Iron in PDB 5djq: The Structure of CBB3 Cytochrome Oxidase.

All present enzymatic activity of The Structure of CBB3 Cytochrome Oxidase.:
1.9.3.1;

The structure of The Structure of CBB3 Cytochrome Oxidase., PDB code: 5djq was solved by S.Buschmann, E.Warkentin, H.Xie, M.Kohlstaedt, J.D.Langer, U.Ermler, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.98 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.475, 279.933, 175.192, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.3

The structure of The Structure of CBB3 Cytochrome Oxidase. also contains other interesting chemical elements:

Calcium	(Ca)	8 atoms
Copper	(Cu)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the The Structure of CBB3 Cytochrome Oxidase. (pdb code 5djq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the The Structure of CBB3 Cytochrome Oxidase., PDB code: 5djq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:59.2 occ:1.00 FE A:HEM501 0.0 59.2 1.0 NE2 A:HIS345 1.9 55.3 1.0 O1 A:PEO505 2.0 74.1 1.0 NC A:HEM501 2.0 69.4 1.0 NB A:HEM501 2.1 60.7 1.0 ND A:HEM501 2.1 67.1 1.0 NA A:HEM501 2.1 64.6 1.0 CD2 A:HIS345 2.9 47.9 1.0 CE1 A:HIS345 2.9 68.7 1.0 C1D A:HEM501 3.0 64.9 1.0 C1C A:HEM501 3.0 73.5 1.0 C4C A:HEM501 3.0 68.0 1.0 C4B A:HEM501 3.1 64.2 1.0 C1B A:HEM501 3.1 66.7 1.0 C4A A:HEM501 3.1 66.3 1.0 C4D A:HEM501 3.1 58.9 1.0 C1A A:HEM501 3.1 58.0 1.0 CHD A:HEM501 3.4 68.7 1.0 CHC A:HEM501 3.4 75.7 1.0 O2 A:PEO505 3.4 74.6 1.0 CHB A:HEM501 3.4 72.1 1.0 CHA A:HEM501 3.5 55.9 1.0 ND1 A:HIS345 4.0 64.8 1.0 CG A:HIS345 4.1 53.0 1.0 C2C A:HEM501 4.2 71.8 1.0 C3C A:HEM501 4.2 68.4 1.0 C2D A:HEM501 4.2 49.2 1.0 C3D A:HEM501 4.3 51.6 1.0 C3B A:HEM501 4.3 60.1 1.0 C2B A:HEM501 4.3 59.0 1.0 C3A A:HEM501 4.3 63.5 1.0 C2A A:HEM501 4.3 55.3 1.0 CU A:CU503 4.7 0.4 1.0 CG2 A:VAL210 4.8 77.3 1.0

Iron binding site 2 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:54.2 occ:1.00 FE A:HEM502 0.0 54.2 1.0 NE2 A:HIS347 1.9 47.2 1.0 NE2 A:HIS60 1.9 62.7 1.0 NA A:HEM502 2.0 45.2 1.0 NB A:HEM502 2.0 52.3 1.0 ND A:HEM502 2.0 48.1 1.0 NC A:HEM502 2.1 49.8 1.0 CE1 A:HIS60 2.7 59.0 1.0 CE1 A:HIS347 2.8 52.7 1.0 CD2 A:HIS347 3.0 49.2 1.0 C4A A:HEM502 3.0 55.6 1.0 C1B A:HEM502 3.0 57.9 1.0 C1D A:HEM502 3.0 54.3 1.0 C1A A:HEM502 3.1 51.7 1.0 C4D A:HEM502 3.1 49.5 1.0 C4C A:HEM502 3.1 47.1 1.0 C4B A:HEM502 3.1 54.5 1.0 C1C A:HEM502 3.1 58.7 1.0 CD2 A:HIS60 3.1 66.9 1.0 CHB A:HEM502 3.4 61.1 1.0 CHD A:HEM502 3.4 45.3 1.0 CHA A:HEM502 3.4 55.4 1.0 CHC A:HEM502 3.5 55.3 1.0 ND1 A:HIS60 3.9 62.1 1.0 ND1 A:HIS347 4.0 49.0 1.0 CG A:HIS347 4.1 49.3 1.0 CG A:HIS60 4.1 63.9 1.0 OH A:TYR395 4.2 58.2 1.0 C3A A:HEM502 4.3 55.3 1.0 C2B A:HEM502 4.3 54.8 1.0 C2A A:HEM502 4.3 53.8 1.0 C2D A:HEM502 4.3 54.4 1.0 C3D A:HEM502 4.3 49.3 1.0 C3B A:HEM502 4.3 55.2 1.0 C3C A:HEM502 4.3 56.8 1.0 C2C A:HEM502 4.3 61.8 1.0

