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Xenon in PDB 4ylh: Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway

Protein crystallography data

The structure of Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway, PDB code: 4ylh was solved by K.Li, N.V.Di Russo, H.L.Condurso, A.E.Roitberg, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.52 / 2.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 139.135, 170.941, 156.003, 90.00, 90.02, 90.00
R / Rfree (%) 17.1 / 20.8

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Xenon atom in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway (pdb code 4ylh). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 14 binding sites of Xenon where determined in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway, PDB code: 4ylh:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 14 in 4ylh

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Xenon binding site 1 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe501

b:58.4
occ:0.32
CZ A:PHE315 1.8 14.3 0.4
CE2 A:PHE315 2.4 15.1 0.4
CE1 A:PHE315 2.9 12.9 0.4
CD1 A:LEU317 3.4 43.0 1.0
CD2 A:PHE315 3.8 15.2 0.4
CG A:LEU317 3.8 47.0 1.0
O A:ALA298 3.9 33.0 1.0
CB A:ALA298 4.0 25.6 1.0
C A:ALA298 4.0 26.8 1.0
CD1 A:PHE315 4.0 13.9 0.4
CD2 A:LEU317 4.1 45.0 1.0
CD1 A:LEU333 4.2 18.4 1.0
CD1 A:LEU302 4.3 34.5 1.0
CD2 A:LEU302 4.3 31.5 1.0
CG A:PHE315 4.4 15.8 0.4
CG A:LEU302 4.5 28.7 1.0
CD2 A:LEU333 4.5 19.3 1.0
N A:GLN299 4.5 26.0 1.0
CA A:ALA298 4.6 27.4 1.0
CB A:ALA329 4.8 21.4 1.0
CA A:GLN299 4.8 27.6 1.0
CG A:LEU333 4.9 19.2 1.0
CD2 A:LEU362 5.0 29.7 1.0

Xenon binding site 2 out of 14 in 4ylh

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Xenon binding site 2 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe501

b:47.5
occ:0.37
CZ A:PHE315 0.9 26.7 0.6
CE2 A:PHE315 1.2 23.3 0.6
CE1 A:PHE315 1.5 25.2 0.6
CD2 A:PHE315 1.9 24.6 0.6
CD1 A:PHE315 2.0 27.3 0.6
CG A:PHE315 2.2 24.4 0.6
C A:TYR314 3.7 24.5 1.0
CB A:PHE315 3.7 24.1 0.6
N A:PHE315 3.8 21.9 0.4
O A:TYR314 3.8 23.8 1.0
N A:PHE315 3.9 23.8 0.6
CB A:PHE315 4.0 17.9 0.4
CA A:TYR314 4.0 27.3 1.0
CB A:ALA313 4.1 32.8 1.0
N A:TYR314 4.2 26.2 1.0
CG2 A:VAL363 4.2 28.0 1.0
CB A:ALA309 4.2 30.1 1.0
CA A:PHE315 4.2 20.4 0.4
CA A:PHE315 4.3 23.9 0.6
C A:ALA313 4.3 28.3 1.0
CG1 A:VAL289 4.4 25.8 1.0
O A:ALA313 4.5 25.0 1.0
CB A:ALA354 4.6 30.6 1.0
CA A:ALA354 4.6 30.3 1.0
O A:ILE352 4.7 22.1 1.0
N A:ALA354 4.8 29.9 1.0
CA A:ALA313 4.9 31.5 1.0
CB A:VAL289 4.9 22.7 1.0

Xenon binding site 3 out of 14 in 4ylh

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Xenon binding site 3 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe501

b:27.6
occ:0.19
CD1 B:PHE315 0.9 16.1 0.4
CE1 B:PHE315 1.3 15.0 0.4
CG B:PHE315 2.1 17.1 0.4
CZ B:PHE315 2.5 13.6 0.4
CD2 B:PHE315 3.0 15.4 0.4
CE2 B:PHE315 3.1 14.0 0.4
O B:PHE315 3.1 27.6 0.6
O B:PHE315 3.1 24.9 0.4
C B:PHE315 3.2 28.9 0.6
C B:PHE315 3.2 25.3 0.4
CB B:PHE315 3.2 19.7 0.4
N B:SER316 3.4 27.5 1.0
CA B:SER316 3.5 28.6 1.0
CB B:PHE315 3.6 29.1 0.6
CG1 B:VAL345 3.8 33.3 1.0
CA B:PHE315 3.8 24.1 0.4
C B:SER316 3.9 28.0 1.0
CA B:PHE315 3.9 30.9 0.6
N B:LEU317 4.1 28.6 1.0
O B:SER316 4.4 26.8 1.0
CD1 B:LEU362 4.4 26.2 1.0
CG B:LEU317 4.4 24.6 1.0
CB B:ALA298 4.5 26.2 1.0
CG2 B:VAL345 4.8 31.4 1.0
CD1 B:LEU317 4.8 23.9 1.0
CB B:SER316 4.8 31.8 1.0
O B:ARG350 4.9 26.0 1.0
CB B:ILE352 4.9 29.1 1.0
CB B:VAL345 5.0 29.9 1.0
CD1 B:ILE352 5.0 32.9 1.0
CG B:PHE315 5.0 32.2 0.6

Xenon binding site 4 out of 14 in 4ylh

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Xenon binding site 4 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe501

b:43.0
occ:0.26
CE2 B:PHE315 0.9 29.8 0.6
CZ B:PHE315 0.9 30.1 0.6
CD2 B:PHE315 1.8 31.1 0.6
CE1 B:PHE315 1.8 29.9 0.6
CD1 B:PHE315 2.4 31.9 0.6
CG B:PHE315 2.4 32.2 0.6
CB B:PHE315 3.9 29.1 0.6
C B:TYR314 3.9 30.3 1.0
O B:TYR314 3.9 34.4 1.0
CB B:ALA309 4.0 33.8 1.0
CG1 B:VAL289 4.1 38.0 1.0
CB B:ALA313 4.1 42.5 1.0
N B:PHE315 4.1 26.3 0.4
CG2 B:VAL363 4.1 30.1 1.0
N B:PHE315 4.2 29.5 0.6
CB B:PHE315 4.3 19.7 0.4
CA B:TYR314 4.4 34.4 1.0
N B:TYR314 4.4 36.1 1.0
CA B:PHE315 4.5 30.9 0.6
CA B:PHE315 4.5 24.1 0.4
CB B:VAL289 4.5 34.6 1.0
C B:ALA313 4.5 38.9 1.0
O B:ALA313 4.8 46.8 1.0
CB B:ALA354 4.8 33.0 1.0
CD1 B:LEU301 4.8 35.9 1.0
CG2 B:VAL289 4.8 38.5 1.0
CA B:ALA354 4.9 27.6 1.0
CA B:ALA313 5.0 38.7 1.0

Xenon binding site 5 out of 14 in 4ylh

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Xenon binding site 5 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe501

b:48.8
occ:0.37
CZ C:PHE315 0.7 24.5 0.6
CE2 C:PHE315 1.1 23.4 0.6
CE1 C:PHE315 1.6 24.9 0.6
CD2 C:PHE315 1.9 24.4 0.6
CD1 C:PHE315 2.3 25.2 0.6
CG C:PHE315 2.4 26.2 0.6
CB C:PHE315 3.9 25.7 0.6
C C:TYR314 3.9 28.8 1.0
CB C:ALA309 3.9 24.6 1.0
O C:TYR314 4.0 32.8 1.0
CG2 C:VAL363 4.1 28.8 1.0
N C:PHE315 4.1 26.4 0.4
CB C:ALA313 4.1 32.3 1.0
N C:PHE315 4.1 29.4 0.6
CB C:PHE315 4.3 19.9 0.4
CA C:TYR314 4.3 27.7 1.0
CG1 C:VAL289 4.3 24.6 1.0
N C:TYR314 4.3 28.2 1.0
C C:ALA313 4.4 32.1 1.0
CA C:PHE315 4.5 23.1 0.4
CA C:PHE315 4.5 27.6 0.6
CB C:ALA354 4.6 20.8 1.0
O C:ALA313 4.6 38.7 1.0
CA C:ALA354 4.7 19.9 1.0
CB C:VAL289 4.7 25.3 1.0
N C:ALA354 4.8 19.2 1.0
CA C:ALA313 5.0 28.9 1.0
O C:ILE352 5.0 27.3 1.0
CD1 C:LEU301 5.0 26.6 1.0

Xenon binding site 6 out of 14 in 4ylh

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Xenon binding site 6 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe501

b:24.3
occ:0.18
CZ D:PHE315 0.6 23.8 0.6
CE2 D:PHE315 1.1 22.5 0.6
CE1 D:PHE315 1.6 22.6 0.6
CD2 D:PHE315 2.0 24.9 0.6
CD1 D:PHE315 2.4 23.2 0.6
CG D:PHE315 2.5 24.6 0.6
CB D:ALA309 3.9 28.2 1.0
C D:TYR314 4.0 27.9 1.0
CB D:PHE315 4.0 24.9 0.6
CG2 D:VAL363 4.0 24.1 1.0
CB D:ALA313 4.1 29.7 1.0
O D:TYR314 4.1 31.3 1.0
N D:PHE315 4.2 25.7 0.4
N D:PHE315 4.2 29.2 0.6
CG1 D:VAL289 4.3 26.8 1.0
CA D:TYR314 4.3 26.6 1.0
N D:TYR314 4.3 26.9 1.0
C D:ALA313 4.4 29.1 1.0
CB D:PHE315 4.4 18.7 0.4
CB D:ALA354 4.5 25.3 1.0
CA D:PHE315 4.6 25.6 0.6
CA D:PHE315 4.6 21.6 0.4
CB D:VAL289 4.6 24.9 1.0
O D:ALA313 4.6 22.7 1.0
CA D:ALA354 4.7 23.4 1.0
N D:ALA354 4.9 22.4 1.0
CA D:ALA313 4.9 28.0 1.0
CG2 D:VAL289 5.0 23.2 1.0

Xenon binding site 7 out of 14 in 4ylh

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Xenon binding site 7 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe501

b:55.2
occ:0.37
CZ E:PHE315 0.7 28.9 0.6
CE2 E:PHE315 1.2 26.8 0.6
CE1 E:PHE315 1.4 26.7 0.6
CD2 E:PHE315 2.0 29.1 0.6
CD1 E:PHE315 2.1 27.7 0.6
CG E:PHE315 2.4 28.0 0.6
C E:TYR314 3.8 25.2 1.0
CB E:PHE315 3.8 24.7 0.6
N E:PHE315 3.9 22.5 0.4
N E:PHE315 4.0 27.0 0.6
O E:TYR314 4.0 29.5 1.0
CB E:ALA309 4.0 25.5 1.0
CG2 E:VAL363 4.1 32.7 1.0
CA E:TYR314 4.1 25.9 1.0
CB E:ALA313 4.1 24.1 1.0
N E:TYR314 4.2 22.6 1.0
CB E:PHE315 4.2 15.4 0.4
C E:ALA313 4.3 21.8 1.0
CA E:PHE315 4.4 25.1 0.6
CA E:PHE315 4.4 18.8 0.4
CG1 E:VAL289 4.5 27.1 1.0
CB E:ALA354 4.5 26.9 1.0
O E:ALA313 4.5 23.5 1.0
CA E:ALA354 4.6 26.4 1.0
N E:ALA354 4.7 28.2 1.0
O E:ILE352 4.8 23.8 1.0
CB E:VAL289 4.9 25.7 1.0
CA E:ALA313 4.9 22.7 1.0

Xenon binding site 8 out of 14 in 4ylh

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Xenon binding site 8 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Xe501

b:39.0
occ:0.39
CE2 F:PHE315 0.7 47.7 0.6
CZ F:PHE315 1.0 48.6 0.6
CD2 F:PHE315 1.6 47.6 0.6
CE1 F:PHE315 1.9 45.3 0.6
CG F:PHE315 2.2 41.6 0.6
CD1 F:PHE315 2.3 45.7 0.6
CB F:PHE315 3.7 32.3 0.6
C F:TYR314 3.9 24.1 1.0
CB F:PHE315 3.9 15.1 0.4
O F:TYR314 4.0 25.5 1.0
CG2 F:VAL363 4.0 28.8 1.0
N F:PHE315 4.0 21.4 0.4
N F:PHE315 4.1 28.4 0.6
CB F:ALA309 4.1 23.2 1.0
CG1 F:VAL289 4.2 24.8 1.0
CA F:PHE315 4.3 19.4 0.4
CA F:PHE315 4.3 31.9 0.6
CB F:ALA313 4.4 25.4 1.0
CA F:TYR314 4.5 24.3 1.0
CB F:VAL289 4.6 23.5 1.0
CD1 F:LEU301 4.6 29.6 1.0
N F:TYR314 4.6 21.6 1.0
CG2 F:VAL289 4.8 23.2 1.0
C F:ALA313 4.8 26.1 1.0
CB F:ALA354 5.0 36.4 1.0
O F:ALA313 5.0 33.6 1.0

Xenon binding site 9 out of 14 in 4ylh

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Xenon binding site 9 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Xe501

b:37.0
occ:0.25
CZ G:PHE315 0.8 22.9 0.6
CE2 G:PHE315 1.4 21.4 0.6
CE1 G:PHE315 1.5 21.5 0.6
CD2 G:PHE315 2.2 21.9 0.6
CD1 G:PHE315 2.2 23.8 0.6
CG G:PHE315 2.5 24.6 0.6
C G:TYR314 3.7 23.4 1.0
CB G:ALA313 3.9 22.6 1.0
O G:TYR314 3.9 26.4 1.0
N G:PHE315 3.9 22.9 0.4
CA G:TYR314 4.0 24.0 1.0
CB G:PHE315 4.0 25.9 0.6
N G:PHE315 4.0 23.9 0.6
N G:TYR314 4.0 24.1 1.0
CB G:ALA309 4.0 24.9 1.0
C G:ALA313 4.1 24.8 1.0
CB G:PHE315 4.2 21.5 0.4
CG2 G:VAL363 4.3 25.5 1.0
O G:ALA313 4.3 28.4 1.0
CB G:ALA354 4.3 22.2 1.0
CG1 G:VAL289 4.4 18.8 1.0
CA G:PHE315 4.5 23.0 0.4
CA G:ALA354 4.5 23.5 1.0
CA G:PHE315 4.5 25.4 0.6
N G:ALA354 4.6 20.2 1.0
CA G:ALA313 4.7 22.3 1.0
O G:ILE352 4.8 25.2 1.0
CB G:VAL289 4.9 17.6 1.0

Xenon binding site 10 out of 14 in 4ylh

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Xenon binding site 10 out of 14 in the Crystal Structure of Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway


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 Dpgc with Bound Substrate Analog and Xe on Oxygen Diffusion Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Xe501

b:47.1
occ:0.28
CZ H:PHE315 0.6 24.3 0.6
CE2 H:PHE315 1.3 21.7 0.6
CE1 H:PHE315 1.4 24.1 0.6
CD2 H:PHE315 2.1 22.5 0.6
CD1 H:PHE315 2.2 25.5 0.6
CG H:PHE315 2.5 25.5 0.6
C H:TYR314 3.9 25.6 1.0
CB H:ALA309 3.9 25.4 1.0
CB H:PHE315 4.0 24.3 0.6
CG2 H:VAL363 4.0 23.3 1.0
N H:PHE315 4.1 22.2 0.4
O H:TYR314 4.1 31.9 1.0
CB H:ALA313 4.1 27.1 1.0
N H:PHE315 4.1 24.3 0.6
CA H:TYR314 4.2 26.8 1.0
N H:TYR314 4.3 25.3 1.0
C H:ALA313 4.3 25.7 1.0
CB H:PHE315 4.3 17.1 0.4
CB H:ALA354 4.4 23.3 1.0
O H:ALA313 4.4 28.8 1.0
CG1 H:VAL289 4.5 38.4 1.0
CA H:ALA354 4.5 22.2 1.0
CA H:PHE315 4.6 20.2 0.4
CA H:PHE315 4.6 24.7 0.6
N H:ALA354 4.7 24.9 1.0
O H:ILE352 4.8 32.4 1.0
CB H:VAL289 4.9 38.7 1.0
CA H:ALA313 4.9 24.7 1.0

Reference:

N.V.Di Russo, H.L.Condurso, K.Li, S.D.Bruner, A.E.Roitberg. Oxygen Diffusion Pathways in A Cofactor-Independent Dioxygenase. Chem Sci V. 6 6341 2015.
ISSN: ISSN 2041-6520
PubMed: 26508997
DOI: 10.1039/C5SC01638J
Page generated: Wed Dec 16 02:40:13 2020

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