Iron in PDB 2gc4: Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
Enzymatic activity of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
All present enzymatic activity of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.:
1.4.99.3;
Protein crystallography data
The structure of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution., PDB code: 2gc4
was solved by
Z.Chen,
R.Durley,
V.L.Davidson,
F.S.Mathews,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.95 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.368,
188.979,
128.836,
90.00,
99.74,
90.00
|
R / Rfree (%)
|
17.3 /
19.7
|
Other elements in 2gc4:
The structure of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution. also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
(pdb code 2gc4). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution., PDB code: 2gc4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2gc4
Go back to
Iron Binding Sites List in 2gc4
Iron binding site 1 out
of 4 in the Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe200
b:25.8
occ:1.00
|
FE
|
H:HEM200
|
0.0
|
25.8
|
1.0
|
ND
|
H:HEM200
|
2.0
|
32.8
|
1.0
|
NC
|
H:HEM200
|
2.0
|
31.2
|
1.0
|
NB
|
H:HEM200
|
2.0
|
28.0
|
1.0
|
NE2
|
H:HIS61
|
2.0
|
24.0
|
1.0
|
NA
|
H:HEM200
|
2.1
|
28.1
|
1.0
|
SD
|
H:MET101
|
2.3
|
30.7
|
1.0
|
C1C
|
H:HEM200
|
3.0
|
31.2
|
1.0
|
C4D
|
H:HEM200
|
3.1
|
31.4
|
1.0
|
C1B
|
H:HEM200
|
3.1
|
28.7
|
1.0
|
C4B
|
H:HEM200
|
3.1
|
28.5
|
1.0
|
C4C
|
H:HEM200
|
3.1
|
31.9
|
1.0
|
C1A
|
H:HEM200
|
3.1
|
29.7
|
1.0
|
CE1
|
H:HIS61
|
3.1
|
25.5
|
1.0
|
C1D
|
H:HEM200
|
3.1
|
33.4
|
1.0
|
C4A
|
H:HEM200
|
3.1
|
28.6
|
1.0
|
CD2
|
H:HIS61
|
3.1
|
25.1
|
1.0
|
CHB
|
H:HEM200
|
3.4
|
26.9
|
1.0
|
CHC
|
H:HEM200
|
3.4
|
28.9
|
1.0
|
CHA
|
H:HEM200
|
3.4
|
29.3
|
1.0
|
CHD
|
H:HEM200
|
3.4
|
31.0
|
1.0
|
CE
|
H:MET101
|
3.5
|
29.3
|
1.0
|
CG
|
H:MET101
|
3.5
|
32.2
|
1.0
|
CB
|
H:MET101
|
4.1
|
36.7
|
1.0
|
CG
|
H:HIS61
|
4.1
|
25.9
|
1.0
|
ND1
|
H:HIS61
|
4.3
|
25.4
|
1.0
|
C3B
|
H:HEM200
|
4.3
|
27.9
|
1.0
|
C3C
|
H:HEM200
|
4.3
|
31.7
|
1.0
|
C2C
|
H:HEM200
|
4.3
|
32.6
|
1.0
|
C2B
|
H:HEM200
|
4.3
|
27.7
|
1.0
|
C3D
|
H:HEM200
|
4.3
|
34.3
|
1.0
|
C3A
|
H:HEM200
|
4.3
|
28.1
|
1.0
|
C2D
|
H:HEM200
|
4.3
|
34.4
|
1.0
|
C2A
|
H:HEM200
|
4.3
|
29.3
|
1.0
|
CA
|
H:MET101
|
4.8
|
40.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 2gc4
Go back to
Iron Binding Sites List in 2gc4
Iron binding site 2 out
of 4 in the Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe200
b:24.4
occ:1.00
|
FE
|
L:HEM200
|
0.0
|
24.4
|
1.0
|
ND
|
L:HEM200
|
2.0
|
25.2
|
1.0
|
NC
|
L:HEM200
|
2.0
|
24.5
|
1.0
|
NB
|
L:HEM200
|
2.0
|
23.6
|
1.0
|
NA
|
L:HEM200
|
2.0
|
22.4
|
1.0
|
