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Copper 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
Sodium (Na) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2gc4

Go back to Copper Binding Sites List in 2gc4
Copper 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 Copper with other atoms in the Cu 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
G:Cu107

b:32.8
occ:1.00
ND1 G:HIS95 2.1 28.9 1.0
ND1 G:HIS53 2.2 23.6 1.0
SG G:CYS92 2.3 29.7 1.0
SD G:MET98 2.6 27.8 1.0
CE1 G:HIS53 3.0 23.0 1.0
CG G:HIS95 3.1 24.6 1.0
CE1 G:HIS95 3.2 26.2 1.0
CB G:CYS92 3.2 24.8 1.0
CG G:HIS53 3.3 25.8 1.0
CB G:HIS95 3.4 26.9 1.0
CE G:MET98 3.6 29.2 1.0
CB G:HIS53 3.7 25.6 1.0
CA G:HIS53 4.0 26.8 1.0
CG G:MET98 4.1 28.3 1.0
O G:PRO52 4.2 26.1 1.0
NE2 G:HIS53 4.2 22.9 1.0
CD2 G:HIS95 4.3 27.7 1.0
NE2 G:HIS95 4.3 26.3 1.0
CD2 G:HIS53 4.3 23.4 1.0
CB G:MET98 4.5 25.4 1.0
CA G:CYS92 4.7 26.6 1.0
CA G:HIS95 4.7 26.6 1.0
N G:HIS95 4.8 27.2 1.0
CE G:MET28 4.9 31.7 1.0
CG G:PRO94 4.9 30.3 1.0
N G:HIS53 4.9 25.5 1.0
N G:ASN54 5.0 26.1 1.0
C G:PRO52 5.0 26.3 1.0

Copper binding site 2 out of 4 in 2gc4

Go back to Copper Binding Sites List in 2gc4
Copper 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 Copper with other atoms in the Cu 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
K:Cu107

b:29.8
occ:1.00
ND1 K:HIS53 2.2 25.8 1.0
ND1 K:HIS95 2.2 26.6 1.0
SG K:CYS92 2.3 24.8 1.0
SD K:MET98 2.6 26.6 1.0
CE1 K:HIS53 3.0 24.3 1.0
CE1 K:HIS95 3.1 25.4 1.0
CG K:HIS95 3.2 27.7 1.0
CB K:CYS92 3.2 20.3 1.0
CG K:HIS53 3.2 24.1 1.0
CB K:HIS95 3.5 26.7 1.0
CE K:MET98 3.6 25.7 1.0
CB K:HIS53 3.7 25.0 1.0
CA K:HIS53 4.0 26.9 1.0
O K:PRO52 4.1 26.4 1.0
CG K:MET98 4.1 27.6 1.0
NE2 K:HIS53 4.2 26.5 1.0
CD2 K:HIS95 4.3 26.3 1.0
NE2 K:HIS95 4.3 27.4 1.0
CD2 K:HIS53 4.3 23.8 1.0
CB K:MET98 4.6 24.3 1.0
CA K:CYS92 4.6 23.6 1.0
CA K:HIS95 4.7 24.9 1.0
N K:HIS95 4.8 27.1 1.0
CG K:PRO94 4.8 25.5 1.0
C K:PRO52 4.9 28.5 1.0
N K:HIS53 4.9 26.9 1.0
N K:ASN54 4.9 25.8 1.0
O K:HIS95 5.0 26.9 1.0
CE K:MET28 5.0 32.2 1.0

Copper binding site 3 out of 4 in 2gc4

Go back to Copper Binding Sites List in 2gc4
Copper 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 Copper with other atoms in the Cu 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
O:Cu107

b:39.1
occ:1.00
ND1 O:HIS53 2.1 34.1 1.0
ND1 O:HIS95 2.2 31.0 1.0
SG O:CYS92 2.4 34.2 1.0
SD O:MET98 2.6 32.9 1.0
CE1 O:HIS53 2.9 36.0 1.0
CG O:HIS95 3.1 29.4 1.0
CG O:HIS53 3.2 37.0 1.0
CE1 O:HIS95 3.2 30.6 1.0
CB O:CYS92 3.3 31.7 1.0
CB O:HIS95 3.4 31.7 1.0
CE O:MET98 3.6 37.5 1.0
CB O:HIS53 3.7 35.6 1.0
CA O:HIS53 4.0 36.3 1.0
CG O:MET98 4.1 35.3 1.0
O O:PRO52 4.1 36.9 1.0
NE2 O:HIS53 4.1 34.9 1.0
CD2 O:HIS53 4.2 34.4 1.0
CD2 O:HIS95 4.3 31.5 1.0
NE2 O:HIS95 4.3 28.2 1.0
CB O:MET98 4.5 37.1 1.0
CA O:HIS95 4.6 32.5 1.0
N O:HIS95 4.7 33.4 1.0
CA O:CYS92 4.7 32.7 1.0
CG O:PRO94 4.7 32.5 1.0
CE O:MET28 4.8 40.5 1.0
O O:HIS95 4.9 34.5 1.0
C O:PRO52 4.9 38.2 1.0
N O:ASN54 4.9 35.7 1.0
N O:HIS53 4.9 35.5 1.0

Copper binding site 4 out of 4 in 2gc4

Go back to Copper Binding Sites List in 2gc4
Copper 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 Copper with other atoms in the Cu 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
C:Cu107

b:33.2
occ:1.00
ND1 C:HIS53 2.1 26.1 1.0
ND1 C:HIS95 2.2 36.0 1.0
SG C:CYS92 2.3 29.6 1.0
SD C:MET98 2.6 31.2 1.0
CE1 C:HIS53 3.0 25.9 1.0
CG C:HIS95 3.1 34.7 1.0
CE1 C:HIS95 3.1 35.7 1.0
CB C:CYS92 3.2 27.0 1.0
CG C:HIS53 3.3 27.0 1.0
CB C:HIS95 3.5 33.2 1.0
CE C:MET98 3.6 28.8 1.0
CB C:HIS53 3.7 28.3 1.0
CA C:HIS53 4.0 29.8 1.0
O C:PRO52 4.1 29.9 1.0
CG C:MET98 4.1 31.2 1.0
NE2 C:HIS53 4.2 26.6 1.0
CD2 C:HIS95 4.2 36.3 1.0
NE2 C:HIS95 4.2 37.1 1.0
CD2 C:HIS53 4.3 25.3 1.0
CB C:MET98 4.5 30.3 1.0
CA C:CYS92 4.6 27.1 1.0
CA C:HIS95 4.7 33.1 1.0
N C:HIS95 4.7 32.6 1.0
CG C:PRO94 4.8 28.7 1.0
C C:PRO52 4.9 30.0 1.0
N C:HIS53 4.9 27.2 1.0
N C:ASN54 5.0 28.9 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: Sun Dec 13 11:04:56 2020

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