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Xenon in PDB 4pwb: Engineered Oxidase Reveals Steric Control of Oxygen Reduction

Protein crystallography data

The structure of Engineered Oxidase Reveals Steric Control of Oxygen Reduction, PDB code: 4pwb was solved by D.Zafred, W.Keller, P.Macheroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 117.640, 117.640, 202.960, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 18.7

Other elements in 4pwb:

The structure of Engineered Oxidase Reveals Steric Control of Oxygen Reduction also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction (pdb code 4pwb). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 2 binding sites of Xenon where determined in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction, PDB code: 4pwb:
Jump to Xenon binding site number: 1; 2;

Xenon binding site 1 out of 2 in 4pwb

Go back to Xenon Binding Sites List in 4pwb
Xenon binding site 1 out of 2 in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Engineered Oxidase Reveals Steric Control of Oxygen Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe606

b:48.4
occ:0.36
HH12 A:ARG440 3.1 21.8 1.0
HA3 A:GLY208 3.2 15.6 1.0
O A:HOH996 3.3 18.6 1.0
O A:GLN491 3.3 19.0 1.0
O A:HOH986 3.4 15.1 1.0
HZ A:PHE467 3.5 13.6 1.0
HZ3 A:TRP462 3.5 16.0 1.0
HE2 A:PHE467 3.5 14.6 1.0
HD2 A:TYR466 3.6 14.3 1.0
NH1 A:ARG440 3.8 18.2 1.0
HE2 A:TYR466 3.8 16.7 1.0
HB1 A:ALA437 3.8 13.7 1.0
CZ3 A:TRP462 4.1 13.3 1.0
HH11 A:ARG440 4.1 21.8 1.0
HH22 A:ARG440 4.1 23.8 1.0
CA A:GLY208 4.1 13.0 1.0
CD2 A:TYR466 4.1 11.9 1.0
CZ A:PHE467 4.1 11.3 1.0
HA A:SER492 4.1 16.2 1.0
CE2 A:PHE467 4.2 12.2 1.0
CE2 A:TYR466 4.2 13.9 1.0
HH2 A:TRP462 4.2 12.6 1.0
HA2 A:GLY208 4.2 15.6 1.0
O A:HOH708 4.4 24.4 1.0
CH2 A:TRP462 4.5 10.5 1.0
C A:GLN491 4.5 15.3 1.0
HB3 A:GLN491 4.6 21.9 1.0
CZ A:ARG440 4.6 20.2 1.0
O A:GLY207 4.6 12.9 1.0
H A:GLY209 4.6 18.8 1.0
NH2 A:ARG440 4.6 19.8 1.0
CB A:ALA437 4.7 11.4 1.0
HB2 A:ALA437 4.7 13.7 1.0
HD11 A:ILE493 4.7 18.7 1.0
C A:GLY208 4.8 14.3 1.0
HG2 A:GLN491 4.9 21.0 1.0
N A:GLY209 4.9 15.7 1.0
HD13 A:ILE493 4.9 18.7 1.0
HG A:SER211 4.9 21.4 1.0
HG12 A:ILE493 5.0 15.8 1.0
CE3 A:TRP462 5.0 12.4 1.0

Xenon binding site 2 out of 2 in 4pwb

Go back to Xenon Binding Sites List in 4pwb
Xenon binding site 2 out of 2 in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Engineered Oxidase Reveals Steric Control of Oxygen Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe607

b:26.4
occ:0.42
H A:ALA186 2.9 18.3 1.0
HB2 A:ASP185 3.1 20.8 1.0
HG23 A:VAL481 3.2 18.7 1.0
HA A:ASP185 3.3 16.8 1.0
HB2 A:ASP482 3.3 16.8 1.0
HB A:VAL481 3.4 21.0 1.0
O A:PHE212 3.5 16.8 1.0
HB3 A:ALA186 3.5 22.0 1.0
HD2 A:PHE487 3.5 18.9 1.0
N A:ALA186 3.6 15.2 1.0
C A:PHE212 3.6 15.6 1.0
HA3 A:GLY213 3.7 16.4 1.0
HG21 A:VAL481 3.7 18.7 1.0
O A:VAL481 3.7 19.0 1.0
N A:GLY213 3.8 12.8 1.0
HA A:PHE212 3.8 15.6 1.0
HA2 A:GLY213 3.8 16.4 1.0
CG2 A:VAL481 3.8 15.6 1.0
HE1 A:HIS200 3.9 18.7 1.0
CB A:ASP185 3.9 17.4 1.0
CA A:ASP185 3.9 14.0 1.0
CA A:GLY213 4.0 13.7 1.0
CB A:VAL481 4.0 17.5 1.0
HB1 A:ALA186 4.1 22.0 1.0
HE2 A:PHE487 4.1 18.2 1.0
CB A:ALA186 4.2 18.3 1.0
C A:ASP185 4.2 15.5 1.0
H A:GLY213 4.2 15.4 1.0
CA A:PHE212 4.3 13.0 1.0
HB3 A:ASP185 4.3 20.8 1.0
C A:VAL481 4.3 16.8 1.0
CB A:ASP482 4.3 14.0 1.0
CE1 A:HIS200 4.3 15.6 1.0
CD2 A:PHE487 4.3 15.7 1.0
NE2 A:HIS200 4.3 16.2 1.0
HD21 A:LEU183 4.4 21.6 1.0
CA A:ALA186 4.4 16.9 1.0
CE2 A:PHE487 4.6 15.1 1.0
O A:SER211 4.7 14.5 1.0
HG22 A:VAL481 4.7 18.7 1.0
HB3 A:ASP482 4.7 16.8 1.0
HA A:ALA186 4.8 20.2 1.0
CA A:VAL481 4.8 16.7 1.0
OD2 A:ASP482 4.8 15.1 1.0
CG A:ASP482 4.9 19.6 1.0
O A:HOH910 5.0 35.9 1.0

Reference:

D.Zafred, W.Keller, P.Macheroux. Engineered Oxidase Reveals Steric Control of Oxygen Reduction To Be Published.
Page generated: Wed Dec 16 02:40:07 2020

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