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Sodium 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 (Fe) 4 atoms
Copper (Cu) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2gc4

Go back to Sodium Binding Sites List in 2gc4
Sodium 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 Sodium with other atoms in the Na 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
L:Na601

b:23.4
occ:1.00
 O L:TYR77 2.5 31.6 1.0
O L:HOH1513 2.6 38.5 1.0
OD2 L:ASP75 2.6 31.1 1.0
O L:HOH1056 2.8 29.3 1.0
O L:GLY72 2.8 26.8 1.0
OE2 K:GLU31 3.0 35.9 1.0
O K:HOH1945 3.2 47.2 1.0
CD K:GLU31 3.5 32.0 1.0
CG L:ASP75 3.5 33.1 1.0
C L:GLY72 3.6 25.3 1.0
C L:TYR77 3.7 30.2 1.0
OE1 K:GLU31 3.8 30.9 1.0
OD1 L:ASP75 3.9 31.9 1.0
N L:LEU73 4.3 24.1 1.0
CA L:LEU73 4.3 23.3 1.0
CA L:TYR77 4.4 29.1 1.0
CB L:TYR77 4.4 31.2 1.0
O L:ASP75 4.4 32.3 1.0
N L:TYR77 4.4 31.4 1.0
CA L:GLY72 4.5 23.7 1.0
N L:ASP75 4.5 30.3 1.0
CD2 L:TYR77 4.5 32.0 1.0
CG K:GLU31 4.5 29.1 1.0
N L:TRP78 4.7 28.0 1.0
N L:GLY72 4.7 23.8 1.0
N L:ASN74 4.8 28.2 1.0
C L:LEU73 4.8 27.2 1.0
CB L:ASP75 4.8 32.1 1.0
C L:ASP75 4.8 32.0 1.0
CA L:ASP75 4.9 31.2 1.0
CA L:TRP78 4.9 28.4 1.0
O L:HOH1752 4.9 38.7 1.0
O2A L:HEM200 5.0 29.9 1.0
CG L:TYR77 5.0 30.8 1.0

Sodium binding site 2 out of 4 in 2gc4

Go back to Sodium Binding Sites List in 2gc4
Sodium 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 Sodium with other atoms in the Na 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
P:Na602

b:28.7
occ:1.00
 O P:TYR77 2.6 36.0 1.0
O P:HOH2138 2.7 51.4 1.0
O P:GLY72 2.8 29.4 1.0
OD2 P:ASP75 2.8 43.6 1.0
O P:HOH1246 2.9 32.0 1.0
O P:HOH1495 3.0 37.5 1.0
OE2 O:GLU31 3.2 40.9 1.0
C P:GLY72 3.6 29.7 1.0
CD O:GLU31 3.6 37.7 1.0
CG P:ASP75 3.6 39.8 1.0
C P:TYR77 3.7 36.2 1.0
OE1 O:GLU31 3.8 38.2 1.0
OD1 P:ASP75 3.9 40.2 1.0
N P:LEU73 4.2 27.8 1.0
CA P:LEU73 4.3 29.6 1.0
CD2 P:TYR77 4.4 38.0 1.0
CB P:TYR77 4.4 36.9 1.0
CA P:GLY72 4.4 28.5 1.0
CA P:TYR77 4.4 36.4 1.0
O P:ASP75 4.5 39.7 1.0
N P:ASP75 4.5 36.6 1.0
N P:TYR77 4.5 36.3 1.0
CG O:GLU31 4.6 35.9 1.0
N P:GLY72 4.7 30.2 1.0
N P:ASN74 4.7 30.5 1.0
C P:LEU73 4.7 30.2 1.0
N P:TRP78 4.8 34.8 1.0
CB P:ASP75 4.8 40.5 1.0
C P:ASP75 4.8 39.8 1.0
CG P:TYR77 4.9 36.4 1.0
CA P:ASP75 4.9 39.6 1.0
O2A P:HEM200 4.9 31.1 1.0
CA P:TRP78 5.0 35.1 1.0

