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Sodium in PDB 2j56: X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin.

Enzymatic activity of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin.

All present enzymatic activity of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin.:
1.4.99.3;

Protein crystallography data

The structure of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin., PDB code: 2j56 was solved by A.R.Pearson, R.Pahl, V.L.Davidson, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.48 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.029, 123.029, 245.303, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.7

Other elements in 2j56:

The structure of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin. also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin. (pdb code 2j56). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin., PDB code: 2j56:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2j56

Go back to Sodium Binding Sites List in 2j56
Sodium binding site 1 out of 2 in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na1132

b:18.5
occ:1.00
O L:HOH2055 2.2 41.2 1.0
O L:ILE106 2.7 19.9 1.0
O L:ASN104 2.8 19.5 1.0
N2 L:TQQ57 3.0 24.1 1.0
CH2 L:TQQ57 3.2 25.5 1.0
O L:ASP32 3.3 24.6 1.0
CZ3 L:TQQ57 3.4 24.7 1.0
C L:ILE106 3.8 20.6 1.0
C L:ASN104 3.8 19.7 1.0
C L:ASP105 3.9 19.8 1.0
CE2 H:PHE55 4.0 22.7 1.0
CZ H:PHE55 4.0 21.7 1.0
O L:ASP105 4.0 19.8 1.0
CG L:ASP32 4.0 28.1 1.0
CB L:ASP32 4.0 24.7 1.0
OD2 L:ASP32 4.1 30.6 1.0
CZ2 L:TQQ57 4.1 24.0 1.0
N L:ILE106 4.3 20.4 1.0
C L:ASP32 4.3 24.1 1.0
CE3 L:TQQ57 4.3 23.3 1.0
CA L:ASP105 4.4 20.1 1.0
CD1 L:ILE107 4.4 14.3 1.0
CA L:ILE107 4.5 20.5 1.0
OD1 L:ASP32 4.5 25.9 1.0
N L:ASP105 4.6 18.9 1.0
OD2 L:ASP76 4.6 28.7 1.0
N L:ILE107 4.6 20.0 1.0
O2 L:TQQ57 4.6 26.6 1.0
CA L:ILE106 4.7 19.2 1.0
CA L:ASN104 4.7 20.0 1.0
CA L:ASP32 4.8 25.2 1.0
CD2 H:PHE55 4.9 21.9 1.0
CE1 H:PHE55 5.0 21.4 1.0
N L:TRP108 5.0 21.2 1.0

Sodium binding site 2 out of 2 in 2j56

Go back to Sodium Binding Sites List in 2j56
Sodium binding site 2 out of 2 in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na1131

b:24.0
occ:1.00
O M:HOH2072 2.4 32.8 1.0
O M:ASN104 2.7 22.9 1.0
O M:ILE106 2.7 18.7 1.0
N2 M:TQQ57 2.9 23.0 1.0
CH2 M:TQQ57 3.2 25.1 1.0
O M:ASP32 3.3 23.2 1.0
CZ3 M:TQQ57 3.4 23.7 1.0
OD2 M:ASP32 3.5 35.5 1.0
C M:ILE106 3.8 20.1 1.0
C M:ASN104 3.8 23.0 1.0
CE2 J:PHE55 3.8 23.9 1.0
CG M:ASP32 3.9 27.4 1.0
C M:ASP105 3.9 21.9 1.0
CZ J:PHE55 3.9 19.3 1.0
CB M:ASP32 4.0 24.9 1.0
O M:ASP105 4.1 20.9 1.0
CZ2 M:TQQ57 4.2 23.9 1.0
N M:ILE106 4.2 21.5 1.0
CA M:ASP105 4.3 22.3 1.0
C M:ASP32 4.3 23.4 1.0
OD2 M:ASP76 4.4 22.1 1.0
CE3 M:TQQ57 4.5 24.3 1.0
N M:ILE107 4.5 19.8 1.0
N M:ASP105 4.5 22.5 1.0
CD1 M:ILE107 4.5 20.0 1.0
CA M:ILE107 4.6 18.6 1.0
O2 M:TQQ57 4.6 26.7 1.0
OD1 M:ASP32 4.7 26.6 1.0
CA M:ILE106 4.7 20.6 1.0
CA M:ASP32 4.8 23.6 1.0
CA M:ASN104 4.8 22.7 1.0
CD2 J:PHE55 4.9 23.4 1.0

Reference:

A.R.Pearson, R.Pahl, E.G.Kovaleva, V.L.Davidson, C.M.Wilmot. Tracking X-Ray-Derived Redox Changes in Crystals of A Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry. J.Synchrotron Radiat. V. 14 92 2007.
ISSN: ISSN 0909-0495
PubMed: 17211075
DOI: 10.1107/S0909049506051259
Page generated: Thu Oct 29 04:12:23 2020

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