Iron in PDB 2gc7: Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
Enzymatic activity of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
All present enzymatic activity of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.:
1.4.99.3;
Protein crystallography data
The structure of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans., PDB code: 2gc7
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)
|
29.94 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.323,
189.127,
128.906,
90.00,
99.75,
90.00
|
R / Rfree (%)
|
17.1 /
19.8
|
Other elements in 2gc7:
The structure of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans. also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
(pdb code 2gc7). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans., PDB code: 2gc7:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2gc7
Go back to
Iron Binding Sites List in 2gc7
Iron binding site 1 out
of 4 in the Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:21.4
occ:1.00
|
FE
|
D:HEM200
|
0.0
|
21.4
|
1.0
|
ND
|
D:HEM200
|
2.0
|
20.8
|
1.0
|
NC
|
D:HEM200
|
2.0
|
20.8
|
1.0
|
NB
|
D:HEM200
|
2.0
|
19.2
|
1.0
|
NE2
|
D:HIS61
|
2.0
|
21.6
|
1.0
|
NA
|
D:HEM200
|
2.0
|
21.5
|
1.0
|
SD
|
D:MET101
|
2.3
|
21.0
|
1.0
|
CE1
|
D:HIS61
|
3.0
|
19.4
|
1.0
|
C4D
|
D:HEM200
|
3.0
|
20.7
|
1.0
|
C1C
|
D:HEM200
|
3.0
|
22.3
|
1.0
|
C4C
|
D:HEM200
|
3.0
|
23.0
|
1.0
|
C1D
|
D:HEM200
|
3.0
|
21.5
|
1.0
|
C1A
|
D:HEM200
|
3.1
|
19.8
|
1.0
|
C1B
|
D:HEM200
|
3.1
|
18.3
|
1.0
|
C4B
|
D:HEM200
|
3.1
|
22.5
|
1.0
|
C4A
|
D:HEM200
|
3.1
|
22.1
|
1.0
|
CD2
|
D:HIS61
|
3.1
|
21.7
|
1.0
|
CHA
|
D:HEM200
|
3.4
|
19.1
|
1.0
|
CHD
|
D:HEM200
|
3.4
|
22.3
|
1.0
|
CHC
|
D:HEM200
|
3.4
|
20.5
|
1.0
|
CHB
|
D:HEM200
|
3.4
|
17.7
|
1.0
|
CE
|
D:MET101
|
3.5
|
23.7
|
1.0
|
CG
|
D:MET101
|
3.5
|
22.8
|
1.0
|
CG
|
D:HIS61
|
4.1
|
22.5
|
1.0
|
CB
|
D:MET101
|
4.2
|
24.6
|
1.0
|
ND1
|
D:HIS61
|
4.2
|
20.5
|
1.0
|
C3C
|
D:HEM200
|
4.3
|
23.8
|
1.0
|
C3D
|
D:HEM200
|
4.3
|
20.6
|
1.0
|
C2D
|
D:HEM200
|
4.3
|
20.4
|
1.0
|
C2C
|
D:HEM200
|
4.3
|
21.4
|
1.0
|
C2A
|
D:HEM200
|
4.3
|
20.1
|
1.0
|
C3B
|
D:HEM200
|
4.3
|
18.5
|
1.0
|
C3A
|
D:HEM200
|
4.3
|
20.6
|
1.0
|
C2B
|
D:HEM200
|
4.3
|
20.2
|
1.0
|
CA
|
D:MET101
|
4.9
|
