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Xenon in PDB 3u52: X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1

Protein crystallography data

The structure of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1, PDB code: 3u52 was solved by M.S.Mccormick, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.942, 141.761, 181.207, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.8

Other elements in 3u52:

The structure of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 2 atoms

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Xenon atom in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 (pdb code 3u52). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 24 binding sites of Xenon where determined in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1, PDB code: 3u52:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 24 in 3u52

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Xenon binding site 1 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe520

b:49.1
occ:0.26
O A:HOH531 3.3 28.1 1.0
CE A:MET211 3.8 29.9 1.0
CE2 A:PHE100 3.9 36.8 1.0
OE1 A:GLU108 4.0 30.7 1.0
CZ A:PHE100 4.1 33.0 1.0
CD2 A:PHE207 4.3 39.4 1.0
NE2 A:GLN145 4.6 20.5 1.0
CG2 A:ILE104 4.6 27.9 1.0
CE2 A:PHE225 4.8 31.4 1.0
CA A:PHE207 4.8 36.2 1.0
CD1 A:LEU206 4.9 41.2 1.0
CE2 A:PHE207 5.0 41.1 1.0

Xenon binding site 2 out of 24 in 3u52

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Xenon binding site 2 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe521

b:47.2
occ:0.38
CE1 A:PHE198 2.8 39.2 1.0
CD1 A:PHE198 2.9 37.0 1.0
CG A:LEU273 3.8 23.1 1.0
O A:GLY269 3.9 18.3 1.0
CD2 A:LEU273 4.0 23.4 1.0
CD2 A:LEU272 4.1 21.3 1.0
CA A:GLY269 4.1 17.7 1.0
CZ A:PHE198 4.2 35.6 1.0
CB A:LEU202 4.2 23.1 1.0
CG A:PHE198 4.2 34.5 1.0
CD1 A:LEU273 4.2 23.9 1.0
CD1 A:LEU202 4.4 22.4 1.0
C A:GLY269 4.4 19.2 1.0
CD2 A:LEU206 4.5 44.7 1.0
CG A:LEU272 4.6 22.4 1.0
CB A:LEU272 4.7 19.9 1.0
CA A:PHE198 4.8 28.6 1.0
CZ A:PHE178 4.9 18.4 1.0
CG A:LEU202 4.9 24.9 1.0

Xenon binding site 3 out of 24 in 3u52

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Xenon binding site 3 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe522

b:42.2
occ:0.43
CZ A:PHE339 3.4 27.3 1.0
CE1 A:PHE339 3.7 28.2 1.0
CG2 A:ILE404 3.9 19.0 1.0
CD A:PRO405 4.0 20.5 1.0
CB A:TYR171 4.0 21.2 1.0
CZ3 A:TRP170 4.2 23.1 1.0
CG2 A:VAL174 4.2 17.7 1.0
CD2 A:LEU275 4.3 34.4 1.0
CE2 A:PHE339 4.3 26.6 1.0
CD2 A:LEU335 4.4 25.8 1.0
CA A:TYR171 4.5 20.4 1.0
CG1 A:ILE404 4.6 18.4 1.0
CB A:ILE404 4.6 18.6 1.0
CA A:ILE404 4.6 16.7 1.0
CH2 A:TRP170 4.7 22.2 1.0
O A:TYR171 4.7 18.9 1.0
CG A:PRO405 4.9 21.6 1.0
CD1 A:PHE339 4.9 24.5 1.0
CE3 A:TRP170 4.9 28.5 1.0

Xenon binding site 4 out of 24 in 3u52

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Xenon binding site 4 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe523

b:32.4
occ:1.00
CD2 A:TRP170 3.7 26.5 1.0
CE2 A:TRP170 3.7 27.2 1.0
CD2 A:TYR342 3.8 18.8 1.0
CG A:TYR342 3.9 18.3 1.0
CD A:PRO396 3.9 22.3 1.0
NE1 A:TRP170 4.0 23.6 1.0
CG A:TRP170 4.0 25.3 1.0
CD1 A:TRP170 4.1 23.5 1.0
CE3 A:TRP170 4.1 28.5 1.0
CZ2 A:TRP170 4.2 23.9 1.0
CD2 A:LEU395 4.2 28.6 1.0
CD1 A:TYR342 4.2 20.0 1.0
CE2 A:TYR342 4.2 17.8 1.0
CB A:TYR342 4.3 18.8 1.0
XE A:XE525 4.4 40.6 1.0
CG A:PRO396 4.5 22.0 1.0
CH2 A:TRP170 4.5 22.2 1.0
CZ3 A:TRP170 4.5 23.1 1.0
CZ A:TYR342 4.6 20.0 1.0
CE1 A:TYR342 4.6 18.8 1.0
XE A:XE524 4.6 42.2 1.0
CB A:TRP170 4.8 22.8 1.0
CB A:ALA345 4.9 24.7 1.0

Xenon binding site 5 out of 24 in 3u52

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Xenon binding site 5 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe524

b:42.2
occ:1.00
CD1 A:ILE457 3.7 27.4 1.0
OH A:TYR475 3.9 24.1 1.0
CB A:ALA345 4.0 24.7 1.0
CE2 A:TYR475 4.1 19.8 1.0
CD2 A:LEU395 4.2 28.6 1.0
CG2 A:VAL471 4.4 22.6 1.0
CZ A:TYR475 4.4 19.2 1.0
CD1 A:TRP170 4.6 23.5 1.0
XE A:XE523 4.6 32.4 1.0
CG1 A:VAL470 4.7 25.4 1.0
CB A:LEU467 4.8 41.2 1.0
CD2 A:LEU467 4.8 30.4 1.0
CG A:LEU467 5.0 40.7 1.0

Xenon binding site 6 out of 24 in 3u52

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Xenon binding site 6 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe525

b:40.6
occ:1.00
O A:ASN392 3.6 22.6 1.0
CD2 A:LEU395 3.9 28.6 1.0
CD1 A:LEU467 3.9 42.6 1.0
C A:ASN393 3.9 24.4 1.0
O A:ASN393 3.9 25.4 1.0
OE1 A:GLN344 4.0 27.9 1.0
CA A:ASN393 4.1 24.5 1.0
CE2 A:TYR342 4.1 17.8 1.0
C A:THR394 4.1 22.6 1.0
CD2 A:TYR342 4.2 18.8 1.0
N A:THR394 4.2 23.6 1.0
N A:LEU395 4.2 22.4 1.0
O A:THR394 4.3 23.5 1.0
XE A:XE523 4.4 32.4 1.0
CG A:LEU395 4.5 23.5 1.0
CA A:LEU395 4.5 22.4 1.0
C A:ASN392 4.6 22.2 1.0
CA A:THR394 4.6 23.4 1.0
CD A:GLN344 4.8 25.3 1.0
N A:ASN393 4.9 23.4 1.0
ND2 A:ASN393 5.0 29.6 1.0

Xenon binding site 7 out of 24 in 3u52

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Xenon binding site 7 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe526

b:48.7
occ:1.00
O A:GLN344 3.5 22.4 1.0
CB A:GLN344 4.2 24.2 1.0
OD1 A:ASN483 4.2 24.6 1.0
CG A:GLN344 4.2 23.9 1.0
CD1 A:ILE479 4.3 27.5 1.0
CG1 A:ILE479 4.3 26.0 1.0
C A:GLN344 4.4 23.3 1.0
CZ A:PHE484 4.5 25.2 1.0
CA A:GLU468 4.5 37.2 1.0
CG2 A:VAL471 4.5 22.6 1.0
CB A:VAL471 4.5 24.1 1.0
CG2 A:ILE479 4.6 25.7 1.0
CG1 A:VAL471 4.6 22.2 1.0
CE1 A:PHE484 4.7 25.1 1.0
CG A:GLU468 4.8 43.4 1.0
CA A:GLN344 4.8 22.8 1.0
N A:GLU468 4.8 37.7 1.0
CB A:GLU468 4.9 38.5 1.0
O A:LEU467 5.0 37.2 1.0