Iron binding site 3 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:0.5 occ:1.00 FE B:HEC301 0.0 0.5 1.0 NE2 B:HIS69 1.9 54.6 1.0 NC B:HEC301 2.1 40.2 1.0 NA B:HEC301 2.1 58.1 1.0 ND B:HEC301 2.1 40.0 1.0 NB B:HEC301 2.1 39.9 1.0 SD B:MET137 2.3 63.1 1.0 CD2 B:HIS69 2.8 54.6 1.0 CE1 B:HIS69 2.9 57.9 1.0 C1A B:HEC301 3.0 57.2 1.0 C1C B:HEC301 3.0 60.2 1.0 C4B B:HEC301 3.0 66.9 1.0 C4D B:HEC301 3.1 72.6 1.0 C4A B:HEC301 3.1 62.9 1.0 C4C B:HEC301 3.1 61.1 1.0 C1D B:HEC301 3.1 69.1 1.0 C1B B:HEC301 3.1 61.7 1.0 CHC B:HEC301 3.4 67.2 1.0 CHA B:HEC301 3.4 65.9 1.0 CHB B:HEC301 3.5 58.6 1.0 CHD B:HEC301 3.5 56.5 1.0 CG B:MET137 3.5 52.0 1.0 CE B:MET137 3.5 62.2 1.0 CG B:HIS69 4.0 42.3 1.0 ND1 B:HIS69 4.0 47.8 1.0 CB B:MET137 4.1 45.3 1.0 C2A B:HEC301 4.4 52.7 1.0 C3B B:HEC301 4.4 58.6 1.0 C2C B:HEC301 4.4 48.8 1.0 C3A B:HEC301 4.4 39.9 1.0 C3C B:HEC301 4.4 52.8 1.0 C3D B:HEC301 4.4 40.6 1.0 C2D B:HEC301 4.4 40.8 1.0 C2B B:HEC301 4.5 54.7 1.0 CE1 B:HIS124 4.6 49.8 1.0

Iron binding site 4 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:57.2 occ:1.00 FE C:HEC401 0.0 57.2 1.0 NE2 C:HIS237 1.9 57.0 1.0 NC C:HEC401 2.1 57.0 1.0 NA C:HEC401 2.1 55.1 1.0 NB C:HEC401 2.1 44.6 1.0 ND C:HEC401 2.1 71.3 1.0 SD C:MET186 2.3 52.4 1.0 CE1 C:HIS237 2.8 59.3 1.0 CG C:MET186 2.9 61.3 1.0 CD2 C:HIS237 3.0 62.9 1.0 C1C C:HEC401 3.1 56.2 1.0 C4A C:HEC401 3.1 57.2 1.0 C4B C:HEC401 3.1 48.6 1.0 C1D C:HEC401 3.1 65.4 1.0 C1A C:HEC401 3.1 57.1 1.0 C4D C:HEC401 3.1 65.6 1.0 C1B C:HEC401 3.1 53.1 1.0 C4C C:HEC401 3.1 62.0 1.0 CHD C:HEC401 3.4 63.4 1.0 CHC C:HEC401 3.4 48.8 1.0 CHB C:HEC401 3.4 59.3 1.0 CHA C:HEC401 3.5 54.9 1.0 CE C:MET186 3.6 54.9 1.0 ND1 C:HIS237 3.9 59.5 1.0 CG C:HIS237 4.1 58.6 1.0 CB C:MET186 4.3 59.0 1.0 C2C C:HEC401 4.4 58.1 1.0 C3B C:HEC401 4.4 53.4 1.0 C3A C:HEC401 4.4 55.7 1.0 C3D C:HEC401 4.4 63.5 1.0 C2D C:HEC401 4.4 63.3 1.0 C2A C:HEC401 4.4 51.5 1.0 C2B C:HEC401 4.4 50.7 1.0 C3C C:HEC401 4.5 57.0 1.0 CA C:MET186 4.8 46.9 1.0

