Iron in PDB 4lmh: Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca, PDB code: 4lmh was solved by M.J.Edwards, N.Baiden, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.97 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.640, 245.380, 135.630, 90.00, 97.89, 90.00
R / Rfree (%)	19.3 / 23

The structure of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca (pdb code 4lmh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca, PDB code: 4lmh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:18.0 occ:1.00 FE A:HEC801 0.0 18.0 1.0 NE2 A:HIS277 1.9 21.8 1.0 NE2 A:HIS232 2.0 25.6 1.0 NC A:HEC801 2.0 19.8 1.0 NA A:HEC801 2.0 18.5 1.0 ND A:HEC801 2.1 18.4 1.0 NB A:HEC801 2.1 20.5 1.0 CE1 A:HIS277 2.8 21.3 1.0 CD2 A:HIS277 2.9 23.8 1.0 CE1 A:HIS232 3.0 25.8 1.0 CD2 A:HIS232 3.0 23.0 1.0 C4C A:HEC801 3.0 20.0 1.0 C4A A:HEC801 3.1 20.8 1.0 C1A A:HEC801 3.1 22.1 1.0 C1C A:HEC801 3.1 22.4 1.0 C1D A:HEC801 3.1 22.1 1.0 C4D A:HEC801 3.1 21.4 1.0 C1B A:HEC801 3.1 20.8 1.0 C4B A:HEC801 3.1 21.1 1.0 CHD A:HEC801 3.4 21.4 1.0 CHA A:HEC801 3.4 23.5 1.0 CHB A:HEC801 3.4 25.5 1.0 CHC A:HEC801 3.5 21.6 1.0 ND1 A:HIS277 3.9 20.2 1.0 CG A:HIS277 4.0 22.9 1.0 ND1 A:HIS232 4.1 26.8 1.0 CG A:HIS232 4.2 25.3 1.0 C3C A:HEC801 4.3 25.7 1.0 C2C A:HEC801 4.3 26.6 1.0 C3A A:HEC801 4.3 22.4 1.0 C2A A:HEC801 4.3 24.4 1.0 C2D A:HEC801 4.3 22.2 1.0 C3D A:HEC801 4.3 21.1 1.0 C2B A:HEC801 4.3 23.4 1.0 C3B A:HEC801 4.3 20.6 1.0

Iron binding site 2 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:17.6 occ:1.00 FE A:HEC802 0.0 17.6 1.0 NB A:HEC802 2.0 22.3 1.0 NA A:HEC802 2.0 18.4 1.0 NE2 A:HIS254 2.0 20.0 1.0 NE2 A:HIS240 2.1 32.9 1.0 NC A:HEC802 2.1 19.1 1.0 ND A:HEC802 2.1 16.6 1.0 CE1 A:HIS240 2.7 32.2 1.0 CE1 A:HIS254 2.9 18.8 1.0 C1B A:HEC802 3.0 24.0 1.0 C4B A:HEC802 3.1 22.4 1.0 C4A A:HEC802 3.1 20.6 1.0 C1A A:HEC802 3.1 21.4 1.0 C1C A:HEC802 3.1 20.8 1.0 C4C A:HEC802 3.1 21.0 1.0 C1D A:HEC802 3.1 20.8 1.0 C4D A:HEC802 3.1 21.4 1.0 CD2 A:HIS254 3.1 17.9 1.0 CD2 A:HIS240 3.3 35.5 1.0 CHB A:HEC802 3.4 23.7 1.0 CHC A:HEC802 3.4 24.1 1.0 CHD A:HEC802 3.5 22.0 1.0 CHA A:HEC802 3.5 19.4 1.0 ND1 A:HIS240 3.9 36.3 1.0 ND1 A:HIS254 4.1 19.5 1.0 CG A:HIS254 4.2 17.5 1.0 CG A:HIS240 4.2 38.3 1.0 C2B A:HEC802 4.3 21.0 1.0 C3B A:HEC802 4.3 22.1 1.0 C3A A:HEC802 4.3 20.0 1.0 C2A A:HEC802 4.3 23.7 1.0 C2C A:HEC802 4.3 22.2 1.0 C3C A:HEC802 4.3 22.9 1.0 C2D A:HEC802 4.4 24.3 1.0 C3D A:HEC802 4.4 26.2 1.0

