Iron in PDB 3wmm: Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form

The structure of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form, PDB code: 3wmm was solved by S.Niwa, K.Takeda, Z.-Y.Wang-Otomo, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.99 / 3.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	227.341, 148.238, 161.792, 90.00, 117.59, 90.00
R / Rfree (%)	31.4 / 33.7

The structure of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form also contains other interesting chemical elements:

Magnesium	(Mg)	36 atoms
Calcium	(Ca)	17 atoms

The binding sites of Iron atom in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form (pdb code 3wmm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form, PDB code: 3wmm:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form


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 LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:62.0 occ:1.00 FE C:HEM501 0.0 62.0 1.0 NA C:HEM501 2.0 65.0 1.0 NB C:HEM501 2.0 65.6 1.0 ND C:HEM501 2.0 60.3 1.0 NC C:HEM501 2.0 63.8 1.0 NE2 C:HIS111 2.1 62.1 1.0 SD C:MET94 2.1 49.1 1.0 C4A C:HEM501 3.0 73.6 1.0 C1D C:HEM501 3.0 59.5 1.0 C1B C:HEM501 3.0 69.9 1.0 C4C C:HEM501 3.0 64.6 1.0 CD2 C:HIS111 3.0 73.0 1.0 C1A C:HEM501 3.0 66.3 1.0 C4D C:HEM501 3.0 57.5 1.0 C1C C:HEM501 3.1 66.1 1.0 C4B C:HEM501 3.1 68.3 1.0 CE1 C:HIS111 3.1 66.1 1.0 CHB C:HEM501 3.3 75.6 1.0 CHD C:HEM501 3.4 65.1 1.0 CHA C:HEM501 3.4 63.1 1.0 CG C:MET94 3.4 58.7 1.0 CE C:MET94 3.5 44.1 1.0 CHC C:HEM501 3.5 70.5 1.0 ND1 C:HIS111 4.2 75.2 1.0 CG C:HIS111 4.2 79.2 1.0 C3A C:HEM501 4.2 73.4 1.0 C2A C:HEM501 4.2 67.9 1.0 C2B C:HEM501 4.3 69.9 1.0 C3D C:HEM501 4.3 54.4 1.0 C2D C:HEM501 4.3 57.1 1.0 C3B C:HEM501 4.3 68.2 1.0 C2C C:HEM501 4.3 62.0 1.0 C3C C:HEM501 4.4 64.0 1.0 CB C:MET94 4.5 53.2 1.0

Iron binding site 2 out of 5 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form


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 LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:59.0 occ:1.00 FE C:HEM502 0.0 59.0 1.0 NA C:HEM502 2.0 47.8 1.0 NC C:HEM502 2.0 51.1 1.0 ND C:HEM502 2.0 44.1 1.0 NB C:HEM502 2.0 51.1 1.0 SD C:MET130 2.0 56.4 1.0 NE2 C:HIS156 2.1 60.2 1.0 C1D C:HEM502 3.0 47.1 1.0 C4C C:HEM502 3.0 54.6 1.0 C4D C:HEM502 3.0 44.7 1.0 C1B C:HEM502 3.0 51.7 1.0 C4A C:HEM502 3.0 50.9 1.0 C1A C:HEM502 3.0 50.2 1.0 C1C C:HEM502 3.0 55.0 1.0 CD2 C:HIS156 3.0 59.2 1.0 C4B C:HEM502 3.1 49.6 1.0 CE1 C:HIS156 3.1 63.1 1.0 CHB C:HEM502 3.3 57.2 1.0 CHA C:HEM502 3.3 49.8 1.0 CHD C:HEM502 3.3 51.5 1.0 CHC C:HEM502 3.4 49.8 1.0 CG C:MET130 3.4 55.3 1.0 CE C:MET130 3.5 39.6 1.0 CG C:HIS156 4.2 63.9 1.0 C3A C:HEM502 4.2 42.4 1.0 ND1 C:HIS156 4.2 65.0 1.0 CB C:MET130 4.2 59.2 1.0 C2A C:HEM502 4.2 44.9 1.0 C2B C:HEM502 4.2 44.3 1.0 C3B C:HEM502 4.3 47.6 1.0 C3D C:HEM502 4.3 44.7 1.0 C2C C:HEM502 4.3 59.2 1.0 C2D C:HEM502 4.3 41.4 1.0 C3C C:HEM502 4.3 55.6 1.0

Iron binding site 3 out of 5 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form


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 LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:67.9 occ:1.00 FE C:HEM503 0.0 67.9 1.0 NC C:HEM503 2.0 64.7 1.0 NA C:HEM503 2.0 67.3 1.0 ND C:HEM503 2.0 65.5 1.0 NB C:HEM503 2.0 71.7 1.0 SD C:MET236 2.1 49.4 1.0 NE2 C:HIS251 2.4 64.9 1.0 C4C C:HEM503 3.0 61.0 1.0 C1D C:HEM503 3.0 64.3 1.0 C4D C:HEM503 3.0 68.8 1.0 C1C C:HEM503 3.0 66.5 1.0 C1B C:HEM503 3.0 72.2 1.0 C4A C:HEM503 3.0 70.6 1.0 C1A C:HEM503 3.0 75.1 1.0 C4B C:HEM503 3.1 70.2 1.0 CE1 C:HIS251 3.1 74.1 1.0 CHD C:HEM503 3.4 62.3 1.0 CHB C:HEM503 3.4 75.2 1.0 CHA C:HEM503 3.4 73.7 1.0 CG C:MET236 3.4 47.0 1.0 CHC C:HEM503 3.4 69.6 1.0 CE C:MET236 3.5 58.9 1.0 CD2 C:HIS251 3.6 67.6 1.0 CB C:MET236 4.2 43.2 1.0 C3A C:HEM503 4.3 71.5 1.0 C2C C:HEM503 4.3 67.0 1.0 C2A C:HEM503 4.3 75.7 1.0 C3C C:HEM503 4.3 62.1 1.0 C3D C:HEM503 4.3 66.4 1.0 C2B C:HEM503 4.3 62.7 1.0 C2D C:HEM503 4.3 62.0 1.0 C3B C:HEM503 4.3 63.3 1.0 ND1 C:HIS251 4.4 78.8 1.0 CG C:HIS251 4.6 71.7 1.0

Iron binding site 4 out of 5 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form


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 LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe504 b:47.9 occ:1.00 FE C:HEM504 0.0 47.9 1.0 NC C:HEM504 2.0 47.8 1.0 NB C:HEM504 2.0 48.9 1.0 NA C:HEM504 2.0 44.3 1.0 ND C:HEM504 2.0 56.3 1.0 NE2 C:HIS311 2.1 55.8 1.0 NE2 C:HIS144 2.1 55.8 1.0 C4C C:HEM504 3.0 54.8 1.0 C1B C:HEM504 3.0 46.6 1.0 C1D C:HEM504 3.0 57.3 1.0 C4A C:HEM504 3.0 46.3 1.0 C1C C:HEM504 3.0 51.3 1.0 C4B C:HEM504 3.0 54.8 1.0 C4D C:HEM504 3.0 57.1 1.0 C1A C:HEM504 3.0 44.7 1.0 CD2 C:HIS311 3.1 51.6 1.0 CE1 C:HIS144 3.1 65.8 1.0 CE1 C:HIS311 3.1 56.0 1.0 CD2 C:HIS144 3.1 58.8 1.0 CHB C:HEM504 3.3 43.9 1.0 CHD C:HEM504 3.3 57.7 1.0 CHA C:HEM504 3.4 44.2 1.0 CHC C:HEM504 3.4 46.8 1.0 ND1 C:HIS144 4.2 61.6 1.0 C2B C:HEM504 4.2 45.8 1.0 ND1 C:HIS311 4.2 54.1 1.0 CG C:HIS311 4.2 54.3 1.0 C3A C:HEM504 4.2 47.4 1.0 C3B C:HEM504 4.2 52.0 1.0 C2A C:HEM504 4.3 48.3 1.0 CG C:HIS144 4.3 59.9 1.0 C2C C:HEM504 4.3 51.2 1.0 C3C C:HEM504 4.3 52.1 1.0 C2D C:HEM504 4.3 55.6 1.0 C3D C:HEM504 4.3 57.0 1.0 CB C:ALA272 4.6 51.0 1.0

Iron binding site 5 out of 5 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form


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 LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe404 b:0.3 occ:1.00 NE2 L:HIS239 2.0 38.2 1.0 NE2 L:HIS199 2.0 41.2 1.0 NE2 M:HIS266 2.0 30.4 1.0 NE2 M:HIS219 2.0 29.2 1.0 OE2 M:GLU234 2.2 17.0 1.0 OE1 M:GLU234 2.2 20.3 1.0 CD M:GLU234 2.4 20.9 1.0 CE1 L:HIS199 2.9 40.2 1.0 CE1 L:HIS239 3.0 44.3 1.0 CD2 L:HIS239 3.0 43.6 1.0 CE1 M:HIS219 3.0 25.4 1.0 CD2 L:HIS199 3.0 42.7 1.0 CE1 M:HIS266 3.0 23.0 1.0 CD2 M:HIS266 3.0 28.9 1.0 CD2 M:HIS219 3.0 22.9 1.0 CG M:GLU234 3.9 29.0 1.0 ND1 L:HIS199 4.1 44.3 1.0 ND1 L:HIS239 4.1 43.2 1.0 CG L:HIS239 4.1 44.0 1.0 ND1 M:HIS219 4.1 24.3 1.0 ND1 M:HIS266 4.1 27.2 1.0 CG L:HIS199 4.1 45.6 1.0 CG M:HIS266 4.2 34.5 1.0 CG M:HIS219 4.2 26.0 1.0 CD1 M:ILE223 4.2 41.8 1.0 CG1 M:ILE223 4.4 34.7 1.0 CG1 L:ILE203 4.7 52.1 1.0 CB M:GLU234 5.0 34.3 1.0

S.Niwa, L.J.Yu, K.Takeda, Y.Hirano, T.Kawakami, Z.Y.Wang-Otomo, K.Miki. Structure of the LH1-Rc Complex From Thermochromatium Tepidum at 3.0 Angstrom Nature V. 508 228 2014.
ISSN: ISSN 0028-0836
PubMed: 24670637
DOI: 10.1038/NATURE13197