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

Protein crystallography data

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

Other elements in 3tfe:

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

Xenon Binding Sites:

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 3tfe

Go back to Xenon Binding Sites List in 3tfe
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 3tfe

Go back to Xenon Binding Sites List in 3tfe
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 3tfe

Go back to Xenon Binding Sites List in 3tfe
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 3tfe

Go back to Xenon Binding Sites List in 3tfe
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

Reference:

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
Page generated: Wed Dec 16 02:40:04 2020

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