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Iron in PDB 2yev: Structure of CAA3-Type Cytochrome Oxidase

Enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase

All present enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase:
1.9.3.1;

Protein crystallography data

The structure of Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev was solved by J.A.Lyons, D.Aragao, T.Soulimane, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.18 / 2.36
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.250, 76.030, 300.267, 90.00, 92.21, 90.00
R / Rfree (%) 17.1 / 21.8

Other elements in 2yev:

The structure of Structure of CAA3-Type Cytochrome Oxidase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Copper (Cu) 6 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of CAA3-Type Cytochrome Oxidase (pdb code 2yev). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2yev

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Iron binding site 1 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1015

b:30.9
occ:1.00
FE A:HAS1015 0.0 30.9 1.0
NE2 A:HIS73 2.0 30.2 1.0
ND A:HAS1015 2.0 30.4 1.0
NE2 A:HIS387 2.1 28.9 1.0
NC A:HAS1015 2.1 36.0 1.0
NA A:HAS1015 2.1 34.6 1.0
NB A:HAS1015 2.2 30.1 1.0
CD2 A:HIS73 3.0 40.2 1.0
CD2 A:HIS387 3.0 33.0 1.0
C4C A:HAS1015 3.0 33.5 1.0
C4D A:HAS1015 3.0 26.3 1.0
C1D A:HAS1015 3.0 38.4 1.0
C1C A:HAS1015 3.1 37.2 1.0
CE1 A:HIS73 3.1 36.2 1.0
C4A A:HAS1015 3.1 33.5 1.0
C1A A:HAS1015 3.1 25.6 1.0
CE1 A:HIS387 3.1 44.2 1.0
C4B A:HAS1015 3.2 30.8 1.0
C1B A:HAS1015 3.2 35.6 1.0
CHD A:HAS1015 3.4 24.9 1.0
CHA A:HAS1015 3.4 28.5 1.0
CHC A:HAS1015 3.5 33.7 1.0
CHB A:HAS1015 3.5 27.0 1.0
CG A:HIS73 4.1 31.6 1.0
CG A:HIS387 4.2 38.9 1.0
ND1 A:HIS73 4.2 33.7 1.0
ND1 A:HIS387 4.2 36.0 1.0
C2D A:HAS1015 4.3 35.0 1.0
C3C A:HAS1015 4.3 35.3 1.0
C3D A:HAS1015 4.3 39.7 1.0
C2C A:HAS1015 4.3 37.9 1.0
C3A A:HAS1015 4.4 35.1 1.0
C2A A:HAS1015 4.4 32.4 1.0
C3B A:HAS1015 4.4 32.9 1.0
C2B A:HAS1015 4.5 25.0 1.0

Iron binding site 2 out of 6 in 2yev

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Iron binding site 2 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1016

b:31.7
occ:1.00
FE A:HAS1016 0.0 31.7 1.0
NA A:HAS1016 2.1 32.0 1.0
ND A:HAS1016 2.1 40.2 1.0
NC A:HAS1016 2.1 28.5 1.0
NB A:HAS1016 2.2 30.2 1.0
O A:HOH2077 2.2 25.9 1.0
NE2 A:HIS385 2.3 28.6 1.0
C1D A:HAS1016 3.1 48.0 1.0
C1A A:HAS1016 3.1 38.2 1.0
C4D A:HAS1016 3.1 35.1 1.0
C4A A:HAS1016 3.1 44.1 1.0
C4C A:HAS1016 3.1 33.7 1.0
C1C A:HAS1016 3.1 35.7 1.0
C1B A:HAS1016 3.1 38.2 1.0
C4B A:HAS1016 3.2 42.2 1.0
CD2 A:HIS385 3.2 35.1 1.0
CE1 A:HIS385 3.2 33.6 1.0
CHA A:HAS1016 3.4 27.8 1.0
CHB A:HAS1016 3.4 30.8 1.0
CHD A:HAS1016 3.5 29.9 1.0
CHC A:HAS1016 3.5 26.0 1.0
C2D A:HAS1016 4.3 38.4 1.0
O A:HOH2076 4.3 49.4 1.0
ND1 A:HIS385 4.4 33.0 1.0
C3A A:HAS1016 4.4 38.1 1.0
CG A:HIS385 4.4 41.9 1.0
C3C A:HAS1016 4.4 35.3 1.0
C3D A:HAS1016 4.4 40.8 1.0
C2A A:HAS1016 4.4 22.1 1.0
C2C A:HAS1016 4.4 35.4 1.0
C2B A:HAS1016 4.4 29.1 1.0
C3B A:HAS1016 4.5 34.0 1.0
CU A:CU1017 4.9 37.6 1.0

