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

Protein crystallography data

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 6 Atm of Xenon, PDB code: 3tfa 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) 43.82 / 2.27
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 123.937, 123.937, 123.937, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19

Other elements in 3tfa:

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 Under 6 Atm of Xenon (pdb code 3tfa). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 6 binding sites of Xenon where determined in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 6 Atm of Xenon, PDB code: 3tfa:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 3tfa

Go back to Xenon Binding Sites List in 3tfa
Xenon binding site 1 out of 6 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe190

b:35.7
occ:0.64
HE2 A:PHE70 3.3 45.0 1.0
HE1 A:MET144 3.4 43.2 1.0
HE3 A:MET144 3.5 43.2 1.0
HG22 A:VAL5 3.6 36.4 1.0
CE2 A:TRP74 3.6 34.2 1.0
C4D A:HEM500 3.7 32.4 1.0
NE1 A:TRP74 3.8 34.8 1.0
CE A:MET144 3.8 36.0 1.0
CD2 A:TRP74 3.8 35.4 1.0
CHA A:HEM500 3.9 31.2 1.0
ND A:HEM500 3.9 34.1 1.0
CZ2 A:TRP74 4.0 28.1 1.0
C1A A:HEM500 4.0 39.2 1.0
CD1 A:TRP74 4.1 36.6 1.0
SD A:MET144 4.1 43.0 1.0
CG A:TRP74 4.1 37.4 1.0
HG13 A:VAL5 4.1 40.3 1.0
HE1 A:TRP74 4.1 41.8 1.0
C3D A:HEM500 4.2 36.1 1.0
NA A:HEM500 4.3 37.4 1.0
CE2 A:PHE70 4.3 37.5 1.0
HADA A:HEM500 4.3 46.5 1.0
HG21 A:VAL5 4.3 36.4 1.0
CE3 A:TRP74 4.3 33.3 1.0
HZ2 A:TRP74 4.4 33.7 1.0
HD11 A:LEU148 4.4 37.0 1.0
HHA A:HEM500 4.4 37.4 1.0
HD21 A:LEU148 4.4 34.2 1.0
CG2 A:VAL5 4.4 30.4 1.0
C1D A:HEM500 4.5 37.2 1.0
CH2 A:TRP74 4.5 30.4 1.0
FE A:HEM500 4.5 35.1 1.0
HZ A:PHE70 4.6 36.9 1.0
C2D A:HEM500 4.6 32.1 1.0
CZ3 A:TRP74 4.7 34.9 1.0
HB2 A:TRP74 4.7 35.9 1.0
HD1 A:TRP74 4.7 43.9 1.0
C2A A:HEM500 4.7 37.1 1.0
HAA A:HEM500 4.8 44.1 1.0
HG11 A:VAL5 4.8 40.3 1.0
CAD A:HEM500 4.8 38.8 1.0
HE2 A:MET144 4.9 43.2 1.0
CG1 A:VAL5 4.9 33.6 1.0
CZ A:PHE70 4.9 30.8 1.0
HE3 A:TRP74 4.9 39.9 1.0
CB A:TRP74 5.0 29.9 1.0
C4A A:HEM500 5.0 38.5 1.0

Xenon binding site 2 out of 6 in 3tfa

Go back to Xenon Binding Sites List in 3tfa
Xenon binding site 2 out of 6 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe191

b:62.0
occ:0.30
HG21 A:THR48 3.2 39.6 1.0
HD11 A:ILE9 3.6 49.8 1.0
HD22 A:LEU141 3.6 47.7 1.0
SD A:MET144 3.6 43.0 1.0
HG22 A:THR48 3.7 39.6 1.0
HE2 A:PHE70 3.7 45.0 1.0
CG2 A:THR48 3.8 33.0 1.0
HE1 A:MET1 3.8 89.5 1.0
HD22 A:LEU67 3.9 46.0 1.0
HG11 A:VAL5 3.9 40.3 1.0
HG23 A:THR48 3.9 39.6 1.0
HD2 A:PHE70 3.9 42.5 1.0
HD23 A:LEU67 4.0 46.0 1.0
HD21 A:LEU67 4.0 46.0 1.0
CE2 A:PHE70 4.1 37.5 1.0
HG13 A:VAL5 4.1 40.3 1.0
CD2 A:LEU67 4.2 38.3 1.0
HD21 A:LEU141 4.2 47.7 1.0
CD2 A:PHE70 4.2 35.4 1.0
CG1 A:VAL5 4.3 33.6 1.0
HG21 A:VAL52 4.3 53.7 1.0
HG12 A:VAL5 4.4 40.3 1.0
CD2 A:LEU141 4.4 39.7 1.0
HE1 A:MET144 4.4 43.2 1.0
CD1 A:ILE9 4.6 41.5 1.0
CE A:MET144 4.7 36.0 1.0
HD13 A:LEU141 4.7 43.2 1.0
CE A:MET1 4.7 74.6 1.0
SD A:MET1 4.9 57.9 1.0
HG22 A:VAL52 4.9 53.7 1.0
HB2 A:MET144 5.0 40.7 1.0
HD23 A:LEU141 5.0 47.7 1.0
HG23 A:VAL52 5.0 53.7 1.0
CG2 A:VAL52 5.0 44.8 1.0

Xenon binding site 3 out of 6 in 3tfa

Go back to Xenon Binding Sites List in 3tfa
Xenon binding site 3 out of 6 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe192

b:77.5
occ:0.44
HB3 A:LEU66 3.1 53.6 1.0
HB2 A:PHE70 3.2 36.3 1.0
HG23 A:ILE9 3.3 48.5 1.0
HG22 A:VAL52 3.3 53.7 1.0
HE1 A:MET12 3.3 80.5 1.0
HG12 A:ILE9 3.5 49.3 1.0
HE2 A:MET12 3.7 80.5 1.0
CE A:MET12 4.0 67.0 1.0
HA A:VAL52 4.0 47.4 1.0
HD13 A:LEU66 4.1 62.9 1.0
CB A:LEU66 4.1 44.7 1.0
HD11 A:ILE13 4.1 59.2 1.0
O A:LEU66 4.2 35.6 1.0
HB2 A:LEU66 4.2 53.6 1.0
HG13 A:VAL52 4.2 50.9 1.0
CB A:PHE70 4.2 30.2 1.0
CG2 A:ILE9 4.2 40.4 1.0
HG21 A:ILE9 4.2 48.5 1.0
HE3 A:MET12 4.3 80.5 1.0
HB3 A:PHE70 4.3 36.3 1.0
HD13 A:ILE9 4.3 49.8 1.0
CG2 A:VAL52 4.4 44.8 1.0
HD23 A:LEU67 4.5 46.0 1.0
CG1 A:ILE9 4.5 41.1 1.0
C A:LEU66 4.5 39.9 1.0
HA A:LEU67 4.6 47.7 1.0
HD1 A:PHE70 4.6 48.4 1.0
HB3 A:ALA55 4.6 41.7 1.0
CG A:PHE70 4.6 35.8 1.0
HD22 A:LEU66 4.7 57.2 1.0
HA A:ILE9 4.8 40.5 1.0
CD1 A:PHE70 4.8 40.3 1.0
CD1 A:ILE9 4.8 41.5 1.0
HG23 A:VAL52 4.8 53.7 1.0
CA A:LEU66 4.9 40.0 1.0
CB A:ILE9 4.9 37.7 1.0
HG21 A:VAL52 4.9 53.7 1.0
CD1 A:LEU66 4.9 52.4 1.0
HD11 A:ILE9 4.9 49.8 1.0
CA A:VAL52 4.9 39.5 1.0
HG13 A:ILE13 4.9 50.4 1.0
HB1 A:ALA55 5.0 41.7 1.0

Xenon binding site 4 out of 6 in 3tfa

Go back to Xenon Binding Sites List in 3tfa
Xenon binding site 4 out of 6 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe190

b:39.0
occ:0.66
HE2 B:PHE70 3.2 50.1 1.0
HE1 B:MET144 3.4 51.1 1.0
HE3 B:MET144 3.6 51.1 1.0
HG22 B:VAL5 3.6 34.6 1.0
CE2 B:TRP74 3.6 36.9 1.0
C4D B:HEM501 3.7 31.1 1.0
NE1 B:TRP74 3.8 36.2 1.0
CD2 B:TRP74 3.8 34.9 1.0
CE B:MET144 3.8 42.5 1.0
CHA B:HEM501 3.9 28.7 1.0
ND B:HEM501 4.0 31.7 1.0
CD1 B:TRP74 4.0 30.9 1.0
C1A B:HEM501 4.0 36.4 1.0
CG B:TRP74 4.1 27.3 1.0
CZ2 B:TRP74 4.1 34.3 1.0
SD B:MET144 4.1 44.1 1.0
C3D B:HEM501 4.1 33.2 1.0
HE1 B:TRP74 4.2 43.5 1.0
CE2 B:PHE70 4.2 41.8 1.0
HG13 B:VAL5 4.2 45.1 1.0
HADA B:HEM501 4.2 39.3 1.0
CE3 B:TRP74 4.3 41.3 1.0
NA B:HEM501 4.3 35.7 1.0
HG21 B:VAL5 4.3 34.6 1.0
HD11 B:LEU148 4.4 44.2 1.0
HHA B:HEM501 4.4 34.5 1.0
HD21 B:LEU148 4.4 38.1 1.0
CG2 B:VAL5 4.5 28.8 1.0
HZ2 B:TRP74 4.5 41.2 1.0
C1D B:HEM501 4.5 34.4 1.0
HZ B:PHE70 4.5 44.3 1.0
CH2 B:TRP74 4.5 35.5 1.0
HB2 B:TRP74 4.6 35.8 1.0
FE B:HEM501 4.6 36.7 1.0
HD1 B:TRP74 4.6 37.1 1.0
C2D B:HEM501 4.6 32.5 1.0
CZ3 B:TRP74 4.7 38.1 1.0
HAA B:HEM501 4.7 47.3 1.0
C2A B:HEM501 4.7 28.0 1.0
CAD B:HEM501 4.8 32.7 1.0
CZ B:PHE70 4.8 36.9 1.0
HG11 B:VAL5 4.9 45.1 1.0
HE3 B:TRP74 4.9 49.5 1.0
CB B:TRP74 4.9 29.8 1.0
HE2 B:MET144 4.9 51.1 1.0
CG1 B:VAL5 5.0 37.6 1.0

Xenon binding site 5 out of 6 in 3tfa

Go back to Xenon Binding Sites List in 3tfa
Xenon binding site 5 out of 6 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 5 of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe191

b:88.5
occ:0.39
HE1 B:MET1 3.0 0.7 1.0
HG21 B:THR48 3.1 51.3 1.0
HD11 B:ILE9 3.6 59.1 1.0
HE3 B:MET1 3.6 0.7 1.0
HG22 B:THR48 3.7 51.3 1.0
CG2 B:THR48 3.7 42.8 1.0
HE2 B:PHE70 3.7 50.1 1.0
SD B:MET144 3.7 44.1 1.0
HG23 B:THR48 3.8 51.3 1.0
CE B:MET1 3.8 83.9 1.0
HD22 B:LEU141 3.8 55.3 1.0
HG11 B:VAL5 3.8 45.1 1.0
HD22 B:LEU67 3.9 60.9 1.0
HD2 B:PHE70 4.0 46.9 1.0
CE2 B:PHE70 4.1 41.8 1.0
HD23 B:LEU67 4.1 60.9 1.0
HG13 B:VAL5 4.1 45.1 1.0
HD21 B:LEU67 4.2 60.9 1.0
CD2 B:PHE70 4.2 39.1 1.0
HE1 B:MET144 4.2 51.1 1.0
HG21 B:VAL52 4.2 66.2 1.0
CD2 B:LEU67 4.3 50.8 1.0
CG1 B:VAL5 4.4 37.6 1.0
HD21 B:LEU141 4.4 55.3 1.0
HG12 B:VAL5 4.4 45.1 1.0
HE2 B:MET1 4.5 0.7 1.0
CD2 B:LEU141 4.6 46.0 1.0
CE B:MET144 4.6 42.5 1.0
CD1 B:ILE9 4.7 49.3 1.0
HD13 B:LEU141 4.7 47.5 1.0
HG23 B:VAL52 4.9 66.2 1.0
CG2 B:VAL52 4.9 55.2 1.0
SD B:MET1 4.9 60.6 1.0
HE2 B:MET144 5.0 51.1 1.0
HG22 B:VAL52 5.0 66.2 1.0
CZ B:PHE70 5.0 36.9 1.0

Xenon binding site 6 out of 6 in 3tfa

Go back to Xenon Binding Sites List in 3tfa
Xenon binding site 6 out of 6 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 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 6 of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe192

b:99.5
occ:0.52
HG22 B:VAL52 2.9 66.2 1.0
HB3 B:LEU66 3.1 62.9 1.0
HB2 B:PHE70 3.2 43.5 1.0
HG23 B:ILE9 3.5 62.5 1.0
HE1 B:MET12 3.5 84.1 1.0
HG12 B:ILE9 3.5 57.0 1.0
HA B:VAL52 4.0 72.7 1.0
HE2 B:MET12 4.0 84.1 1.0
CG2 B:VAL52 4.0 55.2 1.0
O B:LEU66 4.0 45.4 1.0
CB B:PHE70 4.1 36.3 1.0
HB3 B:PHE70 4.1 43.5 1.0
HG13 B:VAL52 4.1 70.2 1.0
CB B:LEU66 4.1 52.4 1.0
HD23 B:LEU67 4.1 60.9 1.0
HB2 B:LEU66 4.2 62.9 1.0
CE B:MET12 4.2 70.1 1.0
HD13 B:ILE9 4.2 59.1 1.0
C B:LEU66 4.3 48.3 1.0
HA B:LEU67 4.4 55.7 1.0
CG2 B:ILE9 4.4 52.1 1.0
HG21 B:ILE9 4.4 62.5 1.0
HD13 B:LEU66 4.4 75.6 1.0
HG23 B:VAL52 4.5 66.2 1.0
CG1 B:ILE9 4.5 47.5 1.0
HD11 B:ILE13 4.5 75.8 1.0
HG21 B:VAL52 4.5 66.2 1.0
CG B:PHE70 4.5 35.3 1.0
HD1 B:PHE70 4.6 51.1 1.0
HE3 B:MET12 4.7 84.1 1.0
CD1 B:ILE9 4.7 49.3 1.0
HD11 B:ILE9 4.8 59.1 1.0
CA B:LEU66 4.8 51.9 1.0
HB3 B:ALA55 4.8 74.5 1.0
CD1 B:PHE70 4.8 42.6 1.0
CB B:VAL52 4.8 57.9 1.0
N B:LEU67 4.8 42.6 1.0
CA B:VAL52 4.9 60.5 1.0
HA B:ILE9 4.9 55.3 1.0
CG1 B:VAL52 4.9 58.5 1.0
CB B:ILE9 5.0 51.0 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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