Iron in PDB 3tfe: Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon, PDB code: 3tfe was solved by M.B.Winter, M.A.Herzik Jr., J.Kuriyan, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.59 / 1.99
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	123.295, 123.295, 123.295, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.3

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon also contains other interesting chemical elements:

Xenon

(Xe)

4 atoms

The binding sites of Iron atom in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon (pdb code 3tfe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon, PDB code: 3tfe:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon


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 An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:29.5 occ:1.00 FE A:HEM500 0.0 29.5 1.0 ND A:HEM500 2.1 26.5 1.0 NA A:HEM500 2.1 24.8 1.0 NB A:HEM500 2.1 26.4 1.0 NC A:HEM500 2.1 30.0 1.0 NE2 A:HIS105 2.2 27.6 1.0 HE1 A:TRP74 3.0 33.2 1.0 C1D A:HEM500 3.1 31.4 1.0 C4D A:HEM500 3.1 30.0 1.0 C1A A:HEM500 3.1 27.2 1.0 C4C A:HEM500 3.1 31.8 1.0 C4A A:HEM500 3.1 25.7 1.0 C4B A:HEM500 3.1 26.5 1.0 C1B A:HEM500 3.1 30.9 1.0 CE1 A:HIS105 3.1 32.1 1.0 C1C A:HEM500 3.1 29.6 1.0 CD2 A:HIS105 3.2 26.6 1.0 HE1 A:HIS105 3.3 38.5 1.0 CHD A:HEM500 3.4 29.5 1.0 CHA A:HEM500 3.5 29.1 1.0 CHB A:HEM500 3.5 25.3 1.0 HD2 A:HIS105 3.5 31.9 1.0 CHC A:HEM500 3.5 34.0 1.0 NE1 A:TRP74 3.8 27.6 1.0 HZ2 A:TRP74 4.2 36.6 1.0 ND1 A:HIS105 4.3 27.0 1.0 C3D A:HEM500 4.3 26.7 1.0 C2D A:HEM500 4.3 31.4 1.0 C3A A:HEM500 4.3 28.4 1.0 C2A A:HEM500 4.3 29.3 1.0 C3C A:HEM500 4.3 31.7 1.0 C3B A:HEM500 4.3 28.5 1.0 C2B A:HEM500 4.4 29.0 1.0 C2C A:HEM500 4.4 32.7 1.0 CG A:HIS105 4.4 29.5 1.0 HG3 A:PRO118 4.4 31.5 1.0 HD3 A:PRO118 4.5 30.7 1.0 HHD A:HEM500 4.5 35.4 1.0 HD2 A:PRO118 4.5 30.7 1.0 HHB A:HEM500 4.5 30.4 1.0 HHA A:HEM500 4.5 35.0 1.0 HHC A:HEM500 4.6 40.8 1.0 CE2 A:TRP74 4.6 33.6 1.0 HD11 A:LEU101 4.6 41.9 1.0 XE A:XE190 4.7 27.9 0.3 CD1 A:TRP74 4.8 28.4 1.0 CZ2 A:TRP74 4.8 30.5 1.0 CD A:PRO118 4.9 25.6 1.0 HD1 A:TRP74 4.9 34.1 1.0 HD22 A:LEU104 4.9 47.0 1.0

Iron binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon


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 An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:27.9 occ:1.00 FE B:HEM501 0.0 27.9 1.0 NA B:HEM501 2.1 26.0 1.0 NB B:HEM501 2.1 28.4 1.0 NC B:HEM501 2.1 29.5 1.0 ND B:HEM501 2.1 25.5 1.0 NE2 B:HIS105 2.2 25.9 1.0 HE1 B:TRP74 3.0 34.6 1.0 C1B B:HEM501 3.1 26.8 1.0 C4A B:HEM501 3.1 28.0 1.0 C4C B:HEM501 3.1 29.7 1.0 C4B B:HEM501 3.1 28.1 1.0 C1C B:HEM501 3.1 26.4 1.0 C1A B:HEM501 3.1 28.7 1.0 C1D B:HEM501 3.1 27.9 1.0 CE1 B:HIS105 3.1 31.0 1.0 C4D B:HEM501 3.1 28.2 1.0 CD2 B:HIS105 3.2 24.2 1.0 HE1 B:HIS105 3.3 37.2 1.0 CHB B:HEM501 3.4 27.6 1.0 CHD B:HEM501 3.4 27.5 1.0 HD2 B:HIS105 3.5 29.0 1.0 CHC B:HEM501 3.5 31.0 1.0 CHA B:HEM501 3.5 29.4 1.0 NE1 B:TRP74 3.9 28.8 1.0 HZ2 B:TRP74 4.1 35.5 1.0 ND1 B:HIS105 4.3 26.7 1.0 C2C B:HEM501 4.3 27.7 1.0 C3C B:HEM501 4.3 26.8 1.0 C3A B:HEM501 4.3 29.5 1.0 C2A B:HEM501 4.3 28.6 1.0 C2B B:HEM501 4.3 29.3 1.0 C3B B:HEM501 4.3 29.5 1.0 CG B:HIS105 4.4 25.8 1.0 C2D B:HEM501 4.4 28.8 1.0 C3D B:HEM501 4.4 31.6 1.0 HD2 B:PRO118 4.4 34.7 1.0 HHD B:HEM501 4.5 33.0 1.0 HHB B:HEM501 4.5 33.1 1.0 HG3 B:PRO118 4.5 33.3 1.0 HHC B:HEM501 4.6 37.2 1.0 HHA B:HEM501 4.6 35.3 1.0 HD3 B:PRO118 4.6 34.7 1.0 CE2 B:TRP74 4.6 29.1 1.0 XE B:XE190 4.6 28.4 0.3 HD12 B:LEU104 4.7 53.7 1.0 HD11 B:LEU101 4.7 66.1 1.0 CZ2 B:TRP74 4.7 29.6 1.0 CD1 B:TRP74 4.8 26.6 1.0 CD B:PRO118 4.9 28.9 1.0 HD1 B:TRP74 5.0 31.9 1.0 HD11 B:LEU104 5.0 53.7 1.0

M.B.Winter, M.A.Herzik, J.Kuriyan, M.A.Marletta. Tunnels Modulate Ligand Flux in A Heme Nitric Oxide/Oxygen Binding (H-Nox) Domain. Proc.Natl.Acad.Sci.Usa V. 108 E881 2011.
ISSN: ISSN 0027-8424
PubMed: 21997213
DOI: 10.1073/PNAS.1114038108