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Copper in PDB 3ehb: A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate

Enzymatic activity of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate

All present enzymatic activity of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate:
1.9.3.1;

Protein crystallography data

The structure of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate, PDB code: 3ehb was solved by J.Koepke, H.Mueller, G.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.69 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.461, 151.332, 157.487, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Other elements in 3ehb:

The structure of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 2 atoms
Calcium (Ca) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate (pdb code 3ehb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate, PDB code: 3ehb:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3ehb

Go back to Copper Binding Sites List in 3ehb
Copper binding site 1 out of 3 in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu561

b:54.4
occ:1.00
 NE2 A:HIS326 2.0 59.8 1.0
ND1 A:HIS276 2.2 63.4 1.0
NE2 A:HIS325 2.2 54.2 1.0
O2 A:PER576 2.4 49.9 1.0
O1 A:PER576 2.5 56.2 1.0
CE1 A:HIS326 2.9 46.6 1.0
CD2 A:HIS326 3.0 44.9 1.0
CE1 A:HIS276 3.1 54.4 1.0
CE1 A:HIS325 3.1 55.6 1.0
CG A:HIS276 3.2 59.8 1.0
CD2 A:HIS325 3.2 61.0 1.0
CB A:HIS276 3.5 51.9 1.0
ND1 A:HIS326 4.0 46.2 1.0
CG A:HIS326 4.1 53.4 1.0
CA A:HIS276 4.1 55.3 1.0
NE2 A:HIS276 4.2 63.0 1.0
NA A:HEA560 4.2 52.6 1.0
ND1 A:HIS325 4.2 53.2 1.0
CD2 A:HIS276 4.3 56.0 1.0
CG A:HIS325 4.3 58.8 1.0
C1A A:HEA560 4.4 52.8 1.0
FE A:HEA560 4.5 51.2 1.0
C4A A:HEA560 4.6 51.6 1.0
ND A:HEA560 4.8 53.3 1.0
CHA A:HEA560 4.8 53.5 1.0
C4D A:HEA560 4.9 53.0 1.0
NB A:HEA560 4.9 51.8 1.0
CG2 A:VAL279 4.9 48.1 1.0

Copper binding site 2 out of 3 in 3ehb

Go back to Copper Binding Sites List in 3ehb
Copper binding site 2 out of 3 in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu270

b:48.7
occ:1.00
 ND1 B:HIS224 2.0 47.4 1.0
SG B:CYS216 2.4 48.1 1.0
SG B:CYS220 2.4 46.9 1.0
O B:GLU218 2.4 46.1 1.0
CE1 B:HIS224 2.7 51.8 1.0
CU B:CU271 2.7 50.0 1.0
CG B:HIS224 3.1 55.5 1.0
CB B:CYS216 3.3 43.1 1.0
C B:GLU218 3.4 52.8 1.0
CB B:CYS220 3.4 43.6 1.0
CB B:HIS224 3.7 53.5 1.0
CA B:HIS224 3.7 49.6 1.0
N B:CYS220 3.7 56.2 1.0
NE2 B:HIS224 3.9 54.9 1.0
N B:GLU218 3.9 52.9 1.0
O B:HIS224 4.0 44.5 1.0
CD2 B:HIS224 4.1 55.0 1.0
ND1 B:HIS181 4.1 34.8 1.0
C B:CYS216 4.1 45.5 1.0
O B:CYS216 4.2 46.8 1.0
N B:LEU219 4.2 51.0 1.0
CA B:CYS220 4.2 54.0 1.0
CA B:LEU219 4.2 49.9 1.0
CA B:GLU218 4.2 47.1 1.0
C B:LEU219 4.3 49.7 1.0
C B:HIS224 4.3 35.4 1.0
CA B:CYS216 4.4 42.1 1.0
SD B:MET227 4.5 48.6 1.0
N B:SER217 4.6 40.0 1.0
CG B:MET227 4.8 44.8 1.0
CE1 B:HIS181 4.9 41.4 1.0
N B:HIS224 4.9 53.8 1.0
CA B:HIS181 4.9 37.8 1.0
C B:SER217 5.0 47.7 1.0

Copper binding site 3 out of 3 in 3ehb

Go back to Copper Binding Sites List in 3ehb
Copper binding site 3 out of 3 in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu271

b:50.0
occ:1.00
 ND1 B:HIS181 1.9 34.8 1.0
SD B:MET227 2.4 48.6 1.0
SG B:CYS216 2.5 48.1 1.0
SG B:CYS220 2.5 46.9 1.0
CE1 B:HIS181 2.7 41.4 1.0
CU B:CU270 2.7 48.7 1.0
CE B:MET227 3.1 38.9 1.0
CG B:HIS181 3.2 42.4 1.0
CB B:CYS220 3.3 43.6 1.0
CB B:CYS216 3.5 43.1 1.0
CG B:MET227 3.5 44.8 1.0
CB B:HIS181 3.7 43.1 1.0
NE2 B:HIS181 3.9 40.4 1.0
O B:GLU218 4.1 46.1 1.0
CD2 B:HIS181 4.1 36.0 1.0
CA B:HIS181 4.3 37.8 1.0
CD1 B:TRP121 4.5 56.2 1.0
ND1 B:HIS224 4.5 47.4 1.0
CA B:CYS220 4.8 54.0 1.0
O B:HIS119 4.8 45.1 1.0
CB B:MET227 4.8 41.3 1.0
O B:ILE180 4.9 47.0 1.0
CA B:CYS216 4.9 42.1 1.0
CA B:HIS224 4.9 49.6 1.0

Reference:

K.L.Durr, J.Koepke, P.Hellwig, H.Muller, H.Angerer, G.Peng, E.Olkhova, O.-M.H.Richter, B.Ludwig, H.Michel. A D-Pathway Mutation Decouples the Paracoccusdenitrificans Cytochrome C Oxidase By Altering the Side-Chain Orientation of A Distant Conserved Glutamate J.Mol.Biol. V. 384 865 2008.
ISSN: ISSN 0022-2836
PubMed: 18930738
DOI: 10.1016/J.JMB.2008.09.074
Page generated: Wed Jul 31 00:51:27 2024

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