Xenon binding site 8 out of 24 in 3u52

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Xenon binding site 8 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe527

b:44.9
occ:0.72
CE A:MET149 3.7 34.9 1.0
CE1 A:PHE100 3.9 33.5 1.0
OG1 A:THR222 3.9 25.8 1.0
CB A:ALA148 4.0 19.0 1.0
CG A:GLN145 4.0 19.9 1.0
CD2 A:PHE225 4.0 29.8 1.0
CG2 A:THR222 4.2 25.9 1.0
CG A:PHE225 4.3 27.0 1.0
CB A:PHE225 4.3 23.1 1.0
CD1 A:PHE100 4.4 33.5 1.0
CA A:THR222 4.4 24.6 1.0
CB A:THR222 4.4 24.3 1.0
CZ A:PHE100 4.5 33.0 1.0
CB A:GLN145 4.5 18.6 1.0
CA A:GLN145 4.5 19.0 1.0
CE2 A:PHE225 4.8 31.4 1.0
CG A:MET149 4.8 28.8 1.0
SD A:MET149 4.8 37.8 1.0
CD A:GLN145 4.9 24.6 1.0
O A:GLN145 4.9 17.5 1.0

Xenon binding site 9 out of 24 in 3u52

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Xenon binding site 9 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe528

b:36.7
occ:1.00
OG A:SER197 3.5 24.9 1.0
CB A:SER197 3.8 24.4 1.0
CB A:PHE266 3.9 17.1 1.0
CA A:PHE266 4.0 17.1 1.0
CA A:SER197 4.1 23.7 1.0
N A:PHE266 4.1 16.1 1.0
CG1 A:VAL201 4.1 21.8 1.0
CE2 A:PHE196 4.2 21.3 1.0
CB A:VAL201 4.2 22.2 1.0
CG2 A:VAL201 4.2 22.6 1.0
O A:ILE262 4.3 17.4 1.0
CZ A:PHE307 4.3 24.6 1.0
CG2 A:ILE262 4.4 20.7 1.0
CD2 A:PHE266 4.5 19.2 1.0
CG A:PRO318 4.7 22.4 1.0
CE1 A:PHE307 4.7 28.3 1.0
CD2 A:PHE196 4.7 20.6 1.0
CG A:PHE266 4.8 14.9 1.0
O A:SER197 4.8 25.5 1.0
C A:TRP265 4.8 16.3 1.0
CA A:ILE262 4.9 18.1 1.0
C A:SER197 4.9 25.1 1.0
CZ A:PHE196 5.0 19.2 1.0
C A:ILE262 5.0 18.0 1.0

Xenon binding site 10 out of 24 in 3u52

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Xenon binding site 10 out of 24 in the X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe529

b:41.2
occ:1.00
CH2 A:TRP47 3.9 29.7 1.0
CE2 A:PHE188 3.9 22.7 1.0
CZ3 A:TRP50 4.0 27.4 1.0
CD2 A:LEU191 4.0 29.1 1.0
CZ3 A:TRP47 4.1 30.6 1.0
CD2 A:PHE188 4.2 19.6 1.0
CD2 A:PHE246 4.2 23.4 1.0
CZ A:PHE122 4.3 27.4 1.0
CG1 A:ILE247 4.4 24.4 1.0
CD1 A:ILE247 4.4 25.3 1.0
CE1 A:PHE122 4.5 24.7 1.0
CE2 A:PHE122 4.6 27.9 1.0
CE2 A:PHE246 4.6 24.5 1.0
CH2 A:TRP50 4.6 26.3 1.0
CG2 A:VAL243 4.6 20.9 1.0
CE3 A:TRP50 4.7 24.4 1.0
CB A:ALA127 4.7 22.5 1.0
CG1 A:VAL243 4.9 22.0 1.0
CD1 A:PHE122 4.9 24.2 1.0
CD2 A:PHE122 4.9 24.2 1.0

Reference:

M.S.Mccormick, S.J.Lippard. Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-Ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase From Pseudomonas Sp. OX1. Biochemistry V. 50 11058 2011.
ISSN: ISSN 0006-2960
PubMed: 22136180
DOI: 10.1021/BI201248B
Page generated: Wed Dec 16 02:40:05 2020

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