25.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 2gc7
Go back to
Iron Binding Sites List in 2gc7
Iron binding site 2 out
of 4 in the Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe200
b:23.8
occ:1.00
|
FE
|
H:HEM200
|
0.0
|
23.8
|
1.0
|
NC
|
H:HEM200
|
2.0
|
28.4
|
1.0
|
ND
|
H:HEM200
|
2.0
|
29.7
|
1.0
|
NB
|
H:HEM200
|
2.0
|
25.1
|
1.0
|
NE2
|
H:HIS61
|
2.0
|
20.9
|
1.0
|
NA
|
H:HEM200
|
2.1
|
24.3
|
1.0
|
SD
|
H:MET101
|
2.3
|
25.6
|
1.0
|
C1C
|
H:HEM200
|
3.0
|
29.1
|
1.0
|
C4C
|
H:HEM200
|
3.1
|
28.5
|
1.0
|
C4B
|
H:HEM200
|
3.1
|
26.8
|
1.0
|
C4D
|
H:HEM200
|
3.1
|
28.5
|
1.0
|
C1B
|
H:HEM200
|
3.1
|
26.1
|
1.0
|
CE1
|
H:HIS61
|
3.1
|
21.7
|
1.0
|
C1D
|
H:HEM200
|
3.1
|
28.8
|
1.0
|
CD2
|
H:HIS61
|
3.1
|
21.0
|
1.0
|
C1A
|
H:HEM200
|
3.1
|
26.7
|
1.0
|
C4A
|
H:HEM200
|
3.1
|
25.7
|
1.0
|
CHC
|
H:HEM200
|
3.4
|
26.6
|
1.0
|
CHD
|
H:HEM200
|
3.4
|
27.7
|
1.0
|
CHA
|
H:HEM200
|
3.4
|
26.0
|
1.0
|
CHB
|
H:HEM200
|
3.4
|
24.0
|
1.0
|
CE
|
H:MET101
|
3.5
|
27.3
|
1.0
|
CG
|
H:MET101
|
3.5
|
30.4
|
1.0
|
CB
|
H:MET101
|
4.1
|
33.5
|
1.0
|
CG
|
H:HIS61
|
4.1
|
24.5
|
1.0
|
ND1
|
H:HIS61
|
4.3
|
22.5
|
1.0
|
C3B
|
H:HEM200
|
4.3
|
25.8
|
1.0
|
C2C
|
H:HEM200
|
4.3
|
29.3
|
1.0
|
C3C
|
H:HEM200
|
4.3
|
27.4
|
1.0
|
C3D
|
H:HEM200
|
4.3
|
30.5
|
1.0
|
C2B
|
H:HEM200
|
4.3
|
27.7
|
1.0
|
C2D
|
H:HEM200
|
4.3
|
31.2
|
1.0
|
C3A
|
H:HEM200
|
4.4
|
26.2
|
1.0
|
C2A
|
H:HEM200
|
4.4
|
27.2
|
1.0
|
CA
|
H:MET101
|
4.7
|
36.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 2gc7
Go back to
Iron Binding Sites List in 2gc7
Iron binding site 3 out
of 4 in the Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe200
b:22.3
occ:1.00
|
FE
|
L:HEM200
|
0.0
|
22.3
|
1.0
|
ND
|
L:HEM200
|
2.0
|
22.8
|
1.0
|
NC
|
L:HEM200
|
2.0
|
20.6
|
1.0
|
NB
|
L:HEM200
|
2.0
|
21.5
|
1.0
|
NA
|
L:HEM200
|
2.0
|
19.3
|
1.0
|
NE2
|
L:HIS61
|
2.1
|
20.0
|
1.0
|
SD
|
L:MET101
|
2.3
|
22.2
|
1.0
|
C4D
|
L:HEM200
|
3.0
|
23.5
|
1.0
|
CE1
|
L:HIS61
|
3.0
|
18.1
|
1.0
|
C4C
|
L:HEM200
|
3.0
|
23.2
|
1.0
|
C1B
|
L:HEM200
|
3.0
|
21.6
|
1.0
|
C1C
|
L:HEM200
|
3.1
|
21.2
|
1.0
|
C1D
|
L:HEM200
|
3.1
|
23.9
|
1.0
|
C1A
|
L:HEM200
|
3.1
|
20.4
|
1.0
|
C4A
|
L:HEM200
|
3.1
|
19.8
|
1.0
|
C4B
|
L:HEM200
|
3.1
|
20.5
|
1.0
|
CD2
|
L:HIS61
|
