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Sodium 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 (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Substrate Reduced, Copper Free Complex of Methylamine Dehydrogenase, Amicyanin and Cytochrome C551I From Paracoccus Denitrificans., PDB code: 2gc7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2gc7

Go back to Sodium Binding Sites List in 2gc7
Sodium 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 Sodium with other atoms in the Na 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:Na602

b:28.6
occ:1.00
 O D:HOH2229 2.0 78.6 1.0
O C:HOH2228 2.0 65.5 1.0
O D:TYR77 2.5 28.6 1.0
OD2 D:ASP75 2.7 27.3 1.0
O D:HOH2007 2.8 46.3 1.0
O D:HOH1003 2.9 18.0 1.0
O D:GLY72 3.1 24.6 1.0
O D:HOH1298 3.1 31.8 1.0
OE2 C:GLU31 3.5 36.4 1.0
CG D:ASP75 3.6 28.2 1.0
C D:TYR77 3.6 28.3 1.0
OE1 C:GLU31 3.7 30.7 1.0
CD C:GLU31 3.7 31.1 1.0
C D:GLY72 3.9 25.1 1.0
OD1 D:ASP75 3.9 27.3 1.0
CD2 D:TYR77 4.1 28.8 1.0
CB D:TYR77 4.1 26.2 1.0
CA D:TYR77 4.2 28.6 1.0
O D:ASP75 4.2 28.7 1.0
N D:TYR77 4.3 30.0 1.0
CA D:LEU73 4.4 22.7 1.0
N D:LEU73 4.4 25.2 1.0
N D:ASP75 4.4 27.0 1.0
CG C:GLU31 4.6 29.6 1.0
N D:TRP78 4.6 26.1 1.0
CG D:TYR77 4.6 28.1 1.0
C D:ASP75 4.7 29.9 1.0
CA D:GLY72 4.7 24.5 1.0
C D:LEU73 4.7 24.7 1.0
CB D:ASP75 4.8 28.1 1.0
N D:ASN74 4.8 25.0 1.0
CA D:ASP75 4.8 28.6 1.0
CA D:TRP78 4.9 26.5 1.0
O2A D:HEM200 4.9 30.1 1.0

Sodium binding site 2 out of 4 in 2gc7

Go back to Sodium Binding Sites List in 2gc7
Sodium 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 Sodium with other atoms in the Na 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:Na604

b:24.1
occ:1.00
 OD2 H:ASP75 2.5 27.0 1.0
O H:HOH1595 2.6 36.2 1.0
O H:TYR77 2.6 32.1 1.0
O G:HOH1641 2.9 32.5 1.0
O H:HOH1084 2.9 25.1 1.0
O H:GLY72 3.0 27.5 1.0
OE2 G:GLU31 3.0 31.5 1.0
CG H:ASP75 3.4 29.3 1.0
CD G:GLU31 3.5 30.8 1.0
C H:GLY72 3.7 28.4 1.0
OE1 G:GLU31 3.7 31.0 1.0
C H:TYR77 3.8 31.1 1.0
OD1 H:ASP75 3.8 25.9 1.0
N H:LEU73 4.3 26.1 1.0
N H:ASP75 4.3 31.2 1.0
CA H:LEU73 4.3 27.5 1.0
O H:ASP75 4.4 31.7 1.0
CA H:TYR77 4.5 32.6 1.0
CA H:GLY72 4.5 28.7 1.0
N H:TYR77 4.5 33.3 1.0
CG G:GLU31 4.5 27.2 1.0
CB H:TYR77 4.5 33.3 1.0
CB H:ASP75 4.6 28.0 1.0
CD2 H:TYR77 4.7 36.2 1.0
N H:ASN74 4.7 29.1 1.0
C H:ASP75 4.7 32.4 1.0
C H:LEU73 4.7 28.1 1.0
O H:HOH1812 4.7 41.9 1.0
CA H:ASP75 4.7 31.6 1.0
N H:GLY72 4.8 26.7 1.0
N H:TRP78 4.8 29.8 1.0
O2A H:HEM200 5.0 30.0 1.0
CA H:TRP78 5.0 30.1 1.0