Iron binding site 3 out of 6 in 2yev

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Iron binding site 3 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe587

b:35.1
occ:1.00
FE B:HEC587 0.0 35.1 1.0
NA B:HEC587 2.0 35.9 1.0
NC B:HEC587 2.0 37.1 1.0
ND B:HEC587 2.0 32.4 1.0
NB B:HEC587 2.0 34.3 1.0
NE2 B:HIS251 2.1 48.6 1.0
SD B:MET303 2.4 37.3 1.0
CD2 B:HIS251 3.0 37.0 1.0
C4D B:HEC587 3.0 39.6 1.0
C1A B:HEC587 3.0 45.8 1.0
C1C B:HEC587 3.0 29.3 1.0
CE1 B:HIS251 3.0 41.6 1.0
C4B B:HEC587 3.1 29.6 1.0
C4C B:HEC587 3.1 37.2 1.0
C1D B:HEC587 3.1 35.1 1.0
C4A B:HEC587 3.1 52.1 1.0
C1B B:HEC587 3.1 37.4 1.0
CHA B:HEC587 3.4 25.9 1.0
CHC B:HEC587 3.4 33.2 1.0
CHD B:HEC587 3.4 40.7 1.0
CG B:MET303 3.5 43.1 1.0
CHB B:HEC587 3.5 34.9 1.0
CE B:MET303 3.5 32.5 1.0
ND1 B:HIS251 4.1 50.8 1.0
CG B:HIS251 4.2 46.5 1.0
CB B:MET303 4.2 28.7 1.0
C2A B:HEC587 4.3 48.2 1.0
C3D B:HEC587 4.3 23.8 1.0
C2C B:HEC587 4.3 30.6 1.0
C3C B:HEC587 4.3 31.9 1.0
C3B B:HEC587 4.3 38.2 1.0
C3A B:HEC587 4.3 48.0 1.0
C2B B:HEC587 4.3 22.8 1.0
C2D B:HEC587 4.3 32.7 1.0
NE1 B:TRP290 5.0 39.2 1.0

Iron binding site 4 out of 6 in 2yev

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Iron binding site 4 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1015

b:42.4
occ:1.00
FE D:HAS1015 0.0 42.4 1.0
NE2 D:HIS387 2.0 34.0 1.0
NC D:HAS1015 2.1 78.6 1.0
NE2 D:HIS73 2.1 33.0 1.0
NA D:HAS1015 2.1 70.9 1.0
ND D:HAS1015 2.1 49.9 1.0
NB D:HAS1015 2.2 58.6 1.0
CD2 D:HIS387 2.9 47.9 1.0
CD2 D:HIS73 3.0 50.9 1.0
C4C D:HAS1015 3.0 72.2 1.0
CE1 D:HIS387 3.1 48.3 1.0
C4A D:HAS1015 3.1 51.2 1.0
C1D D:HAS1015 3.1 44.5 1.0
C1C D:HAS1015 3.1 68.9 1.0
C1A D:HAS1015 3.1 46.2 1.0
C4D D:HAS1015 3.1 62.3 1.0
C1B D:HAS1015 3.1 48.5 1.0
CE1 D:HIS73 3.2 44.2 1.0
C4B D:HAS1015 3.2 68.8 1.0
CHD D:HAS1015 3.4 51.4 1.0
CHA D:HAS1015 3.4 62.0 1.0
CHB D:HAS1015 3.4 55.4 1.0
CHC D:HAS1015 3.5 63.6 1.0
CG D:HIS387 4.1 39.4 1.0
ND1 D:HIS387 4.1 49.1 1.0
CG D:HIS73 4.2 43.3 1.0
ND1 D:HIS73 4.2 46.3 1.0
C3C D:HAS1015 4.3 74.5 1.0
C2C D:HAS1015 4.4 68.8 1.0
C2D D:HAS1015 4.4 61.2 1.0
C3A D:HAS1015 4.4 55.5 1.0
C2A D:HAS1015 4.4 65.5 1.0
C3D D:HAS1015 4.4 53.3 1.0
C2B D:HAS1015 4.4 58.4 1.0
C3B D:HAS1015 4.5 70.3 1.0