3.1
|
20.0
|
1.0
|
CHD
|
L:HEM200
|
3.4
|
23.2
|
1.0
|
CHB
|
L:HEM200
|
3.4
|
20.1
|
1.0
|
CHA
|
L:HEM200
|
3.4
|
17.8
|
1.0
|
CHC
|
L:HEM200
|
3.4
|
17.8
|
1.0
|
CE
|
L:MET101
|
3.5
|
25.0
|
1.0
|
CG
|
L:MET101
|
3.5
|
21.3
|
1.0
|
CB
|
L:MET101
|
4.1
|
24.9
|
1.0
|
CG
|
L:HIS61
|
4.2
|
21.0
|
1.0
|
ND1
|
L:HIS61
|
4.2
|
21.5
|
1.0
|
C3D
|
L:HEM200
|
4.3
|
21.1
|
1.0
|
C2D
|
L:HEM200
|
4.3
|
24.3
|
1.0
|
C3C
|
L:HEM200
|
4.3
|
22.3
|
1.0
|
C2A
|
L:HEM200
|
4.3
|
21.8
|
1.0
|
C3B
|
L:HEM200
|
4.3
|
21.4
|
1.0
|
C2B
|
L:HEM200
|
4.3
|
21.4
|
1.0
|
C3A
|
L:HEM200
|
4.3
|
20.0
|
1.0
|
C2C
|
L:HEM200
|
4.3
|
20.7
|
1.0
|
CA
|
L:MET101
|
4.8
|
25.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 2gc7
Go back to
Iron Binding Sites List in 2gc7
Iron binding site 4 out
of 4 in the Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe200
b:23.0
occ:1.00
|
FE
|
P:HEM200
|
0.0
|
23.0
|
1.0
|
ND
|
P:HEM200
|
2.0
|
26.3
|
1.0
|
NC
|
P:HEM200
|
2.0
|
25.3
|
1.0
|
NE2
|
P:HIS61
|
2.0
|
21.7
|
1.0
|
NB
|
P:HEM200
|
2.1
|
22.4
|
1.0
|
NA
|
P:HEM200
|
2.1
|
24.6
|
1.0
|
SD
|
P:MET101
|
2.4
|
23.5
|
1.0
|
C4D
|
P:HEM200
|
3.0
|
27.1
|
1.0
|
C4C
|
P:HEM200
|
3.0
|
24.3
|
1.0
|
C1C
|
P:HEM200
|
3.0
|
26.0
|
1.0
|
CE1
|
P:HIS61
|
3.1
|
22.0
|
1.0
|
C1D
|
P:HEM200
|
3.1
|
27.9
|
1.0
|
C1A
|
P:HEM200
|
3.1
|
25.9
|
1.0
|
C1B
|
P:HEM200
|
3.1
|
22.8
|
1.0
|
C4A
|
P:HEM200
|
3.1
|
25.6
|
1.0
|
C4B
|
P:HEM200
|
3.1
|
23.8
|
1.0
|
CD2
|
P:HIS61
|
3.1
|
21.6
|
1.0
|
CHD
|
P:HEM200
|
3.4
|
27.3
|
1.0
|
CHA
|
P:HEM200
|
3.4
|
22.9
|
1.0
|
CHB
|
P:HEM200
|
3.4
|
23.9
|
1.0
|
CHC
|
P:HEM200
|
3.4
|
23.0
|
1.0
|
CE
|
P:MET101
|
3.5
|
26.7
|
1.0
|
CG
|
P:MET101
|
3.6
|
24.6
|
1.0
|
CG
|
P:HIS61
|
4.1
|
20.7
|
1.0
|
CB
|
P:MET101
|
4.2
|
23.1
|
1.0
|
ND1
|
P:HIS61
|
4.3
|
22.0
|
1.0
|
C3D
|
P:HEM200
|
4.3
|
26.2
|
1.0
|
C3C
|
P:HEM200
|
4.3
|
26.5
|
1.0
|
C2D
|
P:HEM200
|
4.3
|
27.8
|
1.0
|
C3B
|
P:HEM200
|
4.3
|
21.8
|
1.0
|
C2B
|
P:HEM200
|
4.3
|
23.6
|
1.0
|
C2A
|
P:HEM200
|
4.3
|
26.4
|
1.0
|
C2C
|
P:HEM200
|
4.3
|
25.3
|
1.0
|
C3A
|
P:HEM200
|
4.3
|
27.5
|
1.0
|
CA
|
P:MET101
|
4.9
|
28.6
|
1.0
|
|
Reference:
Z.Chen,
R.Durley,
V.L.Davidson,
F.S.Mathews.
Structral 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 22:30:05 2024
|