Xenon 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:

Iron

(Fe)

2 atoms

The binding sites of Xenon 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 Xenon atom.
In total 4 binding sites of Xenon 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 Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 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 Xenon with other atoms in the Xe 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:Xe190 b:27.9 occ:0.33 HE1 A:MET144 3.4 49.9 1.0 HG22 A:VAL5 3.5 34.1 1.0 CE2 A:TRP74 3.5 33.6 1.0 HE3 A:MET144 3.6 49.9 1.0 CD2 A:TRP74 3.7 29.5 1.0 HE2 A:PHE70 3.7 41.9 1.0 NE1 A:TRP74 3.7 27.6 1.0 C1A A:HEM500 3.7 27.2 1.0 CE A:MET144 3.8 41.5 1.0 HG13 A:VAL5 3.8 37.7 1.0 CHA A:HEM500 3.9 29.1 1.0 SD A:MET144 3.9 39.7 1.0 CZ2 A:TRP74 3.9 30.5 1.0 CG A:TRP74 4.0 26.8 1.0 NA A:HEM500 4.0 24.8 1.0 CD1 A:TRP74 4.0 28.4 1.0 C4D A:HEM500 4.1 30.0 1.0 HE1 A:TRP74 4.1 33.2 1.0 HAAA A:HEM500 4.1 33.8 1.0 C2A A:HEM500 4.2 29.3 1.0 CE3 A:TRP74 4.2 28.0 1.0 HG21 A:VAL5 4.2 34.1 1.0 CG2 A:VAL5 4.3 28.4 1.0 HZ2 A:TRP74 4.3 36.6 1.0 HHA A:HEM500 4.3 35.0 1.0 CH2 A:TRP74 4.4 33.4 1.0 HD11 A:LEU148 4.4 36.7 1.0 ND A:HEM500 4.4 26.5 1.0 CZ3 A:TRP74 4.5 28.9 1.0 C4A A:HEM500 4.5 25.7 1.0 HG11 A:VAL5 4.5 37.7 1.0 HD21 A:LEU148 4.5 31.3 1.0 CE2 A:PHE70 4.5 35.0 1.0 HB2 A:TRP74 4.5 38.0 1.0 C3A A:HEM500 4.6 28.4 1.0 CG1 A:VAL5 4.6 31.4 1.0 HD1 A:TRP74 4.7 34.1 1.0 FE A:HEM500 4.7 29.5 1.0 CAA A:HEM500 4.8 28.1 1.0 HZ A:PHE70 4.8 41.1 1.0 HE3 A:TRP74 4.8 33.6 1.0 C3D A:HEM500 4.8 26.7 1.0 HAD A:HEM500 4.9 34.0 1.0 CB A:TRP74 4.9 31.6 1.0 HE2 A:MET144 4.9 49.9 1.0

Xenon binding site 2 out of 4 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 Xenon with other atoms in the Xe 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 A:Xe191 b:34.0 occ:0.11 HG21 A:THR48 3.0 37.2 1.0 HE2 A:PHE70 3.2 41.9 1.0 HD11 A:ILE9 3.2 41.1 1.0 HD21 A:LEU67 3.2 51.2 1.0 HG22 A:THR48 3.3 37.2 1.0 HG23 A:THR48 3.4 37.2 1.0 CG2 A:THR48 3.4 31.0 1.0 HD2 A:PHE70 3.5 42.3 1.0 HE1 A:MET1 3.6 58.1 1.0 CE2 A:PHE70 3.7 35.0 1.0 HD22 A:LEU67 3.7 51.2 1.0 HD22 A:LEU141 3.7 41.5 1.0 HD23 A:LEU67 3.7 51.2 1.0 CD2 A:LEU67 3.8 42.7 1.0 SD A:MET144 3.8 39.7 1.0 CD2 A:PHE70 3.8 35.3 1.0 HG11 A:VAL5 4.0 37.7 1.0 HG21 A:VAL52 4.0 45.3 1.0 HZ3 A:TRP66 4.2 52.2 1.0 HG13 A:VAL5 4.2 37.7 1.0 HG12 A:VAL5 4.2 37.7 1.0 HG22 A:VAL52 4.2 45.3 1.0 CD1 A:ILE9 4.3 34.3 1.0 HD21 A:LEU141 4.3 41.5 1.0 HG23 A:VAL52 4.3 45.3 1.0 CG1 A:VAL5 4.4 31.4 1.0 CG2 A:VAL52 4.4 37.8 1.0 CD2 A:LEU141 4.5 34.6 1.0 CE A:MET1 4.5 48.4 1.0 HD13 A:ILE9 4.6 41.1 1.0 HE3 A:MET1 4.6 58.1 1.0 CZ A:PHE70 4.7 34.3 1.0 HG12 A:ILE9 4.7 40.6 1.0 HE1 A:MET144 4.8 49.9 1.0 HD12 A:ILE9 4.9 41.1 1.0 HB2 A:MET144 4.9 31.9 1.0 CG A:PHE70 4.9 30.5 1.0 CB A:THR48 4.9 35.1 1.0 HG13 A:ILE9 4.9 40.6 1.0 CG1 A:ILE9 5.0 33.8 1.0 HG3 A:MET144 5.0 39.9 1.0 CE A:MET144 5.0 41.5 1.0