Iron binding site 3 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:20.1 occ:1.00 FE A:HEC803 0.0 20.1 1.0 NE2 A:HIS274 2.0 20.5 1.0 NA A:HEC803 2.0 20.2 1.0 NC A:HEC803 2.0 17.1 1.0 NB A:HEC803 2.1 24.5 1.0 ND A:HEC803 2.1 21.4 1.0 NE2 A:HIS325 2.1 22.7 1.0 CE1 A:HIS274 2.9 20.2 1.0 CE1 A:HIS325 3.0 22.2 1.0 C1A A:HEC803 3.1 21.6 1.0 C1C A:HEC803 3.1 23.0 1.0 CD2 A:HIS274 3.1 21.8 1.0 C4D A:HEC803 3.1 20.2 1.0 C4C A:HEC803 3.1 20.1 1.0 C4A A:HEC803 3.1 22.7 1.0 C4B A:HEC803 3.1 19.1 1.0 C1B A:HEC803 3.1 24.9 1.0 C1D A:HEC803 3.1 20.5 1.0 CD2 A:HIS325 3.2 22.6 1.0 CHA A:HEC803 3.4 21.3 1.0 CHC A:HEC803 3.4 20.2 1.0 CHB A:HEC803 3.5 26.3 1.0 CHD A:HEC803 3.5 19.9 1.0 ND1 A:HIS274 4.0 19.2 1.0 CG A:HIS274 4.1 20.7 1.0 ND1 A:HIS325 4.2 21.6 1.0 CG A:HIS325 4.3 21.2 1.0 C2A A:HEC803 4.3 21.8 1.0 C2C A:HEC803 4.3 16.8 1.0 C3C A:HEC803 4.3 17.9 1.0 C3A A:HEC803 4.3 22.9 1.0 C3D A:HEC803 4.3 21.5 1.0 C3B A:HEC803 4.3 22.3 1.0 C2B A:HEC803 4.3 21.8 1.0 C2D A:HEC803 4.3 23.4 1.0 CMC A:HEC804 4.9 25.9 1.0 CB A:PHE338 5.0 28.8 1.0 CG2 A:THR270 5.0 17.9 1.0

Iron binding site 4 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe804 b:25.8 occ:1.00 FE A:HEC804 0.0 25.8 1.0 NE2 A:HIS384 1.9 25.7 1.0 NE2 A:HIS351 2.0 27.6 1.0 NB A:HEC804 2.0 22.1 1.0 NA A:HEC804 2.0 27.8 1.0 NC A:HEC804 2.1 26.7 1.0 ND A:HEC804 2.1 25.8 1.0 CE1 A:HIS384 2.7 24.3 1.0 CE1 A:HIS351 2.7 22.0 1.0 C1A A:HEC804 3.1 28.5 1.0 C4B A:HEC804 3.1 28.0 1.0 C1B A:HEC804 3.1 27.9 1.0 CD2 A:HIS384 3.1 23.0 1.0 C4D A:HEC804 3.1 29.0 1.0 C4A A:HEC804 3.1 25.3 1.0 C1C A:HEC804 3.1 27.3 1.0 CD2 A:HIS351 3.1 24.9 1.0 C4C A:HEC804 3.1 25.6 1.0 C1D A:HEC804 3.1 27.5 1.0 CHA A:HEC804 3.4 28.8 1.0 CHC A:HEC804 3.4 26.0 1.0 CHB A:HEC804 3.4 29.9 1.0 CHD A:HEC804 3.5 25.1 1.0 ND1 A:HIS384 3.9 19.3 1.0 ND1 A:HIS351 3.9 27.0 1.0 CG A:HIS384 4.1 24.9 1.0 CG A:HIS351 4.1 25.7 1.0 C3B A:HEC804 4.3 25.9 1.0 C2A A:HEC804 4.3 29.3 1.0 C2B A:HEC804 4.3 23.0 1.0 C3A A:HEC804 4.3 28.5 1.0 C2C A:HEC804 4.3 27.4 1.0 C3D A:HEC804 4.3 30.0 1.0 C3C A:HEC804 4.3 28.5 1.0 C2D A:HEC804 4.4 28.9 1.0 CBB A:HEC803 4.6 19.7 1.0

Iron binding site 5 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe805 b:26.9 occ:1.00 FE A:HEC805 0.0 26.9 1.0 NE2 A:HIS359 2.0 25.6 1.0 NA A:HEC805 2.0 29.9 1.0 NB A:HEC805 2.0 30.4 1.0 NE2 A:HIS368 2.1 20.9 1.0 NC A:HEC805 2.1 34.7 1.0 ND A:HEC805 2.1 33.1 1.0 CE1 A:HIS359 2.8 25.8 1.0 C4A A:HEC805 3.0 30.9 1.0 C1A A:HEC805 3.0 32.7 1.0 C1B A:HEC805 3.0 30.6 1.0 CE1 A:HIS368 3.0 20.6 1.0 CD2 A:HIS368 3.1 24.1 1.0 CD2 A:HIS359 3.1 29.8 1.0 C4B A:HEC805 3.1 29.2 1.0 C1C A:HEC805 3.1 36.0 1.0 C4D A:HEC805 3.1 30.6 1.0 C4C A:HEC805 3.1 32.4 1.0 C1D A:HEC805 3.1 33.8 1.0 CHB A:HEC805 3.4 29.6 1.0 CHA A:HEC805 3.4 30.8 1.0 CHC A:HEC805 3.4 34.1 1.0 CHD A:HEC805 3.5 35.7 1.0 ND1 A:HIS359 4.0 26.8 1.0 CG A:HIS359 4.1 25.3 1.0 ND1 A:HIS368 4.2 23.7 1.0 CG A:HIS368 4.2 25.2 1.0 C3A A:HEC805 4.2 30.5 1.0 C2A A:HEC805 4.2 33.4 1.0 C2B A:HEC805 4.3 30.6 1.0 C3B A:HEC805 4.3 30.8 1.0 C2C A:HEC805 4.3 33.0 1.0 C3C A:HEC805 4.3 33.6 1.0 C3D A:HEC805 4.4 29.7 1.0 C2D A:HEC805 4.4 34.0 1.0 CG A:PRO355 4.6 29.1 1.0 C2 B:DMS901 4.7 31.5 1.0

Iron binding site 6 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe806 b:23.1 occ:1.00 FE A:HEC806 0.0 23.1 1.0 NE2 A:HIS618 2.0 33.3 1.0 NE2 A:HIS570 2.0 25.8 1.0 NC A:HEC806 2.0 30.9 1.0 NB A:HEC806 2.0 29.9 1.0 ND A:HEC806 2.1 28.3 1.0 NA A:HEC806 2.1 25.5 1.0 CE1 A:HIS570 2.7 24.1 1.0 CD2 A:HIS618 3.0 34.1 1.0 CE1 A:HIS618 3.0 33.6 1.0 C4B A:HEC806 3.0 28.9 1.0 C1C A:HEC806 3.0 30.6 1.0 C4C A:HEC806 3.1 29.9 1.0 C4D A:HEC806 3.1 27.6 1.0 C1B A:HEC806 3.1 32.4 1.0 C1A A:HEC806 3.1 28.6 1.0 C1D A:HEC806 3.1 26.1 1.0 CD2 A:HIS570 3.2 24.7 1.0 C4A A:HEC806 3.2 28.2 1.0 CHC A:HEC806 3.3 28.4 1.0 CHA A:HEC806 3.5 30.6 1.0 CHD A:HEC806 3.5 25.8 1.0 CHB A:HEC806 3.5 31.6 1.0 ND1 A:HIS570 4.0 23.8 1.0 ND1 A:HIS618 4.1 33.5 1.0 CG A:HIS618 4.1 37.8 1.0 CG A:HIS570 4.2 25.8 1.0 C3B A:HEC806 4.2 28.4 1.0 C2C A:HEC806 4.2 31.4 1.0 C3C A:HEC806 4.3 31.7 1.0 C2B A:HEC806 4.3 29.8 1.0 C3D A:HEC806 4.4 26.7 1.0 C2A A:HEC806 4.4 34.0 1.0 C2D A:HEC806 4.4 28.1 1.0 C3A A:HEC806 4.4 34.2 1.0

