Atomistry » Sodium » PDB 2fmp-2gg2 » 2gc4
Atomistry »
  Sodium »
    PDB 2fmp-2gg2 »
      2gc4 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy