Zinc in PDB 8rja: Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
Enzymatic activity of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
All present enzymatic activity of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum:
1.2.7.12;
1.6.5.11;
3.5.2.5;
Protein crystallography data
The structure of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja
was solved by
O.N.Lemaire,
T.Wagner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
57.38 /
1.97
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.627,
135.636,
149.902,
90,
90.49,
90
|
R / Rfree (%)
|
17.6 /
21
|
Other elements in 8rja:
The structure of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
(pdb code 8rja). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8rja
Go back to
Zinc Binding Sites List in 8rja
Zinc binding site 1 out
of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:42.7
occ:1.00
|
OD1
|
A:ASP383
|
2.1
|
19.2
|
1.0
|
NE2
|
A:HIS60
|
2.3
|
19.0
|
1.0
|
NE2
|
A:HIS58
|
2.3
|
19.0
|
1.0
|
OQ1
|
A:KCX180
|
2.8
|
31.3
|
1.0
|
CG
|
A:ASP383
|
3.1
|
17.1
|
1.0
|
ZN
|
A:ZN602
|
3.1
|
33.6
|
1.0
|
CE1
|
A:HIS60
|
3.2
|
18.7
|
1.0
|
CD2
|
A:HIS58
|
3.3
|
18.4
|
1.0
|
OD2
|
A:ASP383
|
3.3
|
24.2
|
1.0
|
CD2
|
A:HIS60
|
3.4
|
18.5
|
1.0
|
CE1
|
A:HIS58
|
3.4
|
18.1
|
1.0
|
CX
|
A:KCX180
|
3.5
|
28.1
|
1.0
|
OQ2
|
A:KCX180
|
3.5
|
26.0
|
1.0
|
CD2
|
A:HIS269
|
3.8
|
17.4
|
1.0
|
CB
|
A:ALA117
|
4.1
|
21.7
|
1.0
|
ND2
|
A:ASN386
|
4.1
|
16.0
|
1.0
|
NE2
|
A:HIS269
|
4.2
|
18.8
|
1.0
|
ND1
|
A:HIS60
|
4.3
|
19.6
|
1.0
|
CG
|
A:HIS60
|
4.4
|
17.9
|
1.0
|
CB
|
A:ASP383
|
4.5
|
18.3
|
1.0
|
CG
|
A:HIS58
|
4.5
|
17.0
|
1.0
|
ND1
|
A:HIS58
|
4.5
|
19.3
|
1.0
|
O
|
A:HOH991
|
4.5
|
29.9
|
1.0
|
NZ
|
A:KCX180
|
4.5
|
21.0
|
1.0
|
O
|
A:HOH711
|
4.7
|
19.4
|
1.0
|
O
|
A:MET315
|
4.8
|
20.5
|
1.0
|
CA
|
A:ASP383
|
4.9
|
14.8
|
1.0
|
O
|
A:ASP383
|
4.9
|
14.9
|
1.0
|
CG
|
A:ASN386
|
4.9
|
17.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8rja
Go back to
Zinc Binding Sites List in 8rja
Zinc binding site 2 out
of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn602
b:33.6
occ:1.00
|
OQ2
|
A:KCX180
|
2.2
|
26.0
|
1.0
|
NE2
|
A:HIS269
|
2.3
|
18.8
|
1.0
|
ND1
|
A:HIS233
|
2.5
|
19.7
|
1.0
|
O
|
A:HOH991
|
2.9
|
29.9
|
1.0
|
CX
|
A:KCX180
|
3.0
|
28.1
|
1.0
|
CD2
|
A:HIS269
|
3.1
|
17.4
|
1.0
|
OQ1
|
A:KCX180
|
3.1
|
31.3
|
1.0
|
ZN
|
A:ZN601
|
3.1
|
42.7
|
1.0
|
CE1
|
A:HIS233
|
3.3
|
19.8
|
1.0
|
CE1
|
A:HIS269
|
3.4
|
18.1
|
1.0
|
CG
|
A:HIS233
|
3.5
|
21.1
|
1.0
|
OG1
|
A:THR316
|
3.7
|
28.2
|
1.0
|
CB
|
A:HIS233
|
3.8
|
18.5
|
1.0
|
O
|
A:HOH711
|
4.1
|
19.4
|
1.0
|
OD2
|
A:ASP383
|
4.2
|
24.2
|
1.0
|
CG
|
A:HIS269
|
4.3
|
17.0
|
1.0
|
NZ
|
A:KCX180
|
4.3
|
21.0
|
1.0
|
CB
|
A:THR316
|
4.3
|
19.1
|
1.0
|
ND1
|
A:HIS269
|
4.4
|
18.2
|
1.0
|
NE2
|
A:HIS58
|
4.5
|
19.0
|
1.0
|
NE2
|
A:HIS233
|
4.5
|
19.8
|
1.0
|
OD1
|
A:ASP383
|
4.5
|
19.2
|
1.0
|
CG2
|
A:THR268
|
4.6
|
15.5
|
1.0
|
CD2
|
A:HIS233
|
4.6
|
19.7
|
1.0
|
CG
|
A:ASP383
|
4.7
|
17.1
|
1.0
|
CE1
|
A:HIS58
|
4.8
|
18.1
|
1.0
|
NE2
|
A:HIS60
|
4.8
|
19.0
|
1.0
|
CG2
|
A:VAL182
|
4.9
|
18.7
|
1.0
|
CE
|
A:KCX180
|
5.0
|
14.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8rja
Go back to
Zinc Binding Sites List in 8rja
Zinc binding site 3 out
of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn601
b:42.7
occ:1.00
|
NE2
|
G:HIS60
|
2.3
|
22.7
|
1.0
|
NE2
|
G:HIS58
|
2.3
|
22.7
|
1.0
|
OD1
|
G:ASP383
|
2.4
|
20.2
|
1.0
|
OQ2
|
G:KCX180
|
2.6
|
21.4
|
1.0
|
CE1
|
G:HIS60
|
3.0
|
22.1
|
1.0
|
ZN
|
G:ZN602
|
3.2
|
33.2
|
1.0
|
CE1
|
G:HIS58
|
3.2
|
21.2
|
1.0
|
CX
|
G:KCX180
|
3.2
|
26.9
|
1.0
|
CD2
|
G:HIS58
|
3.3
|
16.6
|
1.0
|
CG
|
G:ASP383
|
3.3
|
22.1
|
1.0
|
CD2
|
G:HIS60
|
3.4
|
21.1
|
1.0
|
OQ1
|
G:KCX180
|
3.4
|
27.4
|
1.0
|
OD2
|
G:ASP383
|
3.6
|
22.7
|
1.0
|
CD2
|
G:HIS269
|
3.9
|
16.9
|
1.0
|
CB
|
G:ALA117
|
3.9
|
20.2
|
1.0
|
ND1
|
G:HIS60
|
4.2
|
19.5
|
1.0
|
NE2
|
G:HIS269
|
4.2
|
18.5
|
1.0
|
NZ
|
G:KCX180
|
4.3
|
20.6
|
1.0
|
ND2
|
G:ASN386
|
4.3
|
14.0
|
1.0
|
CG
|
G:HIS60
|
4.4
|
17.4
|
1.0
|
ND1
|
G:HIS58
|
4.4
|
19.5
|
1.0
|
CG
|
G:HIS58
|
4.4
|
18.6
|
1.0
|
O
|
G:HOH709
|
4.5
|
15.9
|
1.0
|
CB
|
G:ASP383
|
4.7
|
15.5
|
1.0
|
O
|
G:MET315
|
4.9
|
18.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8rja
Go back to
Zinc Binding Sites List in 8rja
Zinc binding site 4 out
of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn602
b:33.2
occ:1.00
|
OQ1
|
G:KCX180
|
2.1
|
27.4
|
1.0
|
NE2
|
G:HIS269
|
2.4
|
18.5
|
1.0
|
ND1
|
G:HIS233
|
2.4
|
14.6
|
1.0
|
CX
|
G:KCX180
|
3.0
|
26.9
|
1.0
|
OQ2
|
G:KCX180
|
3.1
|
21.4
|
1.0
|
ZN
|
G:ZN601
|
3.2
|
42.7
|
1.0
|
CD2
|
G:HIS269
|
3.2
|
16.9
|
1.0
|
CE1
|
G:HIS233
|
3.3
|
16.2
|
1.0
|
CE1
|
G:HIS269
|
3.4
|
14.6
|
1.0
|
CG
|
G:HIS233
|
3.5
|
16.7
|
1.0
|
OG1
|
G:THR316
|
3.7
|
25.6
|
1.0
|
CB
|
G:HIS233
|
3.7
|
18.7
|
1.0
|
O
|
G:HOH709
|
3.8
|
15.9
|
1.0
|
NZ
|
G:KCX180
|
4.3
|
20.6
|
1.0
|
CG
|
G:HIS269
|
4.3
|
14.5
|
1.0
|
OD2
|
G:ASP383
|
4.3
|
22.7
|
1.0
|
CB
|
G:THR316
|
4.3
|
19.9
|
1.0
|
ND1
|
G:HIS269
|
4.4
|
12.4
|
1.0
|
NE2
|
G:HIS233
|
4.5
|
16.8
|
1.0
|
NE2
|
G:HIS58
|
4.5
|
22.7
|
1.0
|
CD2
|
G:HIS233
|
4.6
|
14.9
|
1.0
|
CG2
|
G:THR268
|
4.6
|
18.8
|
1.0
|
OD1
|
G:ASP383
|
4.6
|
20.2
|
1.0
|
CE1
|
G:HIS58
|
4.8
|
21.2
|
1.0
|
CG2
|
G:VAL182
|
4.8
|
17.5
|
1.0
|
NE2
|
G:HIS60
|
4.9
|
22.7
|
1.0
|
CG
|
G:ASP383
|
4.9
|
22.1
|
1.0
|
CE
|
G:KCX180
|
4.9
|
14.4
|
1.0
|
|
Reference:
O.N.Lemaire,
G.Wegener,
T.Wagner.
F420 Reduction As A Cellular Driver For Anaerobic Ethanotrophy To Be Published.
Page generated: Thu Oct 31 10:31:24 2024
|