Sodium binding site 3 out of 4 in 2gc4

Go back to Sodium Binding Sites List in 2gc4
Sodium 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 Sodium with other atoms in the Na 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
H:Na603

b:27.6
occ:1.00
 OD2 H:ASP75 2.6 30.6 1.0
O H:TYR77 2.6 36.9 1.0
O H:HOH1763 2.7 36.5 1.0
O H:GLY72 2.9 27.9 1.0
O H:HOH1083 2.9 28.1 1.0
O H:HOH1553 3.0 39.0 1.0
OE2 G:GLU31 3.0 34.5 1.0
CG H:ASP75 3.5 33.2 1.0
CD G:GLU31 3.5 33.3 1.0
C H:GLY72 3.6 29.2 1.0
OE1 G:GLU31 3.7 34.2 1.0
C H:TYR77 3.8 36.3 1.0
OD1 H:ASP75 3.8 31.0 1.0
N H:LEU73 4.2 27.4 1.0
CA H:LEU73 4.3 28.9 1.0
N H:ASP75 4.4 34.1 1.0
O H:ASP75 4.4 34.6 1.0
CA H:GLY72 4.4 29.8 1.0
CG G:GLU31 4.5 29.0 1.0
CA H:TYR77 4.5 36.7 1.0
N H:TYR77 4.5 36.2 1.0
CB H:TYR77 4.6 36.2 1.0
CD2 H:TYR77 4.6 39.6 1.0
CB H:ASP75 4.7 31.9 1.0
N H:ASN74 4.7 31.1 1.0
C H:LEU73 4.7 30.4 1.0
N H:GLY72 4.7 29.4 1.0
C H:ASP75 4.8 35.3 1.0
N H:TRP78 4.8 34.9 1.0
CA H:ASP75 4.8 34.5 1.0
O2A H:HEM200 4.9 31.7 1.0
O H:HOH1710 4.9 44.9 1.0
CB G:GLU31 5.0 27.4 1.0

Sodium binding site 4 out of 4 in 2gc4

Go back to Sodium Binding Sites List in 2gc4
Sodium 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 Sodium with other atoms in the Na 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
D:Na604

b:32.3
occ:1.00
 O D:HOH2140 2.0 53.5 1.0
O C:HOH2139 2.0 55.7 1.0
O D:TYR77 2.5 30.0 1.0
OD2 D:ASP75 2.6 32.0 1.0
O D:HOH1001 2.7 23.6 1.0
O D:HOH2053 2.9 49.8 1.0
O D:GLY72 3.2 28.2 1.0
O D:HOH1172 3.3 31.3 1.0
CG D:ASP75 3.5 32.7 1.0
C D:TYR77 3.6 30.3 1.0
OE2 C:GLU31 3.7 37.9 1.0
OE1 C:GLU31 3.8 33.0 1.0
CD C:GLU31 3.8 34.0 1.0
C D:GLY72 3.9 26.8 1.0
OD1 D:ASP75 3.9 31.6 1.0
CB D:TYR77 4.2 30.3 1.0
O D:ASP75 4.2 32.8 1.0
CA D:TYR77 4.2 31.0 1.0
CD2 D:TYR77 4.2 31.6 1.0
N D:TYR77 4.3 32.3 1.0
CA D:LEU73 4.3 25.4 1.0
N D:ASP75 4.4 29.4 1.0
N D:LEU73 4.4 26.6 1.0
N D:TRP78 4.6 30.2 1.0
C D:ASP75 4.6 32.2 1.0
C D:LEU73 4.7 27.9 1.0
CG D:TYR77 4.7 31.2 1.0
N D:ASN74 4.7 27.8 1.0
CG C:GLU31 4.7 32.4 1.0
CB D:ASP75 4.8 30.0 1.0
CA D:GLY72 4.8 26.6 1.0
CA D:ASP75 4.8 31.2 1.0
CA D:TRP78 4.9 28.7 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: Mon Oct 7 02:33:19 2024

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