Xenon 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:

Iron	(Fe)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Xenon 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 Xenon atom.
In total 2 binding sites of Xenon 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 Xenon binding site number: 1; 2;

Xenon 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 Xenon with other atoms in the Xe 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:Xe190 b:57.3 occ:0.32 HE2 A:PHE70 3.3 72.1 1.0 CE2 A:TRP74 3.6 52.3 1.0 C4D A:HEM500 3.6 51.9 1.0 NE1 A:TRP74 3.7 52.4 1.0 CD2 A:TRP74 3.8 52.8 1.0 SD A:MET144 3.8 64.8 1.0 HG22 A:VAL5 3.8 57.5 1.0 ND A:HEM500 3.8 49.5 1.0 CHA A:HEM500 3.9 41.2 1.0 CD1 A:TRP74 3.9 57.0 1.0 HE1 A:TRP74 3.9 63.0 1.0 CZ2 A:TRP74 4.0 48.9 1.0 CG A:TRP74 4.0 55.4 1.0 C3D A:HEM500 4.1 56.6 1.0 C1A A:HEM500 4.1 45.8 1.0 CE2 A:PHE70 4.2 60.0 1.0 HADA A:HEM500 4.3 65.8 1.0 HD11 A:LEU148 4.3 69.3 1.0 HE1 A:MET144 4.3 0.4 1.0 HG13 A:VAL5 4.3 55.6 1.0 HHA A:HEM500 4.3 49.4 1.0 HZ2 A:TRP74 4.3 58.7 1.0 HG21 A:VAL5 4.3 57.5 1.0 CE3 A:TRP74 4.4 58.5 1.0 C1D A:HEM500 4.4 48.3 1.0 NA A:HEM500 4.4 47.7 1.0 HD1 A:TRP74 4.4 68.4 1.0 HD21 A:LEU148 4.5 55.3 1.0 C2D A:HEM500 4.5 49.7 1.0 CH2 A:TRP74 4.5 53.0 1.0 CG2 A:VAL5 4.5 47.9 1.0 FE A:HEM500 4.5 52.0 1.0 CE A:MET144 4.6 0.5 1.0 HB2 A:TRP74 4.6 62.5 1.0 CZ3 A:TRP74 4.7 57.8 1.0 CAD A:HEM500 4.7 54.8 1.0 HE2 A:MET144 4.8 0.4 1.0 HZ A:PHE70 4.8 70.7 1.0 HG11 A:VAL5 4.8 55.6 1.0 HE1 A:MET1 4.8 0.5 1.0 CB A:TRP74 4.8 52.1 1.0 HE3 A:TRP74 4.9 70.2 1.0 C2A A:HEM500 4.9 51.0 1.0 CG1 A:VAL5 4.9 46.3 1.0 HAA A:HEM500 4.9 56.4 1.0 HE2 A:MET1 5.0 0.5 1.0 HD2 A:PHE70 5.0 58.0 1.0 CZ A:PHE70 5.0 58.9 1.0

Xenon 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 Xenon with other atoms in the Xe 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:Xe190 b:62.8 occ:0.32 HE2 B:PHE70 3.2 65.2 1.0 HE1 B:MET144 3.5 88.2 1.0 CE2 B:TRP74 3.6 64.1 1.0 NE1 B:TRP74 3.7 52.7 1.0 CD2 B:TRP74 3.7 48.6 1.0 HG22 B:VAL5 3.7 57.3 1.0 HE3 B:MET144 3.8 88.2 1.0 C4D B:HEM501 3.9 44.9 1.0 CD1 B:TRP74 3.9 51.0 1.0 CE B:MET144 3.9 73.5 1.0 CG B:TRP74 3.9 45.5 1.0 SD B:MET144 4.0 64.3 1.0 ND B:HEM501 4.0 36.7 1.0 CHA B:HEM501 4.0 45.8 1.0 HE1 B:TRP74 4.0 63.2 1.0 CZ2 B:TRP74 4.1 58.3 1.0 CE2 B:PHE70 4.1 54.3 1.0 C1A B:HEM501 4.1 48.5 1.0 CE3 B:TRP74 4.3 51.9 1.0 HG21 B:VAL5 4.3 57.3 1.0 HG13 B:VAL5 4.3 47.3 1.0 C3D B:HEM501 4.3 43.4 1.0 HD21 B:LEU148 4.4 52.0 1.0 HD1 B:TRP74 4.4 61.3 1.0 NA B:HEM501 4.4 46.0 1.0 HZ2 B:TRP74 4.4 70.0 1.0 HADA B:HEM501 4.5 57.2 1.0 CG2 B:VAL5 4.5 47.7 1.0 HB2 B:TRP74 4.5 58.4 1.0 HHA B:HEM501 4.5 55.0 1.0 C1D B:HEM501 4.5 41.5 1.0 HD11 B:LEU148 4.5 85.2 1.0 CH2 B:TRP74 4.6 59.6 1.0 HZ B:PHE70 4.6 76.6 1.0 FE B:HEM501 4.6 51.1 1.0 CZ3 B:TRP74 4.7 59.1 1.0 HE1 B:MET1 4.7 0.5 1.0 C2D B:HEM501 4.7 45.3 1.0 HE3 B:TRP74 4.7 62.3 1.0 CB B:TRP74 4.7 48.6 1.0 HG11 B:VAL5 4.8 47.3 1.0 HE2 B:MET1 4.8 0.5 1.0 CZ B:PHE70 4.8 63.8 1.0 C2A B:HEM501 4.8 51.7 1.0 HE2 B:MET144 4.9 88.2 1.0 HAA B:HEM501 4.9 66.5 1.0 HB3 B:TRP74 4.9 58.4 1.0 CG1 B:VAL5 4.9 39.5 1.0 HD2 B:PHE70 5.0 64.9 1.0 CAD B:HEM501 5.0 47.6 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