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Xenon in PDB 1vgi: Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex

Enzymatic activity of Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex

All present enzymatic activity of Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex:
1.14.99.3;

Protein crystallography data

The structure of Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex, PDB code: 1vgi was solved by M.Sugishima, H.Sakamoto, M.Noguchi, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.100, 65.100, 120.500, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 21.7

Other elements in 1vgi:

The structure of Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex also contains other interesting chemical elements:

Iron (Fe) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex (pdb code 1vgi). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 3 binding sites of Xenon where determined in the Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex, PDB code: 1vgi:
Jump to Xenon binding site number: 1; 2; 3;

Xenon binding site 1 out of 3 in 1vgi

Go back to Xenon Binding Sites List in 1vgi
Xenon binding site 1 out of 3 in the Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex


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 Xenon Bound Rat Heme-Heme Oxygenase-1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe301

b:42.0
occ:0.32
XE A:XE301 0.0 42.0 0.3
XE A:XE301 1.2 40.4 0.2
XE A:XE301 2.6 42.5 0.3
CG2 A:VAL50 4.0 34.1 1.0
CD1 A:LEU54 4.1 30.9 1.0
O A:HOH368 4.1 52.6 1.0
CZ A:PHE167 4.2 29.7 1.0
CD1 A:LEU147 4.4 37.3 1.0
CE A:MET34 4.6 48.2 1.0
SD A:MET51 4.6 40.4 1.0
CG1 A:VAL50 4.6 35.1 1.0
CE1 A:PHE167 4.7 29.6 1.0
CB A:VAL50 5.0 32.8 1.0

Xenon binding site 2 out of 3 in 1vgi

Go back to Xenon Binding Sites List in 1vgi
Xenon binding site 2 out of 3 in the Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex


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 Xenon Bound Rat Heme-Heme Oxygenase-1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe301

b:42.5
occ:0.27
XE A:XE301 0.0 42.5 0.3
XE A:XE301 1.5 40.4 0.2
XE A:XE301 2.6 42.0 0.3
CE2 A:PHE37 3.3 46.2 1.0
CD2 A:PHE37 3.4 46.1 1.0
CZ A:PHE37 3.7 44.0 1.0
CG A:PHE37 3.9 43.8 1.0
CE1 A:PHE37 4.1 43.8 1.0
CD1 A:LEU147 4.2 37.3 1.0
CD1 A:PHE37 4.2 43.1 1.0
CE1 A:PHE47 4.4 33.2 1.0
CG1 A:VAL50 4.4 35.1 1.0
CE2 A:PHE33 4.6 45.0 1.0
CD1 A:PHE47 4.6 31.8 1.0
SD A:MET34 4.6 44.2 1.0
CZ A:PHE167 4.7 29.7 1.0
CB A:PHE37 4.8 43.0 1.0
CG2 A:VAL50 4.9 34.1 1.0
CE A:MET34 5.0 48.2 1.0
CG A:LEU147 5.0 34.4 1.0

Xenon binding site 3 out of 3 in 1vgi

Go back to Xenon Binding Sites List in 1vgi
Xenon binding site 3 out of 3 in the Crystal Structure of Xenon Bound Rat Heme-Heme Oxygenase-1 Complex


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 Xenon Bound Rat Heme-Heme Oxygenase-1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe301

b:40.4
occ:0.25
XE A:XE301 0.0 40.4 0.2
XE A:XE301 1.2 42.0 0.3
XE A:XE301 1.5 42.5 0.3
CD1 A:LEU147 4.1 37.3 1.0
CZ A:PHE167 4.2 29.7 1.0
CG2 A:VAL50 4.3 34.1 1.0
CG1 A:VAL50 4.3 35.1 1.0
CE2 A:PHE37 4.7 46.2 1.0
CE A:MET34 4.7 48.2 1.0
SD A:MET51 4.7 40.4 1.0
CE1 A:PHE167 4.8 29.6 1.0
CE1 A:PHE47 4.8 33.2 1.0
SD A:MET34 4.8 44.2 1.0
CD2 A:PHE37 4.9 46.1 1.0
CB A:VAL50 4.9 32.8 1.0
CZ A:PHE37 4.9 44.0 1.0
O A:HOH368 5.0 52.6 1.0

Reference:

M.Sugishima, H.Sakamoto, M.Noguchi, K.Fukuyama. Co-Trapping Site in Heme Oxygenase Revealed By Photolysis of Its Co-Bound Heme Complex: Mechanism of Escaping From Product Inhibition J.Mol.Biol. V. 341 7 2004.
ISSN: ISSN 0022-2836
PubMed: 15312758
DOI: 10.1016/J.JMB.2004.05.048
Page generated: Wed Dec 16 02:39:26 2020

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