Iron binding site 5 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:0.6 occ:1.00 FE C:HEC402 0.0 0.6 1.0 NE2 C:HIS147 1.9 60.5 1.0 NA C:HEC402 2.1 60.7 1.0 NC C:HEC402 2.1 43.2 1.0 ND C:HEC402 2.1 57.9 1.0 NB C:HEC402 2.1 51.5 1.0 SD C:MET279 2.3 51.9 1.0 CE1 C:HIS147 2.8 63.1 1.0 CD2 C:HIS147 3.0 72.2 1.0 C4A C:HEC402 3.1 67.1 1.0 C1C C:HEC402 3.1 49.2 1.0 C1A C:HEC402 3.1 65.0 1.0 C4B C:HEC402 3.1 53.5 1.0 C1D C:HEC402 3.1 62.7 1.0 C4D C:HEC402 3.1 61.1 1.0 C4C C:HEC402 3.1 53.6 1.0 C1B C:HEC402 3.1 63.7 1.0 CHB C:HEC402 3.4 72.6 1.0 CHD C:HEC402 3.4 64.8 1.0 CHC C:HEC402 3.4 49.5 1.0 CHA C:HEC402 3.4 63.9 1.0 CG C:MET279 3.5 65.8 1.0 CE C:MET279 3.6 0.6 1.0 ND1 C:HIS147 3.9 57.6 1.0 CG C:HIS147 4.1 59.6 1.0 CB C:MET279 4.1 53.4 1.0 C3A C:HEC402 4.4 56.6 1.0 C3B C:HEC402 4.4 56.2 1.0 C2A C:HEC402 4.4 56.5 1.0 C2C C:HEC402 4.4 42.1 1.0 C2D C:HEC402 4.4 52.7 1.0 C3D C:HEC402 4.4 50.1 1.0 C3C C:HEC402 4.4 44.2 1.0 C2B C:HEC402 4.4 52.5 1.0 CA C:MET279 4.7 49.0 1.0

Iron binding site 6 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:62.4 occ:0.75 FE2 C:FC6403 0.0 62.4 0.8 C24 C:FC6403 1.8 98.1 0.8 C26 C:FC6403 1.8 75.6 0.8 C21 C:FC6403 1.8 73.0 0.8 C23 C:FC6403 1.8 96.4 0.8 C22 C:FC6403 1.8 84.9 0.8 C11 C:FC6403 1.8 60.5 0.8 N24 C:FC6403 2.9 0.5 0.8 N21 C:FC6403 3.0 77.6 0.8 N22 C:FC6403 3.0 84.1 0.8 N25 C:FC6403 3.0 74.0 0.8 N23 C:FC6403 3.0 89.6 0.8 N11 C:FC6403 3.0 63.8 0.8 CG C:GLN266 4.6 70.4 1.0 CG M:PRO215 4.7 67.2 1.0 NH2 M:ARG206 4.8 51.1 1.0 CB M:SER263 5.0 75.6 1.0

