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Copper in PDB 2j57: X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin.

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

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

Protein crystallography data

The structure of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin., PDB code: 2j57 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) 49.39 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.131, 123.439, 246.920, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 24.1

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin. (pdb code 2j57). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin., PDB code: 2j57:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2j57

Go back to Copper Binding Sites List in 2j57
Copper binding site 1 out of 4 in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol 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-Quinol in Complex with Amicyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1106

b:34.9
occ:1.00
 ND1 A:HIS53 2.1 40.1 1.0
SG A:CYS92 2.3 32.3 1.0
ND1 A:HIS95 2.3 28.0 1.0
SD A:MET98 2.6 29.4 1.0
CE1 A:HIS53 3.0 39.1 1.0
CG A:HIS95 3.1 29.6 1.0
CG A:HIS53 3.1 36.3 1.0
CB A:CYS92 3.2 30.9 1.0
CE1 A:HIS95 3.2 29.3 1.0
CE A:MET98 3.3 32.3 1.0
CB A:HIS95 3.4 30.4 1.0
CB A:HIS53 3.6 33.4 1.0
CA A:HIS53 3.9 33.6 1.0
O A:PRO52 3.9 32.5 1.0
NE2 A:HIS53 4.1 38.9 1.0
CD2 A:HIS53 4.2 37.8 1.0
CG A:MET98 4.2 28.4 1.0
CD2 A:HIS95 4.2 29.8 1.0
NE2 A:HIS95 4.3 27.6 1.0
CA A:CYS92 4.6 31.7 1.0
CB A:MET98 4.6 33.1 1.0
CA A:HIS95 4.6 31.1 1.0
N A:HIS95 4.7 31.9 1.0
C A:PRO52 4.8 32.6 1.0
N A:HIS53 4.8 32.6 1.0
N A:ASN54 4.8 34.1 1.0
CG A:PRO94 4.8 34.1 1.0
CE A:MET28 4.9 34.7 1.0
C A:HIS53 4.9 33.4 1.0
CD A:PRO94 4.9 33.5 1.0
O A:HIS95 4.9 32.0 1.0
C A:CYS92 5.0 32.9 1.0

Copper binding site 2 out of 4 in 2j57

Go back to Copper Binding Sites List in 2j57
Copper binding site 2 out of 4 in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol 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-Quinol in Complex with Amicyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1106

b:32.8
occ:1.00
 ND1 B:HIS53 2.1 27.8 1.0
ND1 B:HIS95 2.1 23.8 1.0
SG B:CYS92 2.2 26.4 1.0
SD B:MET98 2.8 32.0 1.0
CE1 B:HIS53 2.9 21.8 1.0
CE1 B:HIS95 3.0 26.6 1.0
CG B:HIS53 3.1 25.9 1.0
CG B:HIS95 3.1 28.0 1.0
CB B:CYS92 3.2 23.7 1.0
CE B:MET98 3.5 28.4 1.0
CB B:HIS95 3.5 29.1 1.0
CB B:HIS53 3.6 25.1 1.0
CA B:HIS53 3.7 24.5 1.0
O B:PRO52 3.9 24.7 1.0
NE2 B:HIS53 4.0 26.3 1.0
NE2 B:HIS95 4.1 21.8 1.0
CD2 B:HIS53 4.2 26.6 1.0
CD2 B:HIS95 4.2 24.3 1.0
CG B:MET98 4.2 30.3 1.0
CG B:PRO94 4.5 25.7 1.0
CA B:CYS92 4.6 23.1 1.0
N B:HIS53 4.6 24.5 1.0
C B:PRO52 4.6 25.5 1.0
CB B:MET98 4.6 29.8 1.0
CE B:MET28 4.7 26.9 1.0
N B:ASN54 4.7 25.4 1.0
C B:HIS53 4.8 24.9 1.0
CA B:HIS95 4.8 30.2 1.0
N B:HIS95 4.9 28.3 1.0