Iron binding site 7 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe807 b:30.8 occ:1.00 FE A:HEC807 0.0 30.8 1.0 NE2 A:HIS576 2.0 32.8 1.0 NC A:HEC807 2.0 36.0 1.0 NE2 A:HIS587 2.1 33.3 1.0 ND A:HEC807 2.1 34.4 1.0 NA A:HEC807 2.1 33.2 1.0 NB A:HEC807 2.1 33.1 1.0 CE1 A:HIS576 2.6 36.8 1.0 CD2 A:HIS587 3.0 35.5 1.0 C4C A:HEC807 3.0 35.7 1.0 C1D A:HEC807 3.1 33.5 1.0 C4D A:HEC807 3.1 34.0 1.0 C1C A:HEC807 3.1 36.4 1.0 C1A A:HEC807 3.1 34.9 1.0 CE1 A:HIS587 3.1 34.0 1.0 C4B A:HEC807 3.1 30.1 1.0 C4A A:HEC807 3.1 32.9 1.0 C1B A:HEC807 3.1 31.7 1.0 CD2 A:HIS576 3.3 36.4 1.0 CHD A:HEC807 3.4 33.2 1.0 CHA A:HEC807 3.4 35.3 1.0 CHC A:HEC807 3.4 33.7 1.0 CHB A:HEC807 3.5 32.7 1.0 ND1 A:HIS576 3.8 35.2 1.0 CG A:HIS587 4.1 37.4 1.0 ND1 A:HIS587 4.2 33.6 1.0 CG A:HIS576 4.2 30.6 1.0 C3C A:HEC807 4.3 37.1 1.0 C2C A:HEC807 4.3 33.6 1.0 C2D A:HEC807 4.3 32.4 1.0 C3D A:HEC807 4.3 37.0 1.0 C2A A:HEC807 4.3 36.7 1.0 C3A A:HEC807 4.3 36.5 1.0 C3B A:HEC807 4.3 31.0 1.0 C2B A:HEC807 4.3 32.6 1.0

Iron binding site 8 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe808 b:34.2 occ:1.00 FE A:HEC808 0.0 34.2 1.0 NE2 A:HIS639 1.9 33.1 1.0 NC A:HEC808 2.0 40.4 1.0 NE2 A:HIS613 2.1 42.4 1.0 ND A:HEC808 2.1 38.9 1.0 NB A:HEC808 2.1 43.6 1.0 NA A:HEC808 2.1 41.9 1.0 CE1 A:HIS613 2.9 41.0 1.0 CE1 A:HIS639 2.9 35.3 1.0 CD2 A:HIS639 2.9 33.7 1.0 C4C A:HEC808 3.0 37.7 1.0 C1C A:HEC808 3.1 38.8 1.0 C1A A:HEC808 3.1 40.5 1.0 C1D A:HEC808 3.1 36.7 1.0 C4D A:HEC808 3.1 37.7 1.0 C4A A:HEC808 3.1 42.5 1.0 C1B A:HEC808 3.1 44.7 1.0 C4B A:HEC808 3.1 42.0 1.0 CD2 A:HIS613 3.2 43.1 1.0 CHD A:HEC808 3.4 36.6 1.0 CHA A:HEC808 3.4 38.9 1.0 CHC A:HEC808 3.5 39.3 1.0 CHB A:HEC808 3.5 43.3 1.0 ND1 A:HIS639 4.0 34.5 1.0 CG A:HIS639 4.0 34.8 1.0 ND1 A:HIS613 4.1 40.5 1.0 CG A:HIS613 4.2 41.1 1.0 C3C A:HEC808 4.3 36.6 1.0 C2C A:HEC808 4.3 33.2 1.0 C3A A:HEC808 4.3 42.4 1.0 C2A A:HEC808 4.3 42.6 1.0 C3D A:HEC808 4.3 38.1 1.0 C2D A:HEC808 4.3 37.1 1.0 C2B A:HEC808 4.3 44.2 1.0 C3B A:HEC808 4.3 42.7 1.0 CG2 A:ILE650 4.9 43.6 1.0