Iron binding site 7 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:0.2 occ:1.00 FE D:HEM501 0.0 0.2 1.0 NE2 D:HIS345 2.0 0.4 1.0 O1 D:PEO506 2.0 0.4 1.0 NA D:HEM501 2.0 0.7 1.0 NB D:HEM501 2.1 0.8 1.0 ND D:HEM501 2.1 0.9 1.0 NC D:HEM501 2.1 0.3 1.0 CD2 D:HIS345 2.9 0.5 1.0 C1A D:HEM501 3.0 0.3 1.0 C4D D:HEM501 3.0 0.6 1.0 C4A D:HEM501 3.0 0.4 1.0 CE1 D:HIS345 3.0 0.3 1.0 C1B D:HEM501 3.0 0.1 1.0 C4B D:HEM501 3.1 0.4 1.0 C1C D:HEM501 3.1 0.8 1.0 C1D D:HEM501 3.1 0.8 1.0 C4C D:HEM501 3.1 0.9 1.0 O2 D:PEO506 3.3 0.9 1.0 CHA D:HEM501 3.4 0.1 1.0 CHB D:HEM501 3.4 1.0 1.0 CHC D:HEM501 3.4 0.8 1.0 CHD D:HEM501 3.5 0.2 1.0 CG D:HIS345 4.0 0.1 1.0 ND1 D:HIS345 4.1 0.0 1.0 C2A D:HEM501 4.2 0.9 1.0 C3A D:HEM501 4.2 0.6 1.0 C2B D:HEM501 4.3 0.4 1.0 C3D D:HEM501 4.3 0.8 1.0 C3B D:HEM501 4.3 0.0 1.0 C2C D:HEM501 4.3 1.0 1.0 C2D D:HEM501 4.3 99.0 1.0 C3C D:HEM501 4.3 0.9 1.0 CU D:CU503 4.6 0.9 1.0 CG2 D:VAL210 4.9 0.3 1.0 ND1 D:HIS207 4.9 0.9 1.0 NE2 D:HIS257 5.0 0.6 1.0

Iron binding site 8 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:99.6 occ:1.00 FE D:HEM502 0.0 99.6 1.0 NE2 D:HIS347 1.9 0.3 1.0 NE2 D:HIS60 2.0 93.8 1.0 NC D:HEM502 2.0 0.7 1.0 ND D:HEM502 2.1 0.6 1.0 NA D:HEM502 2.1 95.8 1.0 NB D:HEM502 2.1 0.5 1.0 CE1 D:HIS60 2.7 89.7 1.0 CE1 D:HIS347 2.9 0.5 1.0 CD2 D:HIS347 2.9 0.4 1.0 C1D D:HEM502 3.0 0.1 1.0 C4C D:HEM502 3.1 0.7 1.0 C4D D:HEM502 3.1 0.1 1.0 C4A D:HEM502 3.1 0.1 1.0 C1B D:HEM502 3.1 0.2 1.0 C1C D:HEM502 3.1 0.7 1.0 C1A D:HEM502 3.1 96.6 1.0 C4B D:HEM502 3.1 0.6 1.0 CD2 D:HIS60 3.1 85.5 1.0 CHD D:HEM502 3.4 0.1 1.0 CHB D:HEM502 3.4 0.5 1.0 CHA D:HEM502 3.4 99.3 1.0 CHC D:HEM502 3.5 0.6 1.0 ND1 D:HIS60 3.9 89.8 1.0 ND1 D:HIS347 4.0 0.5 1.0 CG D:HIS347 4.0 0.2 1.0 CG D:HIS60 4.2 88.5 1.0 OH D:TYR395 4.2 0.2 1.0 C2D D:HEM502 4.3 0.0 1.0 C3C D:HEM502 4.3 0.2 1.0 C2C D:HEM502 4.3 0.8 1.0 C3D D:HEM502 4.3 0.5 1.0 C3A D:HEM502 4.3 99.1 1.0 C2B D:HEM502 4.3 0.1 1.0 C2A D:HEM502 4.3 95.5 1.0 C3B D:HEM502 4.3 0.8 1.0