Xenon binding site 3 out of 4 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 Xenon with other atoms in the Xe binding site number 3 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:Xe190 b:28.4 occ:0.35 HE1 B:MET144 3.4 55.9 1.0 HG22 B:VAL5 3.4 36.4 1.0 CE2 B:TRP74 3.5 29.1 1.0 HE3 B:MET144 3.5 55.9 1.0 CD2 B:TRP74 3.6 27.8 1.0 C4D B:HEM501 3.7 28.2 1.0 NE1 B:TRP74 3.7 28.8 1.0 HE2 B:PHE70 3.7 39.7 1.0 CE B:MET144 3.8 46.5 1.0 CHA B:HEM501 3.8 29.4 1.0 CZ2 B:TRP74 3.8 29.6 1.0 ND B:HEM501 3.9 25.5 1.0 SD B:MET144 3.9 34.8 1.0 CG B:TRP74 4.0 28.9 1.0 CD1 B:TRP74 4.0 26.6 1.0 HE1 B:TRP74 4.0 34.6 1.0 HG13 B:VAL5 4.1 36.2 1.0 C1A B:HEM501 4.1 28.7 1.0 C3D B:HEM501 4.1 31.6 1.0 CE3 B:TRP74 4.2 30.4 1.0 HADA B:HEM501 4.2 33.6 1.0 HD11 B:LEU148 4.2 34.6 1.0 HZ2 B:TRP74 4.3 35.5 1.0 HHA B:HEM501 4.3 35.3 1.0 CH2 B:TRP74 4.3 33.6 1.0 NA B:HEM501 4.3 26.0 1.0 HG21 B:VAL5 4.4 36.4 1.0 CG2 B:VAL5 4.4 30.3 1.0 C1D B:HEM501 4.4 27.9 1.0 CZ3 B:TRP74 4.4 32.3 1.0 HD21 B:LEU148 4.5 31.6 1.0 CE2 B:PHE70 4.5 33.1 1.0 HB2 B:TRP74 4.6 28.9 1.0 C2D B:HEM501 4.6 28.8 1.0 HD1 B:TRP74 4.6 31.9 1.0 FE B:HEM501 4.6 27.9 1.0 CAD B:HEM501 4.7 28.0 1.0 HE3 B:TRP74 4.8 36.5 1.0 HZ B:PHE70 4.8 35.0 1.0 C2A B:HEM501 4.8 28.6 1.0 HG11 B:VAL5 4.8 36.2 1.0 CB B:TRP74 4.9 24.1 1.0 CG1 B:VAL5 4.9 30.2 1.0 HAA B:HEM501 4.9 29.1 1.0 HE2 B:MET144 4.9 55.9 1.0 HH2 B:TRP74 5.0 40.4 1.0

Xenon binding site 4 out of 4 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 Xenon with other atoms in the Xe binding site number 4 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:Xe191 b:27.9 occ:0.12 HG21 B:THR48 3.1 35.3 1.0 HE2 B:PHE70 3.2 39.7 1.0 HD11 B:ILE9 3.3 35.1 1.0 HG22 B:THR48 3.3 35.3 1.0 HG23 B:THR48 3.5 35.3 1.0 CG2 B:THR48 3.5 29.4 1.0 HD21 B:LEU67 3.5 37.5 1.0 HD2 B:PHE70 3.5 37.1 1.0 HD22 B:LEU141 3.6 39.2 1.0 CE2 B:PHE70 3.7 33.1 1.0 HE1 B:MET1 3.7 61.3 1.0 HD22 B:LEU67 3.7 37.5 1.0 HG21 B:VAL52 3.8 37.6 1.0 CD2 B:PHE70 3.8 30.9 1.0 SD B:MET144 3.8 34.8 1.0 HD23 B:LEU67 3.9 37.5 1.0 CD2 B:LEU67 3.9 31.2 1.0 HG11 B:VAL5 4.0 36.2 1.0 HG13 B:VAL5 4.1 36.2 1.0 HZ3 B:TRP66 4.2 40.8 1.0 HD21 B:LEU141 4.2 39.2 1.0 HG22 B:VAL52 4.2 37.6 1.0 HG12 B:VAL5 4.3 36.2 1.0 CG2 B:VAL52 4.3 31.3 1.0 CG1 B:VAL5 4.4 30.2 1.0 HG23 B:VAL52 4.4 37.6 1.0 CD1 B:ILE9 4.4 29.2 1.0 CD2 B:LEU141 4.4 32.7 1.0 CZ B:PHE70 4.7 29.1 1.0 CE B:MET1 4.7 51.1 1.0 HD13 B:LEU141 4.7 40.3 1.0 HD13 B:ILE9 4.8 35.1 1.0 HE1 B:MET144 4.8 55.9 1.0 HG12 B:ILE9 4.9 37.0 1.0 HE3 B:MET1 4.9 61.3 1.0 CG B:PHE70 4.9 28.7 1.0 HB2 B:MET144 4.9 29.6 1.0 HD12 B:ILE9 5.0 35.1 1.0 HD23 B:LEU141 5.0 39.2 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