Atomistry » Copper » PDB 3awt-3erx » 3ehb
Atomistry »
  Copper »
    PDB 3awt-3erx »
      3ehb »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy