Iron in PDB 5ir6: The Structure of Bd Oxidase From Geobacillus Thermodenitrificans

The structure of The Structure of Bd Oxidase From Geobacillus Thermodenitrificans, PDB code: 5ir6 was solved by S.Safarian, H.Mueller, C.Rajendran, J.Preu, S.Ovchinnikov, T.Kusumoto, T.Hirose, J.Langer, J.Sakamoto, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	110.060, 120.860, 122.720, 90.00, 90.00, 90.00
R / Rfree (%)	30.3 / 32.5

The binding sites of Iron atom in the The Structure of Bd Oxidase From Geobacillus Thermodenitrificans (pdb code 5ir6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the The Structure of Bd Oxidase From Geobacillus Thermodenitrificans, PDB code: 5ir6:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the The Structure of Bd Oxidase From Geobacillus Thermodenitrificans


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 Bd Oxidase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:75.5 occ:1.00 FE A:HEB501 0.0 75.5 1.0 NA A:HEB501 2.1 75.5 1.0 NB A:HEB501 2.1 75.5 1.0 NC A:HEB501 2.2 75.5 1.0 ND A:HEB501 2.3 75.5 1.0 NE2 A:HIS186 2.3 64.3 1.0 SD A:MET325 2.4 72.4 1.0 CE1 A:HIS186 2.8 54.7 1.0 CE A:MET325 3.1 55.5 1.0 C1C A:HEB501 3.2 75.5 1.0 C1A A:HEB501 3.2 75.5 1.0 C4A A:HEB501 3.2 75.5 1.0 C4B A:HEB501 3.2 75.5 1.0 C1B A:HEB501 3.2 75.5 1.0 C4C A:HEB501 3.3 75.5 1.0 C4D A:HEB501 3.3 75.5 1.0 C1D A:HEB501 3.4 75.5 1.0 CD2 A:HIS186 3.4 61.5 1.0 CHC A:HEB501 3.6 75.5 1.0 CG A:MET325 3.6 67.4 1.0 CHB A:HEB501 3.7 75.5 1.0 CHA A:HEB501 3.7 75.5 1.0 CHD A:HEB501 3.8 75.5 1.0 ND1 A:HIS186 4.0 45.7 1.0 C2C A:HEB501 4.2 75.5 1.0 C2A A:HEB501 4.2 75.5 1.0 C2B A:HEB501 4.2 75.5 1.0 C3A A:HEB501 4.3 75.5 1.0 CG A:HIS186 4.3 54.3 1.0 C3B A:HEB501 4.3 75.5 1.0 C2D A:HEB501 4.3 75.5 1.0 C3C A:HEB501 4.4 75.5 1.0 C3D A:HEB501 4.5 75.5 1.0 CB A:MET325 5.0 61.5 1.0

Iron binding site 2 out of 3 in the The Structure of Bd Oxidase From Geobacillus Thermodenitrificans


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 Bd Oxidase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:92.3 occ:1.00 FE A:HEB502 0.0 92.3 1.0 NA A:HEB502 2.1 92.3 1.0 NB A:HEB502 2.1 92.3 1.0 NC A:HEB502 2.1 92.3 1.0 ND A:HEB502 2.3 92.3 1.0 OE2 A:GLU101 2.4 1.0 1.0 NE2 A:HIS21 2.7 79.2 1.0 C1B A:HEB502 3.2 92.3 1.0 C1C A:HEB502 3.2 92.3 1.0 C4A A:HEB502 3.2 92.3 1.0 C1A A:HEB502 3.2 92.3 1.0 C4B A:HEB502 3.2 92.3 1.0 C4C A:HEB502 3.3 92.3 1.0 C1D A:HEB502 3.4 92.3 1.0 C4D A:HEB502 3.4 92.3 1.0 CD A:GLU101 3.4 94.4 1.0 CE1 A:HIS21 3.4 85.4 1.0 CHB A:HEB502 3.6 92.3 1.0 CHC A:HEB502 3.7 92.3 1.0 CHD A:HEB502 3.7 92.3 1.0 CHA A:HEB502 3.8 92.3 1.0 CD2 A:HIS21 3.8 68.9 1.0 OE1 A:GLU101 4.0 82.7 1.0 C2C A:HEB502 4.2 92.3 1.0 C2B A:HEB502 4.2 92.3 1.0 C2A A:HEB502 4.2 92.3 1.0 C3A A:HEB502 4.3 92.3 1.0 C3B A:HEB502 4.3 92.3 1.0 C3C A:HEB502 4.3 92.3 1.0 C2D A:HEB502 4.4 92.3 1.0 CG A:GLU101 4.5 76.7 1.0 C3D A:HEB502 4.5 92.3 1.0 ND1 A:HIS21 4.6 63.8 1.0 CA A:GLY72 4.8 68.3 1.0 CG A:HIS21 4.9 59.3 1.0

Iron binding site 3 out of 3 in the The Structure of Bd Oxidase From Geobacillus Thermodenitrificans


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 Bd Oxidase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:0.4 occ:1.00 FE A:HDD503 0.0 0.4 1.0 ND A:HDD503 1.8 0.4 1.0 NA A:HDD503 2.1 0.4 1.0 NC A:HDD503 2.1 0.4 1.0 NB A:HDD503 2.1 0.4 1.0 OE2 A:GLU378 2.7 82.1 1.0 C4D A:HDD503 2.8 0.4 1.0 C1D A:HDD503 2.9 0.4 1.0 CD A:GLU378 3.0 80.0 1.0 C1A A:HDD503 3.0 0.4 1.0 C4C A:HDD503 3.0 0.4 1.0 C1B A:HDD503 3.0 0.4 1.0 C4B A:HDD503 3.1 0.4 1.0 C4A A:HDD503 3.1 0.4 1.0 C1C A:HDD503 3.1 0.4 1.0 CHA A:HDD503 3.3 0.4 1.0 CHD A:HDD503 3.3 0.4 1.0 CHB A:HDD503 3.4 0.4 1.0 CG A:GLU378 3.4 87.0 1.0 CHC A:HDD503 3.5 0.4 1.0 OE1 A:GLU378 3.6 90.5 1.0 CD1 A:LEU18 3.8 0.7 1.0 C3D A:HDD503 3.9 0.4 1.0 C2D A:HDD503 4.0 0.4 1.0 CMD A:HDD503 4.3 0.4 1.0 C2A A:HDD503 4.3 0.4 1.0 C3C A:HDD503 4.3 0.4 1.0 C2B A:HDD503 4.4 0.4 1.0 CAD A:HDD503 4.4 0.4 1.0 C3B A:HDD503 4.4 0.4 1.0 C3A A:HDD503 4.4 0.4 1.0 C2C A:HDD503 4.4 0.4 1.0 CB A:GLU378 4.5 44.1 1.0 CG2 A:THR14 4.9 0.6 1.0 NH1 A:ARG381 4.9 88.7 1.0

S.Safarian, C.Rajendran, H.Muller, J.Preu, J.D.Langer, S.Ovchinnikov, T.Hirose, T.Kusumoto, J.Sakamoto, H.Michel. Structure of A Bd Oxidase Indicates Similar Mechanisms For Membrane-Integrated Oxygen Reductases. Science V. 352 583 2016.
ISSN: ESSN 1095-9203
PubMed: 27126043
DOI: 10.1126/SCIENCE.AAF2477