Iron binding site 9 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:65.9 occ:1.00 FE E:HEC301 0.0 65.9 1.0 NE2 E:HIS69 1.9 87.7 1.0 NA E:HEC301 2.1 69.1 1.0 NC E:HEC301 2.1 63.1 1.0 NB E:HEC301 2.1 67.5 1.0 ND E:HEC301 2.1 68.6 1.0 SD E:MET137 2.3 79.8 1.0 CD2 E:HIS69 2.9 86.3 1.0 CE1 E:HIS69 2.9 85.2 1.0 C1C E:HEC301 3.1 62.9 1.0 C4B E:HEC301 3.1 69.0 1.0 C1A E:HEC301 3.1 71.5 1.0 C4A E:HEC301 3.1 71.5 1.0 C4D E:HEC301 3.1 72.0 1.0 C4C E:HEC301 3.1 65.3 1.0 C1D E:HEC301 3.1 68.0 1.0 C1B E:HEC301 3.2 69.7 1.0 CHC E:HEC301 3.4 64.5 1.0 CHA E:HEC301 3.4 75.0 1.0 CE E:MET137 3.5 66.6 1.0 CHB E:HEC301 3.5 71.6 1.0 CHD E:HEC301 3.5 66.7 1.0 CG E:MET137 3.6 66.2 1.0 ND1 E:HIS69 4.0 84.0 1.0 CG E:HIS69 4.0 83.5 1.0 CB E:MET137 4.2 66.1 1.0 C2C E:HEC301 4.4 69.0 1.0 C3B E:HEC301 4.4 75.5 1.0 C2A E:HEC301 4.4 75.2 1.0 C3A E:HEC301 4.4 73.7 1.0 C3C E:HEC301 4.4 67.3 1.0 C3D E:HEC301 4.5 75.9 1.0 C2D E:HEC301 4.5 75.8 1.0 C2B E:HEC301 4.5 80.0 1.0 CE1 E:HIS124 4.5 75.9 1.0

Iron binding site 10 out of 24 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:85.6 occ:1.00 FE F:HEC401 0.0 85.6 1.0 NE2 F:HIS237 1.9 92.8 1.0 NC F:HEC401 2.1 0.3 1.0 NA F:HEC401 2.1 0.9 1.0 NB F:HEC401 2.1 89.4 1.0 ND F:HEC401 2.1 0.0 1.0 SD F:MET186 2.3 79.9 1.0 CG F:MET186 2.9 75.3 1.0 CE1 F:HIS237 2.9 91.3 1.0 CD2 F:HIS237 2.9 94.9 1.0 C1C F:HEC401 3.1 0.1 1.0 C4B F:HEC401 3.1 93.5 1.0 C1A F:HEC401 3.1 0.3 1.0 C4A F:HEC401 3.1 1.0 1.0 C4D F:HEC401 3.1 1.0 1.0 C1D F:HEC401 3.1 0.9 1.0 C4C F:HEC401 3.1 0.3 1.0 C1B F:HEC401 3.2 93.7 1.0 CHC F:HEC401 3.4 0.2 1.0 CHA F:HEC401 3.4 0.5 1.0 CHB F:HEC401 3.5 0.8 1.0 CHD F:HEC401 3.5 0.8 1.0 CE F:MET186 3.6 89.1 1.0 ND1 F:HIS237 4.0 90.0 1.0 CG F:HIS237 4.1 90.3 1.0 CB F:MET186 4.3 85.7 1.0 C2C F:HEC401 4.4 0.6 1.0 C3B F:HEC401 4.4 94.0 1.0 C3A F:HEC401 4.4 0.3 1.0 C2A F:HEC401 4.4 0.6 1.0 C3D F:HEC401 4.4 0.7 1.0 C2D F:HEC401 4.4 0.1 1.0 C3C F:HEC401 4.4 0.2 1.0 C2B F:HEC401 4.5 96.0 1.0 CA F:MET186 4.8 99.3 1.0

S.Buschmann, E.Warkentin, H.Xie, J.D.Langer, U.Ermler, H.Michel. The Structure of CBB3 Cytochrome Oxidase Provides Insights Into Proton Pumping. Science V. 329 327 2010.
ISSN: ESSN 1095-9203
PubMed: 20576851
DOI: 10.1126/SCIENCE.1187303