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Xenon in PDB 2oqe: Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms

Enzymatic activity of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms

All present enzymatic activity of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms, PDB code: 2oqe was solved by B.J.Johnson, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.68 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.403, 222.751, 103.651, 90.00, 95.85, 90.00
R / Rfree (%) 16.2 / 18.8

Other elements in 2oqe:

The structure of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms also contains other interesting chemical elements:

Copper (Cu) 6 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 Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms (pdb code 2oqe). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 24 binding sites of Xenon where determined in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms, PDB code: 2oqe:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 1 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


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 Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe901

b:34.8
occ:0.55
O5 A:TPQ405 2.9 30.5 0.8
OD1 A:ASP319 3.6 29.4 1.0
CE2 A:TYR323 3.6 17.9 1.0
CE2 A:TRP156 3.8 19.7 1.0
CZ A:TYR323 3.9 18.6 1.0
C5 A:TPQ405 3.9 30.2 1.0
OH A:TYR323 3.9 17.7 1.0
CD2 A:TRP156 4.0 17.9 1.0
CB A:ALA317 4.0 13.1 1.0
O A:ALA402 4.1 20.1 1.0
CZ2 A:TRP156 4.1 18.8 1.0
NE1 A:TRP156 4.1 20.4 1.0
CB A:ALA402 4.2 19.3 1.0
C6 A:TPQ405 4.2 28.1 1.0
CD2 A:TYR323 4.3 17.1 1.0
CE3 A:TRP156 4.3 18.0 1.0
C A:ALA402 4.4 19.3 1.0
CB A:ALA403 4.4 20.0 1.0
CG A:TRP156 4.4 17.6 1.0
XE A:XE902 4.4 39.7 0.2
CH2 A:TRP156 4.4 18.9 1.0
CD1 A:TRP156 4.5 19.1 1.0
CZ3 A:TRP156 4.5 17.9 1.0
CG A:ASP319 4.7 22.6 1.0
CA A:ALA402 4.8 19.0 1.0
CE1 A:TYR323 4.8 17.4 1.0
N A:ALA403 4.9 19.6 1.0
O A:HOH4056 4.9 22.6 1.0
OD1 A:ASN404 5.0 21.6 1.0

Xenon binding site 2 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 2 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


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 Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe902

b:39.7
occ:0.25
CB A:ALA403 3.5 20.0 1.0
CD2 A:LEU121 3.8 23.1 1.0
CD1 A:TRP156 3.8 19.1 1.0
C A:PRO155 3.9 17.9 1.0
N A:TRP156 3.9 16.5 1.0
CD1 A:LEU121 4.0 19.9 1.0
O A:PRO155 4.0 19.3 1.0
CD A:PRO155 4.0 19.1 1.0
CA A:TRP156 4.0 16.3 1.0
N A:PRO155 4.1 18.1 1.0
CE1 A:TYR323 4.2 17.4 1.0
C A:ASP154 4.4 18.1 1.0
CA A:ALA403 4.4 19.6 1.0
XE A:XE901 4.4 34.8 0.6
NE1 A:TRP156 4.4 20.4 1.0
CG A:LEU121 4.4 22.1 1.0
CG A:TRP156 4.4 17.6 1.0
CZ A:TYR323 4.5 18.6 1.0
N A:ALA403 4.5 19.6 1.0
CB A:ASP154 4.5 17.8 1.0
OH A:TYR323 4.6 17.7 1.0
CA A:PRO155 4.6 18.2 1.0
CA A:ASP154 4.7 18.0 1.0
CG A:PRO155 4.8 18.3 1.0
CB A:TRP156 4.8 17.4 1.0
CD1 A:TYR323 4.8 16.9 1.0
O A:ASP154 4.9 17.5 1.0

Xenon binding site 3 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 3 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


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 Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe903

b:17.7
occ:0.30
CD1 A:LEU643 3.5 21.9 1.0
CD1 A:ILE296 3.7 23.4 1.0
CG2 A:ILE419 3.8 17.9 1.0
CD1 A:LEU641 3.9 16.7 1.0
N A:LEU421 3.9 16.0 1.0
O A:ILE419 4.0 16.8 1.0
CZ3 A:TRP411 4.0 15.8 1.0
C A:ARG420 4.0 17.3 1.0
CB A:LEU421 4.1 15.4 1.0
C A:ILE419 4.2 16.6 1.0
CE3 A:TRP411 4.2 15.1 1.0
CG A:LEU643 4.3 17.7 1.0
O A:ARG420 4.3 17.1 1.0
N A:ARG420 4.3 17.0 1.0
CA A:ARG420 4.4 17.3 1.0
CB A:ILE419 4.5 16.6 1.0
CA A:LEU421 4.5 15.8 1.0
CG1 A:ILE296 4.7 16.5 1.0
CD2 A:LEU462 4.8 13.0 1.0
CB A:LEU643 4.9 16.5 1.0
CD1 A:LEU462 5.0 13.2 1.0

Xenon binding site 4 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 4 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


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 Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe904

b:36.5
occ:0.30
O B:HOH4641 3.2 40.5 1.0
N A:LYS226 3.3 22.6 1.0
CD A:PRO225 3.7 20.6 1.0
CG A:LYS226 3.7 25.7 1.0
CB A:LYS226 3.8 23.9 1.0
N A:PRO225 3.8 21.0 1.0
CB A:TYR224 3.9 19.5 1.0
CB A:PRO225 4.0 21.8 1.0
CA A:LYS226 4.2 23.7 1.0
CD A:LYS226 4.2 27.0 1.0
CG A:PRO225 4.2 21.2 1.0
C A:PRO225 4.2 21.6 1.0
CA A:PRO225 4.2 21.0 1.0
CD1 A:TYR224 4.3 18.9 1.0
C A:TYR224 4.4 20.3 1.0
CG2 B:THR664 4.5 23.1 1.0
CG A:TYR224 4.6 20.2 1.0
CA A:TYR224 4.7 20.1 1.0
CE A:LYS226 4.8 27.7 1.0
OE2 B:GLU667 5.0 35.9 1.0

Xenon binding site 5 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 5 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


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 Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe901

b:34.7
occ:0.55
O5 B:TPQ405 3.0 33.0 1.0
OD1 B:ASP319 3.5 27.2 1.0
CE2 B:TYR323 3.6 17.1 1.0
CE2 B:TRP156 3.8 19.3 1.0
C5 B:TPQ405 3.9 31.8 1.0
CZ B:TYR323 4.0 16.3 1.0
CD2 B:TRP156 4.0 17.7 1.0
CB B:ALA317 4.0 14.2 1.0
OH B:TYR323 4.0 16.7 1.0
CZ2 B:TRP156 4.1 18.6 1.0
O B:ALA402 4.1 20.0 1.0
NE1 B:TRP156 4.1 19.1 1.0
C6 B:TPQ405 4.1 30.0 1.0
CB B:ALA402 4.1 18.9 1.0
CD2 B:TYR323 4.3 17.8 1.0
C B:ALA402 4.3 19.4 1.0
CE3 B:TRP156 4.4 17.6 1.0
CB B:ALA403 4.4 19.4 1.0
CG B:TRP156 4.4 17.1 1.0
XE B:XE902 4.4 29.0 0.1
CH2 B:TRP156 4.4 18.8 1.0
CD1 B:TRP156 4.5 18.4 1.0
CZ3 B:TRP156 4.6 18.5 1.0
CG B:ASP319 4.7 22.8 1.0
CA B:ALA402 4.8 18.9 1.0
O B:HOH4142 4.8 23.0 1.0
N B:ALA403 4.9 19.8 1.0
CE1 B:TYR323 4.9 16.0 1.0
OD1 B:ASN404 5.0 21.1 1.0

Xenon binding site 6 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 6 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


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 Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe902

b:29.0
occ:0.15
CB B:ALA403 3.5 19.4 1.0
CD2 B:LEU121 3.7 25.6 1.0
CD1 B:TRP156 3.8 18.4 1.0
N B:TRP156 3.9 17.2 1.0
C B:PRO155 3.9 18.0 1.0
CA B:TRP156 3.9 16.5 1.0
CD1 B:LEU121 4.0 22.7 1.0
O B:PRO155 4.0 19.1 1.0
CD B:PRO155 4.0 19.1 1.0
N B:PRO155 4.1 18.0 1.0
CE1 B:TYR323 4.1 16.0 1.0
C B:ASP154 4.4 18.3 1.0
XE B:XE901 4.4 34.7 0.6
CG B:TRP156 4.4 17.1 1.0
CG B:LEU121 4.4 23.3 1.0
CZ B:TYR323 4.4 16.3 1.0
CA B:ALA403 4.4 19.8 1.0
NE1 B:TRP156 4.4 19.1 1.0
OH B:TYR323 4.5 16.7 1.0
N B:ALA403 4.5 19.8 1.0
CB B:ASP154 4.6 18.0 1.0
CA B:PRO155 4.6 18.2 1.0
CD1 B:TYR323 4.7 15.2 1.0
CA B:ASP154 4.8 18.4 1.0
CB B:TRP156 4.8 17.1 1.0
CG B:PRO155 4.8 18.2 1.0
O B:ASP154 4.9 17.6 1.0

Xenon binding site 7 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 7 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe903

b:17.7
occ:0.30
CD1 B:LEU643 3.5 20.8 1.0
CD1 B:ILE296 3.7 20.9 1.0
CG2 B:ILE419 3.8 18.4 1.0
CD1 B:LEU641 3.8 16.5 1.0
N B:LEU421 3.9 15.5 1.0
O B:ILE419 4.0 17.0 1.0
CZ3 B:TRP411 4.0 15.7 1.0
C B:ARG420 4.0 16.9 1.0
CB B:LEU421 4.1 14.5 1.0
C B:ILE419 4.2 16.7 1.0
CE3 B:TRP411 4.2 13.6 1.0
CG B:LEU643 4.3 16.7 1.0
O B:ARG420 4.3 17.0 1.0
N B:ARG420 4.4 16.6 1.0
CA B:ARG420 4.4 16.9 1.0
CB B:ILE419 4.5 17.1 1.0
CA B:LEU421 4.5 14.8 1.0
CG1 B:ILE296 4.7 16.0 1.0
CD2 B:LEU462 4.8 14.4 1.0
CB B:LEU643 4.9 15.6 1.0
CD1 B:LEU462 5.0 15.7 1.0

Xenon binding site 8 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 8 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe904

b:28.2
occ:0.20
O A:HOH4602 3.1 38.1 1.0
N B:LYS226 3.3 23.1 1.0
CB B:LYS226 3.7 23.8 1.0
CD B:PRO225 3.7 21.3 1.0
CG B:LYS226 3.8 25.7 1.0
N B:PRO225 3.9 21.6 1.0
CB B:TYR224 3.9 20.6 1.0
CB B:PRO225 4.0 22.1 1.0
CD B:LYS226 4.0 27.1 1.0
CA B:LYS226 4.1 23.6 1.0
CG B:PRO225 4.2 22.0 1.0
C B:PRO225 4.2 22.1 1.0
CA B:PRO225 4.3 21.8 1.0
CD1 B:TYR224 4.3 18.3 1.0
C B:TYR224 4.4 20.9 1.0
CG2 A:THR664 4.4 22.7 1.0
CG B:TYR224 4.6 20.8 1.0
CA B:TYR224 4.7 20.7 1.0
CE B:LYS226 4.8 29.0 1.0
O B:HOH4267 4.9 29.6 1.0

Xenon binding site 9 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 9 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe901

b:39.3
occ:0.50
O5 C:TPQ405 2.9 30.4 0.7
OD1 C:ASP319 3.6 26.8 1.0
CE2 C:TYR323 3.8 18.6 1.0
CE2 C:TRP156 3.8 18.2 1.0
C5 C:TPQ405 3.8 29.2 0.7
XE C:XE902 3.9 52.3 0.1
CZ2 C:TRP156 4.0 18.4 1.0
CB C:ALA317 4.0 14.9 1.0
O C:ALA402 4.0 20.2 1.0
CD2 C:TRP156 4.0 17.9 1.0
OH C:TYR323 4.1 17.7 1.0
NE1 C:TRP156 4.1 17.3 1.0
CZ C:TYR323 4.1 19.1 1.0
CB C:ALA402 4.2 19.4 1.0
C6 C:TPQ405 4.2 28.4 0.7
CH2 C:TRP156 4.3 19.0 1.0
CE3 C:TRP156 4.3 18.1 1.0
C C:ALA402 4.4 19.2 1.0
CZ3 C:TRP156 4.4 18.2 1.0
CG C:TRP156 4.4 17.4 1.0
CD2 C:TYR323 4.5 19.8 1.0
CD1 C:TRP156 4.5 19.1 1.0
CB C:ALA403 4.6 19.9 1.0
CG C:ASP319 4.6 22.1 1.0
O C:HOH4454 4.6 30.5 1.0
CA C:ALA402 4.8 19.1 1.0
O C:HOH4408 4.9 30.0 1.0
OD1 C:ASN404 4.9 21.6 1.0
OD2 C:ASP319 5.0 27.3 1.0

Xenon binding site 10 out of 24 in 2oqe

Go back to Xenon Binding Sites List in 2oqe
Xenon binding site 10 out of 24 in the Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Crystal Structure of Hansenula Polymorpha Amine Oxidase in Complex with Xe to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe902

b:52.3
occ:0.15
O C:PRO155 3.6 21.9 1.0
CE1 C:TYR323 3.7 17.0 1.0
CB C:ALA403 3.7 19.9 1.0
N C:ALA403 3.8 19.5 1.0
CZ C:TYR323 3.9 19.1 1.0
CD1 C:TYR323 3.9 19.7 1.0
XE C:XE901 3.9 39.3 0.5
C C:ALA402 4.1 19.2 1.0
CA C:ALA403 4.2 19.4 1.0
CE2 C:TYR323 4.3 18.6 1.0
CG C:TYR323 4.3 17.0 1.0
O C:HOH4157 4.3 26.5 1.0
OH C:TYR323 4.4 17.7 1.0
CA C:ALA402 4.4 19.1 1.0
CD2 C:TYR323 4.5 19.8 1.0
CD2 C:LEU121 4.5 32.2 0.5
C C:PRO155 4.7 20.5 1.0
O C:ALA402 4.7 20.2 1.0
CD1 C:LEU121 4.8 31.0 0.5
CB C:ALA402 4.8 19.4 1.0
CE C:MET328 4.9 17.8 0.4
CD1 C:TRP156 4.9 19.1 1.0
CA C:TRP156 5.0 17.0 1.0

Reference:

B.J.Johnson, J.Cohen, R.W.Welford, A.R.Pearson, K.Schulten, J.P.Klinman, C.M.Wilmot. Exploring Molecular Oxygen Pathways in Hansenula Polymorpha Copper-Containing Amine Oxidase J.Biol.Chem. V. 282 17767 2007.
ISSN: ISSN 0021-9258
PubMed: 17409383
DOI: 10.1074/JBC.M701308200
Page generated: Wed Dec 16 02:39:45 2020

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