Iron binding site 9 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe809 b:45.4 occ:1.00 FE A:HEC809 0.0 45.4 1.0 NE2 A:HIS685 1.9 43.0 1.0 NE2 A:HIS733 2.0 48.9 1.0 NA A:HEC809 2.0 56.3 1.0 NB A:HEC809 2.0 52.4 1.0 NC A:HEC809 2.1 51.1 1.0 ND A:HEC809 2.1 54.2 1.0 CE1 A:HIS685 2.8 47.8 1.0 CE1 A:HIS733 2.9 49.2 1.0 CD2 A:HIS733 3.0 51.8 1.0 CD2 A:HIS685 3.0 46.6 1.0 C4A A:HEC809 3.0 58.6 1.0 C1B A:HEC809 3.1 52.6 1.0 C1A A:HEC809 3.1 56.1 1.0 C4B A:HEC809 3.1 53.5 1.0 C1C A:HEC809 3.1 52.4 1.0 C4C A:HEC809 3.1 47.2 1.0 C4D A:HEC809 3.1 54.3 1.0 C1D A:HEC809 3.1 48.5 1.0 CHB A:HEC809 3.4 55.8 1.0 CHA A:HEC809 3.4 57.2 1.0 CHC A:HEC809 3.4 53.4 1.0 CHD A:HEC809 3.5 47.0 1.0 ND1 A:HIS685 3.9 47.9 1.0 ND1 A:HIS733 4.0 51.8 1.0 CG A:HIS685 4.1 48.1 1.0 CG A:HIS733 4.1 50.7 1.0 C3A A:HEC809 4.3 60.3 1.0 C2A A:HEC809 4.3 63.1 1.0 C2B A:HEC809 4.3 56.9 1.0 C3B A:HEC809 4.3 53.4 1.0 C2C A:HEC809 4.3 48.9 1.0 C3C A:HEC809 4.3 49.8 1.0 C3D A:HEC809 4.3 53.9 1.0 C2D A:HEC809 4.4 49.0 1.0 CBB A:HEC808 5.0 42.6 1.0

Iron binding site 10 out of 40 in the Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Outer Membrane Decaheme Cytochrome Omca within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe810 b:65.6 occ:1.00 FE A:HEC810 0.0 65.6 1.0 NE2 A:HIS696 1.8 67.0 1.0 NE2 A:HIS724 1.8 56.3 1.0 NC A:HEC810 2.0 70.7 1.0 NA A:HEC810 2.1 62.5 1.0 NB A:HEC810 2.1 63.2 1.0 ND A:HEC810 2.1 69.2 1.0 CD2 A:HIS696 2.6 60.9 1.0 CE1 A:HIS724 2.7 59.9 1.0 CD2 A:HIS724 2.9 60.6 1.0 CE1 A:HIS696 3.0 66.8 1.0 C4C A:HEC810 3.0 67.2 1.0 C1C A:HEC810 3.1 72.4 1.0 C1D A:HEC810 3.1 67.8 1.0 C1A A:HEC810 3.1 64.6 1.0 C4A A:HEC810 3.1 65.0 1.0 C4B A:HEC810 3.1 67.1 1.0 C4D A:HEC810 3.1 65.9 1.0 C1B A:HEC810 3.1 65.0 1.0 CHD A:HEC810 3.4 64.9 1.0 CHC A:HEC810 3.4 67.2 1.0 CHA A:HEC810 3.5 65.9 1.0 CHB A:HEC810 3.5 63.6 1.0 ND1 A:HIS724 3.7 59.3 1.0 CG A:HIS696 3.8 60.4 1.0 CG A:HIS724 3.9 57.8 1.0 ND1 A:HIS696 4.0 66.7 1.0 C2C A:HEC810 4.2 71.2 1.0 C3C A:HEC810 4.3 69.7 1.0 C3A A:HEC810 4.3 61.1 1.0 C2A A:HEC810 4.3 58.5 1.0 C3B A:HEC810 4.3 68.3 1.0 C2D A:HEC810 4.3 68.6 1.0 C2B A:HEC810 4.3 65.8 1.0 C3D A:HEC810 4.3 68.1 1.0 CMB A:HEC809 4.9 54.9 1.0

M.J.Edwards, N.Baiden, T.A.Clarke, D.J.Richardson. Insights Into Electron Transfer at the Microbe-Mineral Interface: the X-Ray Crystal Structures of Shewanella Oneidensis Mtrc and Omca Febs Letters 2014.