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Xenon in PDB 2w0q: E. Coli Copper Amine Oxidase in Complex with Xenon

Enzymatic activity of E. Coli Copper Amine Oxidase in Complex with Xenon

All present enzymatic activity of E. Coli Copper Amine Oxidase in Complex with Xenon:
1.4.3.4;

Protein crystallography data

The structure of E. Coli Copper Amine Oxidase in Complex with Xenon, PDB code: 2w0q was solved by P.Pirrat, M.A.Smith, A.R.Pearson, M.J.Mcpherson, S.E.V.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 2.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.588, 166.871, 80.330, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 21.9

Other elements in 2w0q:

The structure of E. Coli Copper Amine Oxidase in Complex with Xenon also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Calcium (Ca) 4 atoms

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Xenon atom in the E. Coli Copper Amine Oxidase in Complex with Xenon (pdb code 2w0q). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 11 binding sites of Xenon where determined in the E. Coli Copper Amine Oxidase in Complex with Xenon, PDB code: 2w0q:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 1 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe901

b:58.8
occ:0.45
 O A:TYR387 3.4 37.9 1.0
CE1 A:PHE192 3.7 51.0 1.0
N A:LEU189 3.8 44.9 1.0
O A:VAL187 3.8 42.7 1.0
C A:LEU188 3.9 43.9 1.0
CD2 A:LEU189 4.0 48.9 1.0
O A:HOH2086 4.0 38.4 1.0
CD1 A:LEU392 4.1 34.8 1.0
CA A:LEU189 4.1 46.3 1.0
O A:LEU188 4.2 44.5 1.0
CG A:LEU189 4.2 49.1 1.0
CA A:LEU188 4.3 43.2 1.0
C A:TYR387 4.3 37.9 1.0
C A:VAL187 4.3 42.9 1.0
CA A:TYR387 4.4 38.7 1.0
CD1 A:PHE192 4.4 51.5 1.0
CB A:TYR387 4.4 38.8 1.0
CD2 A:TYR387 4.5 40.3 1.0
CZ A:PHE192 4.5 51.5 1.0
N A:LEU188 4.6 42.7 1.0
CG A:LEU392 4.6 34.1 1.0
CG1 A:VAL187 4.7 42.9 1.0
CD2 A:LEU392 4.8 33.3 1.0
CB A:LEU189 4.8 46.2 1.0
CB A:VAL187 5.0 42.9 1.0
CG A:TYR387 5.0 39.5 1.0

Xenon binding site 2 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 2 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe903

b:43.1
occ:0.30
 O A:HOH2164 3.4 40.6 1.0
C A:PHE330 3.6 21.2 1.0
O A:PHE330 3.7 20.5 1.0
O A:HOH2169 3.7 37.5 1.0
O A:HOH2159 3.7 43.1 1.0
CA A:PHE330 3.8 21.1 1.0
CG A:MET322 3.8 32.2 1.0
N A:PHE330 3.8 20.4 1.0
OG1 A:THR344 3.9 24.4 1.0
O A:THR344 4.0 25.2 1.0
N A:HIS331 4.0 22.9 1.0
SD A:MET322 4.2 37.7 1.0
C A:ASP329 4.3 21.3 1.0
CB A:ASP329 4.3 22.5 1.0
CB A:MET322 4.4 27.5 1.0
CD2 A:HIS94 4.4 22.6 1.0
NE2 A:HIS94 4.5 26.5 1.0
CB A:HIS331 4.5 24.3 1.0
CE A:MET322 4.5 43.1 1.0
CA A:HIS331 4.6 23.8 1.0
O A:ASP329 4.7 20.1 1.0
CA A:ASP329 4.9 21.8 1.0
CB A:THR344 4.9 24.3 1.0
O A:SER343 4.9 26.4 1.0
CA A:MET322 5.0 27.6 1.0

Xenon binding site 3 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 3 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe904

b:58.4
occ:0.35
 CE1 A:TYR381 3.4 58.0 1.0
OH A:TYR381 3.6 59.8 1.0
CA A:GLY464 3.8 36.3 1.0
OG1 A:THR223 3.8 50.6 1.0
CE2 A:TYR387 3.9 41.3 1.0
O A:PRO224 3.9 44.9 1.0
OH A:TYR387 4.0 42.9 1.0
CZ A:TYR387 4.0 44.0 1.0
CZ A:TYR381 4.0 57.8 1.0
N A:GLY464 4.0 37.1 1.0
CE2 A:PHE192 4.3 50.6 1.0
CZ A:PHE192 4.3 51.5 1.0
CG1 A:VAL463 4.4 37.8 1.0
CD1 A:TYR381 4.4 57.8 1.0
CD A:PRO224 4.5 43.6 1.0
CD2 A:TYR387 4.6 40.3 1.0
C A:VAL463 4.6 37.4 1.0
CE1 A:TYR387 4.7 42.4 1.0
O A:VAL463 4.8 38.5 1.0

Xenon binding site 4 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 4 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe907

b:49.7
occ:0.20
 CD2 A:LEU638 3.3 43.0 1.0
CG A:LEU638 3.4 40.0 1.0
CD2 A:LEU543 3.4 35.7 1.0
O A:ALA576 3.5 39.0 1.0
CD A:GLN578 3.6 46.0 1.0
NE2 A:GLN578 3.6 47.5 1.0
OE1 A:GLN578 3.8 48.2 1.0
CD1 A:LEU543 3.9 38.1 1.0
CG A:LEU543 3.9 36.5 1.0
CG A:GLN578 4.2 41.0 1.0
CD A:ARG586 4.2 28.1 1.0
CG2 A:VAL640 4.2 29.9 1.0
CA A:ALA576 4.3 37.6 1.0
C A:ALA576 4.3 37.9 1.0
CB A:LEU638 4.3 35.0 1.0
XE A:XE909 4.4 41.6 0.1
CD1 A:LEU638 4.4 42.6 1.0
CB A:ALA576 4.5 36.4 1.0
CD1 A:ILE570 4.5 40.7 1.0
CG A:ARG586 4.7 26.7 1.0
NE A:ARG586 4.8 26.9 1.0
CB A:ARG586 4.9 26.4 1.0

Xenon binding site 5 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 5 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe908

b:27.2
occ:0.15
 O A:ALA426 2.7 23.5 1.0
N A:ILE460 2.8 25.6 1.0
O A:SER394 2.9 25.1 1.0
O A:ILE460 3.4 28.6 1.0
CD1 A:ILE396 3.5 30.4 1.0
CA A:ILE460 3.5 25.8 1.0
CB A:ILE460 3.6 24.6 1.0
C A:ALA426 3.6 23.5 1.0
CG1 A:ILE396 3.6 27.1 1.0
CG2 A:THR393 3.8 20.9 1.0
C A:TRP459 3.8 24.7 1.0
CD1 A:TRP459 3.9 23.2 1.0
CA A:TRP459 3.9 23.6 1.0
C A:ILE460 3.9 27.6 1.0
CG1 A:ILE460 3.9 23.6 1.0
C A:SER394 4.0 25.2 1.0
O A:ARG425 4.0 26.1 1.0
CA A:ALA426 4.2 23.6 1.0
N A:ILE396 4.4 26.2 1.0
N A:ILE427 4.5 23.0 1.0
N A:SER394 4.5 23.7 1.0
CG A:TRP459 4.6 24.7 1.0
NE1 A:TRP459 4.6 25.9 1.0
CB A:ILE396 4.6 26.0 1.0
O A:ARG458 4.7 22.3 1.0
C A:PRO395 4.8 26.1 1.0
CB A:TRP459 4.8 22.8 1.0
CD1 A:ILE460 4.8 21.6 1.0
CA A:SER394 4.8 24.5 1.0
CA A:ILE396 4.9 25.6 1.0
CA A:ILE427 4.9 23.0 1.0
CA A:PRO395 4.9 25.3 1.0
N A:PRO395 4.9 25.8 1.0
O A:TRP459 4.9 23.7 1.0
N A:TRP459 5.0 22.8 1.0
CG2 A:ILE460 5.0 24.8 1.0

Xenon binding site 6 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 6 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe909

b:41.6
occ:0.10
 CG1 A:ILE605 2.8 29.9 1.0
CD1 A:LEU543 3.2 38.1 1.0
CB A:ILE605 3.6 30.3 1.0
CD1 A:ILE605 3.9 29.1 1.0
CD1 A:LEU638 3.9 42.6 1.0
CG2 A:ILE605 4.1 29.5 1.0
CD2 A:LEU638 4.1 43.0 1.0
CG2 A:VAL681 4.1 26.0 1.0
CG2 A:VAL640 4.2 29.9 1.0
CG1 A:VAL681 4.4 26.8 1.0
CG A:LEU638 4.4 40.0 1.0
XE A:XE907 4.4 49.7 0.2
CB A:ARG586 4.5 26.4 1.0
N A:LEU588 4.6 26.4 1.0
C A:LEU587 4.6 27.0 1.0
O A:LEU587 4.6 26.7 1.0
CG A:LEU543 4.7 36.5 1.0
CB A:LEU588 4.7 28.2 1.0
O A:ARG586 4.7 28.5 1.0
C A:ARG586 4.7 27.5 1.0
N A:LEU587 4.9 26.6 1.0
CB A:VAL681 4.9 27.3 1.0

Xenon binding site 7 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 7 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe902

b:50.2
occ:0.30
 O B:TYR387 3.2 40.0 1.0
O B:VAL187 3.6 48.8 1.0
CE1 B:PHE192 3.7 55.8 1.0
N B:LEU189 3.8 48.5 1.0
C B:LEU188 3.9 47.5 1.0
CD1 B:LEU392 4.0 33.4 1.0
O B:HOH2069 4.1 46.4 1.0
C B:TYR387 4.2 39.9 1.0
CA B:LEU189 4.2 49.8 1.0
CD2 B:TYR387 4.2 41.5 1.0
C B:VAL187 4.2 48.8 1.0
CD1 B:LEU189 4.2 53.9 1.0
CA B:LEU188 4.3 47.4 1.0
CB B:TYR387 4.3 40.9 1.0
CA B:TYR387 4.3 40.5 1.0
O B:LEU188 4.4 46.8 1.0
CD1 B:PHE192 4.5 54.7 1.0
CD2 B:LEU392 4.5 32.2 1.0
CG1 B:VAL187 4.5 48.2 1.0
CG B:LEU392 4.6 34.2 1.0
N B:LEU188 4.6 48.3 1.0
CZ B:PHE192 4.6 54.9 1.0
CG B:TYR387 4.8 40.3 1.0
CB B:LEU189 4.8 50.9 1.0
CB B:VAL187 4.8 48.9 1.0

Xenon binding site 8 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 8 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe905

b:48.8
occ:0.15
 CD2 B:LEU638 2.9 41.0 1.0
CD2 B:LEU543 3.2 44.1 1.0
CG B:LEU638 3.3 38.7 1.0
O B:ALA576 3.5 43.6 1.0
NE2 B:GLN578 3.5 50.4 1.0
CD B:GLN578 3.7 48.7 1.0
CD1 B:LEU543 3.7 44.9 1.0
CG B:LEU543 3.9 41.4 1.0
OE1 B:GLN578 4.1 49.5 1.0
CG2 B:VAL640 4.1 33.2 1.0
CD B:ARG586 4.2 28.6 1.0
CA B:ALA576 4.2 42.1 1.0
CG B:GLN578 4.2 44.7 1.0
CD1 B:ILE570 4.2 36.8 1.0
C B:ALA576 4.3 42.7 1.0
CB B:ALA576 4.3 41.6 1.0
CD1 B:LEU638 4.3 38.6 1.0
CB B:LEU638 4.4 35.8 1.0
CG B:ARG586 4.7 31.2 1.0
NE B:ARG586 4.9 31.7 1.0
CB B:ARG586 4.9 31.1 1.0

Xenon binding site 9 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 9 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe906

b:57.3
occ:0.30
 O B:HOH2121 3.6 45.1 1.0
C B:PHE330 3.7 23.1 1.0
O B:PHE330 3.8 22.3 1.0
OG1 B:THR344 3.8 31.0 1.0
CA B:PHE330 3.9 23.3 1.0
N B:PHE330 3.9 23.3 1.0
O B:THR344 3.9 30.1 1.0
CG B:MET322 4.0 35.3 1.0
SD B:MET322 4.1 44.6 1.0
N B:HIS331 4.1 24.1 1.0
O B:HOH2115 4.3 39.7 1.0
CB B:HIS331 4.3 25.6 1.0
C B:ASP329 4.3 24.3 1.0
CB B:ASP329 4.4 25.7 1.0
CB B:MET322 4.4 30.1 1.0
CE1 B:HIS94 4.4 33.1 1.0
ND1 B:HIS94 4.5 32.6 1.0
CA B:HIS331 4.6 25.9 1.0
CB B:THR344 4.7 31.5 1.0
O B:ASP329 4.8 24.4 1.0
CA B:ASP329 5.0 25.6 1.0
O B:SER343 5.0 31.9 1.0

Xenon binding site 10 out of 11 in 2w0q

Go back to Xenon Binding Sites List in 2w0q
Xenon binding site 10 out of 11 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe910

b:46.6
occ:0.15
 NE2 B:GLN620 3.4 63.4 1.0
O A:VAL549 3.5 41.4 1.0
CB A:MET563 3.6 38.9 1.0
CB A:PRO548 3.6 39.7 1.0
N A:VAL549 3.6 40.9 1.0
CG B:GLN620 3.7 58.6 1.0
C A:PRO548 3.8 40.9 1.0
C A:VAL549 3.8 41.8 1.0
CB B:GLN620 3.9 54.8 1.0
CA A:MET563 3.9 38.5 1.0
CG A:MET563 4.0 39.9 1.0
CA A:PRO548 4.0 40.2 1.0
CD B:GLN620 4.1 64.3 1.0
O A:GLN564 4.2 38.8 1.0
CA A:VAL549 4.2 41.1 1.0
O A:PRO548 4.3 41.2 1.0
N A:GLN564 4.4 38.5 1.0
N A:VAL550 4.4 42.0 1.0
C A:MET563 4.5 38.2 1.0
SD A:MET563 4.6 43.0 1.0
CG2 B:THR688 4.6 31.8 1.0
CG2 A:VAL550 4.8 41.7 1.0
CA A:VAL550 5.0 43.4 1.0

Reference:

P.Pirrat, M.A.Smith, A.R.Pearson, M.J.Mcpherson, S.E.V.Phillips. Structure of A Xenon Derivative of Escherichia Coli Copper Amine Oxidase: Confirmation of the Proposed Oxygen-Entry Pathway. Acta Crystallogr.,Sect.F V. 64 1105 2008.
ISSN: ISSN 1744-3091
PubMed: 19052360
DOI: 10.1107/S1744309108036373
Page generated: Wed Dec 16 02:39:41 2020

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