Copper binding site 3 out of 4 in 2j57

Go back to Copper Binding Sites List in 2j57
Copper binding site 3 out of 4 in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1106

b:34.8
occ:1.00
 ND1 C:HIS95 2.0 27.8 1.0
ND1 C:HIS53 2.2 26.4 1.0
SG C:CYS92 2.3 28.8 1.0
SD C:MET98 2.8 30.6 1.0
CE1 C:HIS53 2.9 27.1 1.0
CE1 C:HIS95 3.0 23.0 1.0
CG C:HIS95 3.0 26.6 1.0
CB C:CYS92 3.2 24.8 1.0
CG C:HIS53 3.3 25.0 1.0
CB C:HIS95 3.3 30.1 1.0
CE C:MET98 3.6 23.2 1.0
CB C:HIS53 3.8 29.4 1.0
CA C:HIS53 3.9 27.1 1.0
O C:PRO52 4.0 27.5 1.0
NE2 C:HIS95 4.1 23.0 1.0
CD2 C:HIS95 4.1 24.6 1.0
NE2 C:HIS53 4.1 22.5 1.0
CG C:MET98 4.2 29.0 1.0
CD2 C:HIS53 4.3 24.8 1.0
CG C:PRO94 4.5 23.5 1.0
CA C:HIS95 4.6 30.8 1.0
CA C:CYS92 4.6 26.0 1.0
CE C:MET28 4.6 23.0 1.0
CB C:MET98 4.6 30.2 1.0
N C:HIS95 4.6 30.9 1.0
O C:HIS95 4.8 32.2 1.0
N C:HIS53 4.8 26.9 1.0
C C:PRO52 4.8 28.2 1.0
CD C:PRO94 4.9 26.4 1.0
N C:ASN54 4.9 28.3 1.0
C C:CYS92 4.9 25.6 1.0
O C:CYS92 5.0 25.5 1.0
C C:HIS53 5.0 27.8 1.0

Copper binding site 4 out of 4 in 2j57

Go back to Copper Binding Sites List in 2j57
Copper binding site 4 out of 4 in the X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Quinol in Complex with Amicyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1106

b:38.2
occ:1.00
 ND1 D:HIS53 2.3 36.4 1.0
SG D:CYS92 2.3 36.9 1.0
ND1 D:HIS95 2.3 35.4 1.0
SD D:MET98 2.4 32.8 1.0
CG D:HIS53 3.2 33.6 1.0
CB D:CYS92 3.2 37.1 1.0
CG D:HIS95 3.2 32.7 1.0
CE1 D:HIS95 3.2 34.9 1.0
CE1 D:HIS53 3.3 32.6 1.0
CE D:MET98 3.3 31.3 1.0
CB D:HIS53 3.4 31.8 1.0
CB D:HIS95 3.5 30.7 1.0
CA D:HIS53 3.7 32.4 1.0
O D:PRO52 3.8 35.0 1.0
CG D:MET98 4.1 30.6 1.0
NE2 D:HIS95 4.3 34.0 1.0
CD2 D:HIS53 4.3 32.6 1.0
CD2 D:HIS95 4.4 33.5 1.0
NE2 D:HIS53 4.4 33.0 1.0
C D:PRO52 4.6 34.1 1.0
N D:HIS53 4.6 33.6 1.0
CA D:CYS92 4.6 37.2 1.0
CA D:HIS95 4.7 31.8 1.0
CG D:PRO94 4.7 32.1 1.0
N D:ASN54 4.7 31.9 1.0
CB D:MET98 4.8 33.4 1.0
CE D:MET28 4.8 30.0 1.0
C D:HIS53 4.8 31.9 1.0
N D:HIS95 4.8 31.4 1.0
CD D:PRO94 4.8 33.6 1.0
O D:HIS95 4.9 30.6 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: Tue Jul 30 23:44:47 2024

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