Iron in PDB 5jru: Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus

The structure of Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus, PDB code: 5jru was solved by J.Bruegger, C.Hespen, C.M.Phillips-Piro, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.92 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.264, 70.446, 108.419, 90.00, 104.93, 90.00
R / Rfree (%)	19.2 / 25.4

The binding sites of Iron atom in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus (pdb code 5jru). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus, PDB code: 5jru:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus


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 Fe(II) Unliganded H-Nox Protein From C. Subterraneus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:16.5 occ:1.00 FE A:HEM201 0.0 16.5 1.0 NC A:HEM201 2.0 20.1 1.0 ND A:HEM201 2.0 20.1 1.0 NB A:HEM201 2.0 17.1 1.0 NA A:HEM201 2.0 15.2 1.0 NE2 A:HIS102 2.0 21.9 1.0 CE1 A:HIS102 2.8 18.0 1.0 C4C A:HEM201 3.0 20.4 1.0 C4A A:HEM201 3.0 17.9 1.0 C1D A:HEM201 3.0 18.6 1.0 C1B A:HEM201 3.0 16.2 1.0 C4D A:HEM201 3.0 18.3 1.0 C4B A:HEM201 3.1 21.1 1.0 C1A A:HEM201 3.1 18.2 1.0 C1C A:HEM201 3.1 17.8 1.0 CD2 A:HIS102 3.2 15.3 1.0 CHD A:HEM201 3.3 17.9 1.0 CHB A:HEM201 3.4 16.2 1.0 CHA A:HEM201 3.5 15.7 1.0 CHC A:HEM201 3.5 19.3 1.0 ND1 A:HIS102 4.0 16.1 1.0 C3C A:HEM201 4.2 15.2 1.0 CG A:HIS102 4.2 18.0 1.0 C3A A:HEM201 4.2 18.2 1.0 C2D A:HEM201 4.3 16.7 1.0 C3D A:HEM201 4.3 13.3 1.0 C2B A:HEM201 4.3 18.9 1.0 C2C A:HEM201 4.3 16.9 1.0 C3B A:HEM201 4.3 16.6 1.0 C2A A:HEM201 4.3 14.6 1.0 CE2 A:PHE78 4.5 20.3 1.0 CB A:PRO114 4.7 16.8 1.0 CD1 A:LEU144 4.8 19.1 1.0 CZ A:PHE78 4.9 19.9 1.0 CD A:PRO115 5.0 15.5 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus


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 Fe(II) Unliganded H-Nox Protein From C. Subterraneus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:19.3 occ:1.00 FE B:HEM201 0.0 19.3 1.0 NC B:HEM201 2.0 21.3 1.0 ND B:HEM201 2.0 21.7 1.0 NB B:HEM201 2.0 16.8 1.0 NE2 B:HIS102 2.0 22.8 1.0 NA B:HEM201 2.0 15.5 1.0 CE1 B:HIS102 2.6 20.9 1.0 C4C B:HEM201 3.0 20.6 1.0 C1D B:HEM201 3.0 22.5 1.0 C1B B:HEM201 3.0 21.0 1.0 C4A B:HEM201 3.0 16.9 1.0 C4D B:HEM201 3.1 22.8 1.0 C4B B:HEM201 3.1 18.7 1.0 C1C B:HEM201 3.1 22.4 1.0 C1A B:HEM201 3.1 19.3 1.0 CD2 B:HIS102 3.3 20.7 1.0 CHD B:HEM201 3.3 19.4 1.0 CHB B:HEM201 3.4 18.2 1.0 CHA B:HEM201 3.5 15.9 1.0 CHC B:HEM201 3.5 18.6 1.0 ND1 B:HIS102 3.8 17.2 1.0 C2D B:HEM201 4.2 20.1 1.0 C3C B:HEM201 4.2 23.4 1.0 CG B:HIS102 4.2 17.3 1.0 C3D B:HEM201 4.2 22.0 1.0 C2B B:HEM201 4.2 20.9 1.0 C3B B:HEM201 4.3 19.0 1.0 C3A B:HEM201 4.3 23.2 1.0 C2C B:HEM201 4.3 22.4 1.0 C2A B:HEM201 4.3 20.7 1.0 CE2 B:PHE78 4.5 15.8 1.0 CB B:PRO114 4.6 20.1 1.0 CD1 B:LEU144 4.8 23.4 1.0 CZ B:PHE78 4.8 17.4 1.0 CE B:MET98 4.9 20.5 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus


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 Fe(II) Unliganded H-Nox Protein From C. Subterraneus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:18.6 occ:1.00 FE C:HEM201 0.0 18.6 1.0 ND C:HEM201 2.0 20.6 1.0 NC C:HEM201 2.0 22.6 1.0 NB C:HEM201 2.0 20.6 1.0 NA C:HEM201 2.0 18.8 1.0 NE2 C:HIS102 2.0 21.6 1.0 CE1 C:HIS102 2.6 21.3 1.0 C1D C:HEM201 3.0 24.8 1.0 C4C C:HEM201 3.0 20.9 1.0 C4A C:HEM201 3.0 22.8 1.0 C1B C:HEM201 3.0 24.7 1.0 C4B C:HEM201 3.1 23.1 1.0 C4D C:HEM201 3.1 19.7 1.0 C1A C:HEM201 3.1 17.6 1.0 C1C C:HEM201 3.1 20.2 1.0 CD2 C:HIS102 3.3 20.5 1.0 CHD C:HEM201 3.3 21.2 1.0 CHB C:HEM201 3.4 20.2 1.0 CHA C:HEM201 3.5 13.7 1.0 CHC C:HEM201 3.5 18.4 1.0 ND1 C:HIS102 3.8 21.1 1.0 CG C:HIS102 4.2 21.5 1.0 C2D C:HEM201 4.2 18.8 1.0 C3C C:HEM201 4.2 23.5 1.0 C3B C:HEM201 4.3 22.7 1.0 C2B C:HEM201 4.3 20.8 1.0 C3A C:HEM201 4.3 19.2 1.0 C3D C:HEM201 4.3 19.2 1.0 C2C C:HEM201 4.3 23.8 1.0 C2A C:HEM201 4.3 19.4 1.0 CE2 C:PHE78 4.4 17.7 1.0 CB C:PRO114 4.7 18.0 1.0 CD1 C:LEU144 4.7 19.4 1.0 CZ C:PHE78 4.8 20.3 1.0 CE C:MET98 4.8 24.1 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus


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 Fe(II) Unliganded H-Nox Protein From C. Subterraneus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:16.8 occ:1.00 FE D:HEM201 0.0 16.8 1.0 NA D:HEM201 2.0 16.4 1.0 ND D:HEM201 2.0 13.4 1.0 NC D:HEM201 2.0 16.4 1.0 NB D:HEM201 2.0 16.8 1.0 NE2 D:HIS102 2.0 22.5 1.0 CE1 D:HIS102 2.7 19.7 1.0 C4C D:HEM201 3.0 18.3 1.0 C1D D:HEM201 3.0 15.7 1.0 C4A D:HEM201 3.0 18.7 1.0 C1A D:HEM201 3.0 13.8 1.0 C4B D:HEM201 3.1 19.5 1.0 C4D D:HEM201 3.1 16.7 1.0 C1B D:HEM201 3.1 16.8 1.0 C1C D:HEM201 3.1 17.8 1.0 CD2 D:HIS102 3.2 18.3 1.0 CHD D:HEM201 3.4 16.6 1.0 CHA D:HEM201 3.4 13.2 1.0 CHB D:HEM201 3.4 17.3 1.0 CHC D:HEM201 3.5 16.0 1.0 ND1 D:HIS102 3.9 21.0 1.0 CG D:HIS102 4.2 16.7 1.0 C3A D:HEM201 4.2 14.8 1.0 C2D D:HEM201 4.3 16.6 1.0 C3C D:HEM201 4.3 14.7 1.0 C3B D:HEM201 4.3 14.7 1.0 C2A D:HEM201 4.3 13.9 1.0 C2B D:HEM201 4.3 16.3 1.0 C3D D:HEM201 4.3 16.2 1.0 C2C D:HEM201 4.3 17.4 1.0 CE2 D:PHE78 4.5 20.0 1.0 CB D:PRO114 4.7 19.0 1.0 CD1 D:LEU144 4.8 13.8 1.0 CZ D:PHE78 4.9 18.1 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus


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 Fe(II) Unliganded H-Nox Protein From C. Subterraneus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:22.4 occ:1.00 FE E:HEM201 0.0 22.4 1.0 NC E:HEM201 2.0 24.6 1.0 NA E:HEM201 2.0 27.6 1.0 NB E:HEM201 2.0 26.6 1.0 NE2 E:HIS102 2.0 27.3 1.0 ND E:HEM201 2.0 30.3 1.0 CE1 E:HIS102 2.8 26.9 1.0 C4C E:HEM201 3.0 26.4 1.0 C4A E:HEM201 3.0 24.6 1.0 C1D E:HEM201 3.0 27.2 1.0 C1B E:HEM201 3.0 22.7 1.0 C1A E:HEM201 3.1 28.4 1.0 C4D E:HEM201 3.1 26.3 1.0 C4B E:HEM201 3.1 25.8 1.0 C1C E:HEM201 3.1 24.6 1.0 CD2 E:HIS102 3.2 23.8 1.0 CHD E:HEM201 3.3 23.0 1.0 CHB E:HEM201 3.4 26.5 1.0 CHA E:HEM201 3.4 28.1 1.0 CHC E:HEM201 3.5 19.5 1.0 ND1 E:HIS102 4.0 21.0 1.0 C3C E:HEM201 4.2 24.5 1.0 C3A E:HEM201 4.2 26.8 1.0 CG E:HIS102 4.2 25.1 1.0 C2D E:HEM201 4.3 22.6 1.0 C2A E:HEM201 4.3 26.1 1.0 C2B E:HEM201 4.3 22.1 1.0 C3D E:HEM201 4.3 22.3 1.0 C2C E:HEM201 4.3 25.7 1.0 C3B E:HEM201 4.3 21.0 1.0 CE2 E:PHE78 4.6 18.8 1.0 CB E:PRO114 4.6 26.5 1.0 CD1 E:LEU144 4.8 19.7 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Fe(II) Unliganded H-Nox Protein From C. Subterraneus


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 Fe(II) Unliganded H-Nox Protein From C. Subterraneus within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:19.9 occ:1.00 FE F:HEM201 0.0 19.9 1.0 NC F:HEM201 2.0 20.1 1.0 NB F:HEM201 2.0 18.1 1.0 NA F:HEM201 2.0 18.5 1.0 NE2 F:HIS102 2.0 22.6 1.0 ND F:HEM201 2.0 24.1 1.0 CE1 F:HIS102 2.7 19.0 1.0 C4A F:HEM201 3.0 21.7 1.0 C1B F:HEM201 3.0 21.7 1.0 C1D F:HEM201 3.0 20.5 1.0 C4C F:HEM201 3.0 20.5 1.0 C1A F:HEM201 3.1 23.0 1.0 C1C F:HEM201 3.1 22.1 1.0 C4D F:HEM201 3.1 21.4 1.0 C4B F:HEM201 3.1 18.7 1.0 CD2 F:HIS102 3.2 20.3 1.0 CHD F:HEM201 3.3 22.8 1.0 CHB F:HEM201 3.3 22.5 1.0 CHA F:HEM201 3.5 22.6 1.0 CHC F:HEM201 3.6 13.1 1.0 ND1 F:HIS102 3.9 17.8 1.0 C3A F:HEM201 4.2 22.8 1.0 CG F:HIS102 4.2 18.5 1.0 C2B F:HEM201 4.2 20.2 1.0 C3C F:HEM201 4.2 23.9 1.0 C2D F:HEM201 4.2 26.0 1.0 C2C F:HEM201 4.3 22.1 1.0 C2A F:HEM201 4.3 19.4 1.0 C3B F:HEM201 4.3 20.1 1.0 C3D F:HEM201 4.3 19.7 1.0 CE2 F:PHE78 4.5 18.8 1.0 CB F:PRO114 4.7 20.3 1.0 CZ F:PHE78 4.9 20.2 1.0 CD1 F:LEU144 4.9 17.9 1.0

C.W.Hespen, J.J.Bruegger, C.M.Phillips-Piro, M.A.Marletta. Structural and Functional Evidence Indicates Selective Oxygen Signaling in Caldanaerobacter Subterraneus H-Nox. Acs Chem.Biol. V. 11 2337 2016.
ISSN: ESSN 1554-8937
PubMed: 27328180
DOI: 10.1021/ACSCHEMBIO.6B00431