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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:

Copper (Cu) 4 atoms
Sodium (Na) 4 atoms

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: Sun Dec 13 14:45:11 2020

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