
|
3.3
|
18.7
|
1.0
|
C
|
A:SER396
|
3.6
|
21.4
|
1.0
|
CD1
|
A:LEU287
|
3.6
|
22.9
|
1.0
|
CG2
|
A:THR374
|
3.7
|
10.8
|
1.0
|
CB
|
A:ALA400
|
3.8
|
18.9
|
1.0
|
CB
|
A:SER396
|
3.8
|
23.7
|
1.0
|
CD1
|
A:TYR388
|
3.9
|
28.5
|
1.0
|
CD1
|
A:ILE386
|
4.0
|
16.1
|
1.0
|
CE1
|
A:TYR388
|
4.0
|
36.3
|
1.0
|
N
|
A:ALA397
|
4.0
|
20.2
|
1.0
|
CA
|
A:ALA397
|
4.1
|
20.0
|
1.0
|
CA
|
A:SER396
|
4.2
|
22.7
|
1.0
|
SG
|
A:CYS350
|
4.2
|
16.8
|
1.0
|
CG2
|
A:ILE386
|
4.4
|
15.6
|
1.0
|
CD1
|
A:ILE291
|
4.4
|
26.9
|
1.0
|
CB
|
A:ILE386
|
4.5
|
16.9
|
1.0
|
CB
|
A:THR374
|
4.8
|
12.2
|
1.0
|
CG1
|
A:ILE386
|
4.9
|
18.3
|
1.0
|
CA
|
A:ALA400
|
4.9
|
21.3
|
1.0
|
N
|
A:ALA400
|
5.0
|
21.0
|
1.0
|
C
|
A:ALA397
|
5.0
|
20.7
|
1.0
|
|
Xenon binding site 8 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 8 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 8 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Xe1001
b:32.3
occ:0.13
|
SG
|
B:CYS468
|
3.3
|
21.7
|
1.0
|
CB
|
B:ALA580
|
3.4
|
14.3
|
1.0
|
CG2
|
B:THR602
|
3.5
|
8.9
|
1.0
|
N
|
B:ALA580
|
3.7
|
14.4
|
1.0
|
CD1
|
B:TRP595
|
3.9
|
11.6
|
1.0
|
CA
|
B:GLY592
|
3.9
|
13.8
|
1.0
|
O
|
B:HIS603
|
4.0
|
15.8
|
1.0
|
C
|
B:SER579
|
4.0
|
14.9
|
1.0
|
CA
|
B:ALA580
|
4.1
|
15.6
|
1.0
|
N
|
B:SER579
|
4.2
|
13.6
|
1.0
|
N
|
B:GLY592
|
4.3
|
14.9
|
1.0
|
CA
|
B:SER579
|
4.4
|
14.5
|
1.0
|
CG2
|
B:ILE591
|
4.4
|
12.9
|
1.0
|
CB
|
B:ALA578
|
4.5
|
10.9
|
1.0
|
O
|
B:SER579
|
4.5
|
15.0
|
1.0
|
C
|
B:ALA578
|
4.5
|
13.8
|
1.0
|
NE1
|
B:TRP595
|
4.5
|
10.7
|
1.0
|
O
|
B:ALA578
|
4.8
|
12.0
|
1.0
|
C
|
B:ILE591
|
4.8
|
15.1
|
1.0
|
CG
|
B:TRP595
|
4.8
|
10.0
|
1.0
|
CB
|
B:THR602
|
4.9
|
13.8
|
1.0
|
O
|
B:ILE591
|
5.0
|
17.5
|
1.0
|
|
Xenon binding site 9 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 9 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 9 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Xe1002
b:25.3
occ:1.00
|
CG
|
B:PRO608
|
3.7
|
16.5
|
1.0
|
CZ
|
B:PHE632
|
3.8
|
7.6
|
1.0
|
O
|
B:ALA589
|
3.8
|
12.9
|
1.0
|
OG1
|
B:THR593
|
3.9
|
16.5
|
1.0
|
CG2
|
B:VAL102
|
3.9
|
10.1
|
1.0
|
CB
|
B:PRO608
|
4.0
|
12.4
|
1.0
|
CB
|
B:ALA589
|
4.0
|
9.4
|
1.0
|
CA
|
B:ALA589
|
4.1
|
11.6
|
1.0
|
CE1
|
B:PHE632
|
4.2
|
5.0
|
1.0
|
C
|
B:ALA589
|
4.4
|
12.6
|
1.0
|
CE2
|
B:PHE632
|
4.5
|
7.5
|
1.0
|
CD1
|
B:ILE106
|
4.8
|
3.4
|
1.0
|
CG1
|
B:ILE106
|
4.9
|
6.8
|
1.0
|
|
Xenon binding site 10 out
of 42 in 2z8y
Go back to
Xenon Binding Sites List in 2z8y
Xenon binding site 10 out
of 42 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica
 Mono view
 Stereo pair view
|
A full contact list of Xenon with other atoms in the Xe binding
site number 10 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Xe1003
b:26.6
occ:0.56
|
XE
|
B:XE1003
|
0.0
|
26.6
|
0.6
|
XE
|
B:XE1003
|
2.7
|
25.7
|
0.3
|
CD1
|
B:ILE106
|
3.7
|
3.4
|
1.0
|
CD2
|
B:LEU620
|
3.7
|
18.5
|
1.0
|
CB
|
B:ALA234
|
4.1
|
12.7
|
1.0
|
CG2
|
B:THR593
|
4.1
|
10.1
|
1.0
|
OG1
|
B:THR593
|
4.3
|
16.5
|
1.0
|
CG1
|
B:VAL102
|
4.4
|
10.9
|
1.0
|
CD1
|
B:LEU620
|
4.4
|
14.0
|
1.0
|
XE
|
B:XE1004
|
4.5
|
29.9
|
0.9
|
CG1
|
B:VAL231
|
4.5
|
8.7
|
1.0
|
CG
|
B:LEU620
|
4.7
|
17.1
|
1.0
|
O
|
B:VAL231
|
4.9
|
13.7
|
1.0
|
CB
|
B:THR593
|
4.9
|
14.5
|
1.0
|
|
Reference:
T.I.Doukov,
L.C.Blasiak,
J.Seravalli,
S.W.Ragsdale,
C.L.Drennan.
Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase Biochemistry V. 47 3474 2008.
ISSN: ISSN 0006-2960
PubMed: 18293927
DOI: 10.1021/BI702386T
Page generated: Sat Oct 12 18:32:29 2024
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