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Copper 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:

Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 2 binding sites of Copper where determined in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex with Amicyanin., PDB code: 2j56:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2j56

Go back to Copper Binding Sites List in 2j56
Copper 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 Copper with other atoms in the Cu 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
A:Cu1106

b:32.2
occ:1.00
ND1 A:HIS53 2.1 34.1 1.0
SG A:CYS92 2.2 31.3 1.0
ND1 A:HIS95 2.2 26.5 1.0
SD A:MET98 2.5 27.3 1.0
CG A:HIS53 3.0 32.6 1.0
CE1 A:HIS53 3.2 34.1 1.0
CG A:HIS95 3.2 30.2 1.0
CB A:CYS92 3.2 29.8 1.0
CE1 A:HIS95 3.2 26.3 1.0
CB A:HIS53 3.3 30.1 1.0
CE A:MET98 3.4 30.0 1.0
CB A:HIS95 3.4 30.7 1.0
CA A:HIS53 3.7 31.1 1.0
O A:PRO52 3.9 31.3 1.0
CG A:MET98 4.2 24.6 1.0
CD2 A:HIS53 4.2 33.2 1.0
NE2 A:HIS53 4.2 33.6 1.0
NE2 A:HIS95 4.3 28.1 1.0
CD2 A:HIS95 4.3 29.2 1.0
CG A:PRO94 4.5 31.4 1.0
CA A:CYS92 4.6 30.8 1.0
N A:HIS53 4.6 30.6 1.0
CB A:MET98 4.7 27.7 1.0
CA A:HIS95 4.7 31.0 1.0
C A:PRO52 4.7 31.1 1.0
N A:ASN54 4.8 30.5 1.0
CE A:MET28 4.8 30.2 1.0
N A:HIS95 4.8 30.9 1.0
C A:HIS53 4.8 30.6 1.0
O A:HIS95 5.0 32.4 1.0

Copper binding site 2 out of 2 in 2j56

Go back to Copper Binding Sites List in 2j56
Copper 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 Copper with other atoms in the Cu 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
B:Cu1106

b:28.7
occ:1.00
ND1 B:HIS53 2.0 20.0 1.0
ND1 B:HIS95 2.1 16.1 1.0
SG B:CYS92 2.3 26.0 1.0
SD B:MET98 2.8 27.3 1.0
CE1 B:HIS95 2.8 20.6 1.0
CE1 B:HIS53 2.9 20.0 1.0
CG B:HIS53 3.1 21.6 1.0
CG B:HIS95 3.2 23.1 1.0
CB B:CYS92 3.2 22.9 1.0
CB B:HIS53 3.5 20.6 1.0
CB B:HIS95 3.6 24.1 1.0
CE B:MET98 3.7 26.1 1.0
CA B:HIS53 3.7 21.9 1.0
O B:PRO52 3.8 22.2 1.0
NE2 B:HIS95 4.0 21.8 1.0
NE2 B:HIS53 4.1 20.4 1.0
CD2 B:HIS53 4.2 21.7 1.0
CD2 B:HIS95 4.2 18.9 1.0
CG B:MET98 4.2 27.5 1.0
CG B:PRO94 4.6 23.7 1.0
CA B:CYS92 4.6 22.2 1.0
C B:PRO52 4.6 23.6 1.0
N B:HIS53 4.7 23.0 1.0
N B:ASN54 4.7 22.2 1.0
CB B:MET98 4.7 25.8 1.0
C B:HIS53 4.8 22.2 1.0
CA B:HIS95 4.8 24.8 1.0
N B:HIS95 4.8 24.4 1.0
CE B:MET28 4.9 24.1 1.0
CD B:PRO94 5.0 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: Wed Oct 28 14:20:11 2020
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