Iron binding site 5 out of 6 in 2yev

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Iron binding site 5 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1016

b:42.5
occ:1.00
FE D:HAS1016 0.0 42.5 1.0
NC D:HAS1016 2.1 32.8 1.0
ND D:HAS1016 2.1 37.5 1.0
NA D:HAS1016 2.1 29.3 1.0
NB D:HAS1016 2.1 40.4 1.0
NE2 D:HIS385 2.3 56.9 1.0
O D:HOH2054 2.7 35.8 1.0
C1D D:HAS1016 3.0 57.7 1.0
C1C D:HAS1016 3.0 24.3 1.0
C4C D:HAS1016 3.1 41.1 1.0
C1A D:HAS1016 3.1 39.8 1.0
C4A D:HAS1016 3.1 46.3 1.0
C4D D:HAS1016 3.1 36.9 1.0
C1B D:HAS1016 3.1 42.3 1.0
C4B D:HAS1016 3.1 35.8 1.0
CE1 D:HIS385 3.2 49.2 1.0
CD2 D:HIS385 3.3 52.9 1.0
CHB D:HAS1016 3.4 33.2 1.0
CHD D:HAS1016 3.4 32.2 1.0
CHC D:HAS1016 3.4 47.3 1.0
CHA D:HAS1016 3.4 28.8 1.0
C2D D:HAS1016 4.3 32.8 1.0
C3C D:HAS1016 4.3 27.1 1.0
C2C D:HAS1016 4.3 42.2 1.0
ND1 D:HIS385 4.3 48.2 1.0
C3A D:HAS1016 4.4 26.8 1.0
CG D:HIS385 4.4 45.9 1.0
C3D D:HAS1016 4.4 62.8 1.0
C2B D:HAS1016 4.4 33.9 1.0
C2A D:HAS1016 4.4 39.9 1.0
C3B D:HAS1016 4.4 49.7 1.0
CU D:CU1017 4.8 42.6 1.0
O D:HOH2053 4.9 50.7 1.0

Iron binding site 6 out of 6 in 2yev

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Iron binding site 6 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe587

b:48.3
occ:1.00
FE E:HEC587 0.0 48.3 1.0
NC E:HEC587 2.0 62.2 1.0
NE2 E:HIS251 2.1 41.3 1.0
ND E:HEC587 2.1 91.2 1.0
NA E:HEC587 2.1 81.9 1.0
NB E:HEC587 2.1 78.1 1.0
SD E:MET303 2.4 48.5 1.0
CD2 E:HIS251 3.0 42.4 1.0
C4C E:HEC587 3.0 65.2 1.0
C1D E:HEC587 3.0 44.2 1.0
C4A E:HEC587 3.1 80.3 1.0
C1C E:HEC587 3.1 66.8 1.0
C1B E:HEC587 3.1 63.8 1.0
C4B E:HEC587 3.1 56.3 1.0
CE1 E:HIS251 3.1 55.1 1.0
C4D E:HEC587 3.1 58.5 1.0
C1A E:HEC587 3.1 76.6 1.0
CHD E:HEC587 3.3 57.7 1.0
CHB E:HEC587 3.4 80.2 1.0
CG E:MET303 3.5 48.7 1.0
CE E:MET303 3.5 52.4 1.0
CHC E:HEC587 3.5 54.4 1.0
CHA E:HEC587 3.5 47.8 1.0
CG E:HIS251 4.1 47.5 1.0
ND1 E:HIS251 4.2 52.6 1.0
CB E:MET303 4.2 41.7 1.0
C3C E:HEC587 4.2 70.9 1.0
C2C E:HEC587 4.3 55.8 1.0
C2D E:HEC587 4.3 73.8 1.0
C3A E:HEC587 4.3 69.4 1.0
C3B E:HEC587 4.3 55.4 1.0
C2B E:HEC587 4.3 69.6 1.0
C3D E:HEC587 4.3 54.1 1.0
C2A E:HEC587 4.3 57.0 1.0

Reference:

J.A.Lyons, D.Aragao, O.Slattery, A.V.Pisliakov, T.Soulimane, M.Caffrey. Structural Insights Into Electron Transfer in CAA3-Type Cytochrome Oxidases. Nature V. 487 514 2012.
ISSN: ISSN 0028-0836
PubMed: 22763450
DOI: 10.1038/NATURE11182
Page generated: Sun Dec 13 14:58:07 2020

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