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Copper in PDB 3c75: Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin

Enzymatic activity of Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin

All present enzymatic activity of Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin:
1.4.99.3;

Protein crystallography data

The structure of Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin, PDB code: 3c75 was solved by C.Cavalieri, N.Biermann, M.D.Vlasie, O.Einsle, A.Merli, D.Ferrari, G.L.Rossi, M.Ubbink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.15 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.573, 131.038, 171.689, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28.3

Copper Binding Sites:

The binding sites of Copper atom in the Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin (pdb code 3c75). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin, PDB code: 3c75:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 3c75

Go back to Copper Binding Sites List in 3c75
Copper binding site 1 out of 2 in the Paracoccus Versutus Methylamine Dehydrogenase 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 Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu107

b:34.7
occ:1.00
ND1 A:HIS54 2.0 34.4 1.0
SG A:CYS93 2.1 35.5 1.0
ND1 A:HIS96 2.3 32.8 1.0
SD A:MET99 2.8 42.1 1.0
CE1 A:HIS54 2.9 34.6 1.0
CB A:CYS93 3.1 32.2 1.0
CG A:HIS96 3.1 33.1 1.0
CG A:HIS54 3.1 33.6 1.0
CB A:HIS96 3.2 34.4 1.0
CE1 A:HIS96 3.3 30.9 1.0
CE A:MET99 3.3 39.9 1.0
CB A:HIS54 3.6 31.8 1.0
CA A:HIS54 3.7 31.7 1.0
O A:PRO53 3.9 31.6 1.0
NE2 A:HIS54 4.0 34.0 1.0
CD2 A:HIS54 4.2 32.5 1.0
CD2 A:HIS96 4.3 31.0 1.0
NE2 A:HIS96 4.4 31.6 1.0
CG A:MET99 4.4 38.9 1.0
CA A:CYS93 4.5 33.3 1.0
CA A:HIS96 4.5 36.2 1.0
N A:HIS96 4.5 36.3 1.0
N A:ASN55 4.6 31.7 1.0
CG A:PRO95 4.6 33.7 1.0
CB A:MET99 4.7 38.7 1.0
N A:HIS54 4.7 31.8 1.0
C A:PRO53 4.7 32.1 1.0
C A:HIS54 4.8 30.7 1.0
CE A:MET29 4.8 39.3 1.0
O A:HIS96 4.9 37.4 1.0
CD A:PRO95 5.0 34.0 1.0

Copper binding site 2 out of 2 in 3c75

Go back to Copper Binding Sites List in 3c75
Copper binding site 2 out of 2 in the Paracoccus Versutus Methylamine Dehydrogenase 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 Paracoccus Versutus Methylamine Dehydrogenase in Complex with Amicyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu107

b:38.9
occ:1.00
ND1 B:HIS54 2.0 34.0 1.0
SG B:CYS93 2.2 32.0 1.0
ND1 B:HIS96 2.2 34.1 1.0
CE1 B:HIS54 2.9 31.8 1.0
SD B:MET99 2.9 43.6 1.0
CB B:CYS93 3.0 31.2 1.0
CG B:HIS96 3.1 34.1 1.0
CG B:HIS54 3.1 32.6 1.0
CB B:HIS96 3.3 34.3 1.0
CE1 B:HIS96 3.3 32.7 1.0
CE B:MET99 3.4 40.5 1.0
CB B:HIS54 3.5 31.6 1.0
CA B:HIS54 3.7 31.1 1.0
O B:PRO53 3.9 29.4 1.0
NE2 B:HIS54 4.0 31.5 1.0
CD2 B:HIS54 4.2 31.7 1.0
CD2 B:HIS96 4.3 34.1 1.0
NE2 B:HIS96 4.4 33.9 1.0
CA B:CYS93 4.5 32.0 1.0
CG B:MET99 4.5 38.5 1.0
CA B:HIS96 4.5 37.0 1.0
N B:HIS96 4.5 37.4 1.0
N B:ASN55 4.6 31.1 1.0
CG B:PRO95 4.6 34.9 1.0
N B:HIS54 4.7 30.2 1.0
C B:PRO53 4.7 29.2 1.0
C B:HIS54 4.7 31.4 1.0
CB B:MET99 4.8 39.0 1.0
O B:HIS96 4.9 38.3 1.0
CD B:PRO95 4.9 36.3 1.0
CE B:MET29 4.9 35.8 1.0

Reference:

C.Cavalieri, N.Biermann, M.D.Vlasie, O.Einsle, A.Merli, D.Ferrari, G.L.Rossi, M.Ubbink. Structural Comparison of Crystal and Solution States of the 138 kDa Complex of Methylamine Dehydrogenase and Amicyanin From Paracoccus Versutus. Biochemistry V. 47 6560 2008.
ISSN: ISSN 0006-2960
PubMed: 18512962
DOI: 10.1021/BI7023749
Page generated: Sun Dec 13 11:09:15 2020

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