NE2
|
L:HIS61
|
2.1
|
19.9
|
1.0
|
SD
|
L:MET101
|
2.3
|
25.6
|
1.0
|
C4D
|
L:HEM200
|
3.0
|
26.0
|
1.0
|
C1D
|
L:HEM200
|
3.1
|
26.3
|
1.0
|
C1C
|
L:HEM200
|
3.1
|
25.6
|
1.0
|
CE1
|
L:HIS61
|
3.1
|
22.2
|
1.0
|
C4C
|
L:HEM200
|
3.1
|
25.9
|
1.0
|
C1B
|
L:HEM200
|
3.1
|
24.2
|
1.0
|
C4A
|
L:HEM200
|
3.1
|
23.2
|
1.0
|
C1A
|
L:HEM200
|
3.1
|
23.8
|
1.0
|
C4B
|
L:HEM200
|
3.1
|
24.3
|
1.0
|
CD2
|
L:HIS61
|
3.2
|
20.6
|
1.0
|
CHD
|
L:HEM200
|
3.4
|
25.8
|
1.0
|
CHB
|
L:HEM200
|
3.4
|
22.8
|
1.0
|
CHA
|
L:HEM200
|
3.4
|
21.6
|
1.0
|
CHC
|
L:HEM200
|
3.4
|
21.8
|
1.0
|
CG
|
L:MET101
|
3.5
|
25.4
|
1.0
|
CE
|
L:MET101
|
3.5
|
30.0
|
1.0
|
CB
|
L:MET101
|
4.1
|
28.7
|
1.0
|
CG
|
L:HIS61
|
4.2
|
23.5
|
1.0
|
ND1
|
L:HIS61
|
4.3
|
24.3
|
1.0
|
C3D
|
L:HEM200
|
4.3
|
27.7
|
1.0
|
C2D
|
L:HEM200
|
4.3
|
29.1
|
1.0
|
C3A
|
L:HEM200
|
4.3
|
22.9
|
1.0
|
C2A
|
L:HEM200
|
4.3
|
23.8
|
1.0
|
C3C
|
L:HEM200
|
4.3
|
25.9
|
1.0
|
C3B
|
L:HEM200
|
4.3
|
24.2
|
1.0
|
C2B
|
L:HEM200
|
4.3
|
23.5
|
1.0
|
C2C
|
L:HEM200
|
4.3
|
24.9
|
1.0
|
CA
|
L:MET101
|
4.8
|
28.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 2gc4
Go back to
Iron Binding Sites List in 2gc4
Iron binding site 3 out
of 4 in the Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:24.6
occ:1.00
|
FE
|
D:HEM200
|
0.0
|
24.6
|
1.0
|
ND
|
D:HEM200
|
2.0
|
25.1
|
1.0
|
NC
|
D:HEM200
|
2.0
|
25.4
|
1.0
|
NB
|
D:HEM200
|
2.0
|
23.7
|
1.0
|
NE2
|
D:HIS61
|
2.0
|
21.9
|
1.0
|
NA
|
D:HEM200
|
2.0
|
23.7
|
1.0
|
SD
|
D:MET101
|
2.3
|
25.0
|
1.0
|
CE1
|
D:HIS61
|
3.0
|
21.9
|
1.0
|
C4D
|
D:HEM200
|
3.0
|
25.5
|
1.0
|
C1D
|
D:HEM200
|
3.0
|
25.7
|
1.0
|
C1A
|
D:HEM200
|
3.0
|
21.9
|
1.0
|
C4C
|
D:HEM200
|
3.1
|
26.0
|
1.0
|
C1C
|
D:HEM200
|
3.1
|
26.8
|
1.0
|
C1B
|
D:HEM200
|
3.1
|
22.7
|
1.0
|
C4A
|
D:HEM200
|
3.1
|
22.3
|
1.0
|
C4B
|
D:HEM200
|
3.1
|
24.2
|
1.0
|
CD2
|
D:HIS61
|
3.2
|
22.2
|
1.0
|
CHA
|
D:HEM200
|
3.4
|
24.2
|
1.0
|
CHD
|
D:HEM200
|
3.4
|
27.1
|
1.0
|
CHB
|
D:HEM200
|
3.4
|
22.5
|
1.0
|
CHC
|
D:HEM200
|
3.4
|
23.6
|
1.0
|
CE
|
D:MET101
|
3.5
|
28.4
|
1.0
|
CG
|
D:MET101
|
3.5
|
25.9
|
1.0
|
CG
|
D:HIS61
|
4.1
|
23.0
|
1.0
|
CB
|
D:MET101
|
4.2
|
26.7
|
1.0
|
ND1
|
D:HIS61
|
4.2
|
20.1
|
1.0
|
C3D
|
D:HEM200
|
4.3
|
25.5
|
1.0
|
C2A
|
D:HEM200
|
4.3
|
23.6
|
1.0
|
C2D
|
D:HEM200
|
4.3
|
25.5
|
1.0
|
C3C
|
D:HEM200
|
4.3
|
26.6
|
1.0
|
C3A
|
D:HEM200
|
4.3
|
22.3
|
1.0
|
C3B
|
D:HEM200
|
4.3
|
22.0
|
1.0
|
C2B
|
D:HEM200
|
4.3
|
21.9
|
1.0
|
C2C
|
D:HEM200
|
4.3
|
25.3
|
1.0
|
CA
|
D:MET101
|
4.9
|
28.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 2gc4
Go back to
Iron Binding Sites List in 2gc4
Iron binding site 4 out
of 4 in the Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution.