Sodium binding site 3 out of 4 in 2gc7

Go back to Sodium Binding Sites List in 2gc7
Sodium 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 Sodium with other atoms in the Na 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:Na601

b:21.9
occ:1.00
 O L:TYR77 2.5 28.7 1.0
O L:HOH1475 2.6 32.9 1.0
OD2 L:ASP75 2.6 25.5 1.0
O L:HOH1051 2.7 23.1 1.0
O L:GLY72 2.8 24.6 1.0
OE2 K:GLU31 2.9 30.1 1.0
O L:HOH1839 3.2 46.6 1.0
CD K:GLU31 3.5 27.3 1.0
CG L:ASP75 3.5 30.4 1.0
C L:GLY72 3.7 22.9 1.0
C L:TYR77 3.7 28.5 1.0
OE1 K:GLU31 3.7 26.9 1.0
OD1 L:ASP75 3.9 26.2 1.0
N L:LEU73 4.3 22.3 1.0
CA L:LEU73 4.4 23.4 1.0
CA L:TYR77 4.4 27.6 1.0
O L:ASP75 4.5 29.1 1.0
N L:ASP75 4.5 28.7 1.0
N L:TYR77 4.5 29.6 1.0
CG K:GLU31 4.5 24.3 1.0
CB L:TYR77 4.5 29.1 1.0
CA L:GLY72 4.5 21.1 1.0
CD2 L:TYR77 4.5 26.9 1.0
N L:TRP78 4.7 26.2 1.0
C L:LEU73 4.7 25.0 1.0
N L:ASN74 4.8 24.2 1.0
CB L:ASP75 4.8 29.3 1.0
C L:ASP75 4.8 29.4 1.0
N L:GLY72 4.8 21.5 1.0
CA L:ASP75 4.9 28.9 1.0
CA L:TRP78 4.9 27.3 1.0
O2A L:HEM200 5.0 25.4 1.0

Sodium binding site 4 out of 4 in 2gc7

Go back to Sodium Binding Sites List in 2gc7
Sodium 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 Sodium with other atoms in the Na 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:Na603

b:28.4
occ:1.00
 O P:TYR77 2.6 35.3 1.0
OD2 P:ASP75 2.7 38.5 1.0
O P:GLY72 2.7 27.6 1.0
O O:HOH1447 2.8 34.7 1.0
O P:HOH1330 2.8 28.8 1.0
O P:HOH2230 3.1 59.7 1.0
OE2 O:GLU31 3.1 36.3 1.0
C P:GLY72 3.5 27.4 1.0
CG P:ASP75 3.5 33.4 1.0
CD O:GLU31 3.6 34.4 1.0
C P:TYR77 3.7 34.9 1.0
OE1 O:GLU31 3.8 33.7 1.0
OD1 P:ASP75 3.9 33.0 1.0
N P:LEU73 4.2 24.7 1.0
CA P:LEU73 4.2 26.8 1.0
CA P:GLY72 4.4 26.3 1.0
CB P:TYR77 4.4 33.9 1.0
CA P:TYR77 4.4 34.1 1.0
CD2 P:TYR77 4.5 36.9 1.0
O P:ASP75 4.5 34.0 1.0
N P:ASP75 4.5 31.1 1.0
N P:TYR77 4.5 35.4 1.0
N P:GLY72 4.7 25.7 1.0
C P:LEU73 4.7 27.9 1.0
CG O:GLU31 4.7 30.7 1.0
N P:ASN74 4.7 26.8 1.0
N P:TRP78 4.7 33.2 1.0
CB P:ASP75 4.8 34.2 1.0
C P:ASP75 4.8 35.0 1.0
CA P:ASP75 4.9 34.8 1.0
O2A P:HEM200 4.9 27.6 1.0
CG P:TYR77 4.9 35.0 1.0
CA P:TRP78 4.9 31.9 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: Tue Dec 15 05:49:32 2020

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