Iron in PDB 3tf9: Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon, PDB code: 3tf9 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)	43.98 / 2.59
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	124.404, 124.404, 124.404, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.5

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon also contains other interesting chemical elements:

Xenon	(Xe)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Iron atom in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon (pdb code 3tf9). 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 Under 1 Atm of Xenon, PDB code: 3tf9:
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 Under 1 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 Under 1 Atm of Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:52.0 occ:1.00 FE A:HEM500 0.0 52.0 1.0 NC A:HEM500 2.1 53.1 1.0 NA A:HEM500 2.1 47.7 1.0 ND A:HEM500 2.1 49.5 1.0 NE2 A:HIS105 2.2 52.0 1.0 NB A:HEM500 2.3 54.2 1.0 CE1 A:HIS105 3.0 50.1 1.0 HE1 A:HIS105 3.0 60.1 1.0 C4C A:HEM500 3.1 49.2 1.0 C1D A:HEM500 3.1 48.3 1.0 C1A A:HEM500 3.1 45.8 1.0 C4D A:HEM500 3.1 51.9 1.0 C1C A:HEM500 3.1 46.0 1.0 C4A A:HEM500 3.2 54.9 1.0 C4B A:HEM500 3.2 51.9 1.0 HE1 A:TRP74 3.3 63.0 1.0 C1B A:HEM500 3.3 54.0 1.0 CD2 A:HIS105 3.3 48.1 1.0 CHD A:HEM500 3.4 46.8 1.0 CHA A:HEM500 3.5 41.2 1.0 CHC A:HEM500 3.5 39.2 1.0 HD2 A:HIS105 3.6 57.7 1.0 CHB A:HEM500 3.6 59.3 1.0 NE1 A:TRP74 4.0 52.4 1.0 ND1 A:HIS105 4.2 59.2 1.0 HHD A:HEM500 4.3 56.1 1.0 C3C A:HEM500 4.3 54.6 1.0 C2A A:HEM500 4.3 51.0 1.0 C2D A:HEM500 4.3 49.7 1.0 C2C A:HEM500 4.3 56.3 1.0 C3D A:HEM500 4.3 56.6 1.0 C3A A:HEM500 4.3 50.5 1.0 CG A:HIS105 4.4 49.9 1.0 HHA A:HEM500 4.4 49.4 1.0 C3B A:HEM500 4.5 51.9 1.0 HZ2 A:TRP74 4.5 58.7 1.0 HHB A:HEM500 4.5 71.2 1.0 HD2 A:PRO118 4.5 73.3 1.0 HHC A:HEM500 4.5 47.1 1.0 C2B A:HEM500 4.5 56.5 1.0 XE A:XE190 4.5 57.3 0.3 HG3 A:PRO118 4.6 70.1 1.0 HD3 A:PRO118 4.7 73.3 1.0 HD11 A:LEU101 4.7 61.4 0.7 CE2 A:TRP74 4.8 52.3 1.0 CD A:PRO118 4.9 61.0 1.0 CD1 A:TRP74 4.9 57.0 1.0 CZ2 A:TRP74 5.0 48.9 1.0 HD1 A:TRP74 5.0 68.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 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 Under 1 Atm of Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:51.1 occ:1.00 FE B:HEM501 0.0 51.1 1.0 NC B:HEM501 2.0 48.8 1.0 NA B:HEM501 2.0 46.0 1.0 ND B:HEM501 2.2 36.7 1.0 NB B:HEM501 2.2 48.5 1.0 NE2 B:HIS105 2.2 50.9 1.0 C1C B:HEM501 3.0 46.5 1.0 C1A B:HEM501 3.0 48.5 1.0 C4C B:HEM501 3.1 47.9 1.0 CE1 B:HIS105 3.1 52.4 1.0 C4A B:HEM501 3.1 40.3 1.0 C4D B:HEM501 3.2 44.9 1.0 C4B B:HEM501 3.2 49.2 1.0 C1D B:HEM501 3.2 41.5 1.0 HE1 B:HIS105 3.2 62.9 1.0 HE1 B:TRP74 3.2 63.2 1.0 C1B B:HEM501 3.2 54.5 1.0 CD2 B:HIS105 3.3 38.5 1.0 CHC B:HEM501 3.4 48.4 1.0 CHA B:HEM501 3.4 45.8 1.0 HD2 B:HIS105 3.5 46.2 1.0 CHD B:HEM501 3.5 44.3 1.0 CHB B:HEM501 3.6 50.8 1.0 NE1 B:TRP74 3.9 52.7 1.0 C2C B:HEM501 4.2 56.9 1.0 C3C B:HEM501 4.3 49.4 1.0 ND1 B:HIS105 4.3 51.9 1.0 HD3 B:PRO118 4.3 78.3 1.0 C2A B:HEM501 4.3 51.7 1.0 C3A B:HEM501 4.3 44.9 1.0 CG B:HIS105 4.4 46.8 1.0 HZ2 B:TRP74 4.4 70.0 1.0 HHC B:HEM501 4.4 58.1 1.0 HHD B:HEM501 4.4 53.2 1.0 HHA B:HEM501 4.4 55.0 1.0 HG3 B:PRO118 4.4 76.8 1.0 C3B B:HEM501 4.4 54.0 1.0 C3D B:HEM501 4.4 43.4 1.0 HHB B:HEM501 4.4 61.0 1.0 C2D B:HEM501 4.5 45.3 1.0 HD2 B:PRO118 4.5 78.3 1.0 C2B B:HEM501 4.5 56.8 1.0 XE B:XE190 4.6 62.8 0.3 CE2 B:TRP74 4.7 64.1 1.0 CD B:PRO118 4.7 65.2 1.0 CD1 B:TRP74 4.8 51.0 1.0 HD11 B:LEU101 4.8 76.2 1.0 HD1 B:TRP74 4.9 61.3 1.0 CZ2 B:TRP74 4.9 58.3 1.0 CG B:PRO118 5.0 64.0 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