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Iron 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
Copper (Cu) 3 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3ehb

Go back to Iron Binding Sites List in 3ehb
Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe559

b:47.1
occ:1.00
 FE A:HEA559 0.0 47.1 1.0
NE2 A:HIS94 1.9 56.7 1.0
NE2 A:HIS413 2.0 58.1 1.0
NB A:HEA559 2.0 47.0 1.0
ND A:HEA559 2.1 47.0 1.0
NA A:HEA559 2.1 49.2 1.0
NC A:HEA559 2.1 48.7 1.0
CE1 A:HIS94 2.9 55.5 1.0
CE1 A:HIS413 2.9 62.4 1.0
C4B A:HEA559 2.9 46.8 1.0
CD2 A:HIS413 3.0 58.7 1.0
CD2 A:HIS94 3.0 50.4 1.0
C4D A:HEA559 3.0 47.2 1.0
C1A A:HEA559 3.0 45.3 1.0
C1B A:HEA559 3.0 49.8 1.0
C1C A:HEA559 3.0 46.4 1.0
C1D A:HEA559 3.1 49.5 1.0
C4A A:HEA559 3.1 48.4 1.0
C4C A:HEA559 3.1 47.9 1.0
CHA A:HEA559 3.5 47.1 1.0
CHC A:HEA559 3.5 45.5 1.0
CHD A:HEA559 3.6 48.3 1.0
CHB A:HEA559 3.6 48.5 1.0
ND1 A:HIS94 4.0 59.1 1.0
ND1 A:HIS413 4.0 56.8 1.0
CG A:HIS94 4.1 57.0 1.0
CG A:HIS413 4.1 56.7 1.0
C3B A:HEA559 4.2 48.1 1.0
C2A A:HEA559 4.3 49.2 1.0
C3D A:HEA559 4.3 46.7 1.0
C3A A:HEA559 4.3 45.0 1.0
C2B A:HEA559 4.3 45.4 1.0
C2C A:HEA559 4.3 49.0 1.0
C3C A:HEA559 4.3 46.8 1.0
C2D A:HEA559 4.4 45.8 1.0
OG1 A:THR50 4.6 51.0 1.0
CE1 A:PHE412 4.8 45.0 1.0

Iron binding site 2 out of 2 in 3ehb

Go back to Iron Binding Sites List in 3ehb
Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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
A:Fe560

b:51.2
occ:1.00
 FE A:HEA560 0.0 51.2 1.0
NE2 A:HIS411 2.0 46.4 1.0
ND A:HEA560 2.1 53.3 1.0
NB A:HEA560 2.1 51.8 1.0
NC A:HEA560 2.1 54.0 1.0
NA A:HEA560 2.2 52.6 1.0
O2 A:PER576 2.2 49.9 1.0
O1 A:PER576 2.9 56.2 1.0
CE1 A:HIS411 3.0 53.8 1.0
C4B A:HEA560 3.0 52.7 1.0
C4D A:HEA560 3.0 53.0 1.0
C1C A:HEA560 3.0 53.3 1.0
C1A A:HEA560 3.1 52.8 1.0
C1D A:HEA560 3.1 54.0 1.0
CD2 A:HIS411 3.1 51.9 1.0
C4C A:HEA560 3.1 53.9 1.0
C1B A:HEA560 3.1 54.2 1.0
C4A A:HEA560 3.2 51.6 1.0
CHC A:HEA560 3.4 50.5 1.0
CHA A:HEA560 3.5 53.5 1.0
CHD A:HEA560 3.6 52.7 1.0
CHB A:HEA560 3.7 52.2 1.0
ND1 A:HIS411 4.1 45.0 1.0
CG A:HIS411 4.2 45.1 1.0
C3D A:HEA560 4.3 54.0 1.0
C3B A:HEA560 4.3 53.3 1.0
C2D A:HEA560 4.3 52.9 1.0
C3C A:HEA560 4.4 53.2 1.0
C2C A:HEA560 4.4 54.6 1.0
C2A A:HEA560 4.4 54.1 1.0
C2B A:HEA560 4.5 53.6 1.0
C3A A:HEA560 4.5 53.4 1.0
CU A:CU561 4.5 54.4 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: Tue Aug 5 00:58:55 2025

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