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe200
b:26.2
occ:1.00
|
FE
|
P:HEM200
|
0.0
|
26.2
|
1.0
|
ND
|
P:HEM200
|
2.0
|
31.2
|
1.0
|
NC
|
P:HEM200
|
2.0
|
27.2
|
1.0
|
NE2
|
P:HIS61
|
2.0
|
26.0
|
1.0
|
NA
|
P:HEM200
|
2.0
|
27.4
|
1.0
|
NB
|
P:HEM200
|
2.0
|
24.5
|
1.0
|
SD
|
P:MET101
|
2.4
|
25.9
|
1.0
|
C4C
|
P:HEM200
|
3.0
|
28.6
|
1.0
|
C1C
|
P:HEM200
|
3.0
|
28.6
|
1.0
|
C4D
|
P:HEM200
|
3.1
|
29.3
|
1.0
|
CE1
|
P:HIS61
|
3.1
|
27.2
|
1.0
|
C1A
|
P:HEM200
|
3.1
|
26.4
|
1.0
|
C1D
|
P:HEM200
|
3.1
|
31.1
|
1.0
|
C1B
|
P:HEM200
|
3.1
|
24.3
|
1.0
|
C4A
|
P:HEM200
|
3.1
|
26.7
|
1.0
|
C4B
|
P:HEM200
|
3.1
|
26.4
|
1.0
|
CD2
|
P:HIS61
|
3.1
|
26.6
|
1.0
|
CHD
|
P:HEM200
|
3.4
|
32.0
|
1.0
|
CHA
|
P:HEM200
|
3.4
|
25.6
|
1.0
|
CHB
|
P:HEM200
|
3.4
|
26.0
|
1.0
|
CHC
|
P:HEM200
|
3.4
|
26.7
|
1.0
|
CE
|
P:MET101
|
3.5
|
31.3
|
1.0
|
CG
|
P:MET101
|
3.6
|
25.6
|
1.0
|
CG
|
P:HIS61
|
4.1
|
24.7
|
1.0
|
CB
|
P:MET101
|
4.2
|
24.9
|
1.0
|
ND1
|
P:HIS61
|
4.3
|
26.0
|
1.0
|
C3C
|
P:HEM200
|
4.3
|
30.1
|
1.0
|
C3B
|
P:HEM200
|
4.3
|
24.8
|
1.0
|
C3D
|
P:HEM200
|
4.3
|
29.1
|
1.0
|
C2A
|
P:HEM200
|
4.3
|
28.1
|
1.0
|
C2C
|
P:HEM200
|
4.3
|
29.0
|
1.0
|
C2B
|
P:HEM200
|
4.3
|
24.7
|
1.0
|
C3A
|
P:HEM200
|
4.3
|
27.6
|
1.0
|
C2D
|
P:HEM200
|
4.3
|
30.8
|
1.0
|
CA
|
P:MET101
|
4.9
|
30.8
|
1.0
|
|
Reference:
Z.Chen,
R.Durley,
V.L.Davidson,
F.S.Mathews.
Structural Comparison of the Oxidized Ternary Electron Transfer Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans with the Substrate-Reduced, Copper Free Complex at 1.9 A Resolution. To Be Published.
Page generated: Sat Aug 3 22:30:04 2024
|