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Xenon in PDB 1e9v: Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris

Protein crystallography data

The structure of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris, PDB code: 1e9v was solved by S.J.Cooper, S.Bailey, P.J.Rizkallah, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.07 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.620, 64.598, 152.254, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.7

Other elements in 1e9v:

The structure of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Xenon Binding Sites:

Pages:

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

Binding sites:

The binding sites of Xenon atom in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris (pdb code 1e9v). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 14 binding sites of Xenon where determined in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris, PDB code: 1e9v:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 14 in 1e9v

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Xenon binding site 1 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe700

b:25.7
occ:0.80
CD2 A:LEU472 3.8 24.8 1.0
CG A:LYS471 4.0 24.5 1.0
CB A:ALA385 4.1 22.8 1.0
CG1 A:VAL381 4.1 18.9 1.0
CA A:ALA385 4.1 23.7 1.0
CD2 A:LEU382 4.2 24.8 1.0
CG A:LEU472 4.2 24.0 1.0
O A:VAL381 4.4 20.1 1.0
CG2 A:ILE468 4.6 16.4 1.0
CG1 A:VAL388 4.6 24.8 1.0
CB A:VAL388 4.6 25.4 1.0
CB A:LYS471 4.7 22.5 1.0
CA A:LEU382 4.8 21.2 1.0
O A:ILE468 4.8 18.6 1.0
C A:VAL381 4.9 18.9 1.0
O A:ALA385 5.0 24.3 1.0
CD1 A:LEU472 5.0 24.4 1.0
N A:ALA385 5.0 20.9 1.0

Xenon binding site 2 out of 14 in 1e9v

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Xenon binding site 2 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe701

b:19.6
occ:0.80
O A:SER462 3.9 13.2 1.0
CB A:ALA503 4.0 13.5 1.0
CE A:MET210 4.0 17.3 1.0
CB A:ALA466 4.0 15.5 1.0
CD2 A:LEU504 4.0 14.5 1.0
C A:SER462 4.1 12.3 1.0
N A:TYR463 4.2 11.6 1.0
SD A:MET210 4.2 19.2 1.0
CA A:TYR463 4.3 13.8 1.0
CD1 A:LEU507 4.3 15.5 1.0
CG A:LEU504 4.4 14.2 1.0
CB A:SER462 4.4 14.8 1.0
O A:VAL500 4.6 12.1 1.0
CG1 A:VAL500 4.6 13.9 1.0
N A:LEU504 4.6 12.7 1.0
C A:ALA503 4.9 14.1 1.0
CA A:SER462 4.9 13.2 1.0

Xenon binding site 3 out of 14 in 1e9v

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Xenon binding site 3 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe702

b:26.7
occ:0.50
O A:HOH2726 3.7 36.0 1.0
CD1 A:LEU522 3.9 18.8 1.0
CG2 A:ILE536 3.9 22.7 1.0
O A:HOH2398 3.9 38.2 1.0
CB A:ILE536 4.1 22.1 1.0
O A:ALA527 4.1 25.1 1.0
CB A:LEU530 4.2 25.8 1.0
CG2 A:VAL531 4.2 27.7 1.0
CB A:ALA527 4.3 21.7 1.0
CA A:ALA527 4.4 22.7 1.0
CD1 A:LEU518 4.4 19.9 1.0
CD2 A:LEU518 4.5 19.6 1.0
CD1 A:LEU530 4.6 26.1 1.0
C A:ALA527 4.7 24.6 1.0
O A:ILE536 4.7 19.2 1.0
CD1 A:ILE536 4.8 23.9 1.0
N A:VAL531 4.9 26.2 1.0
CG A:LEU518 5.0 19.3 1.0

Xenon binding site 4 out of 14 in 1e9v

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Xenon binding site 4 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe703

b:27.1
occ:0.50
CD1 A:LEU384 3.7 24.0 1.0
CG2 A:VAL388 3.7 25.0 1.0
CE1 A:PHE376 3.9 20.0 1.0
CD1 A:PHE376 4.0 21.0 1.0
CG2 A:ILE450 4.1 26.4 1.0
CB A:LEU384 4.2 22.3 1.0
CD1 A:LEU454 4.3 15.9 1.0
CG A:LEU384 4.6 24.2 1.0
CG1 A:ILE450 4.6 26.5 1.0
CG2 A:VAL381 4.6 16.8 1.0
CD2 A:LEU454 4.6 15.9 1.0
CG1 A:VAL381 4.7 18.9 1.0
CA A:VAL381 4.8 17.9 1.0
O A:HOH2659 4.8 44.1 1.0
CD1 A:ILE450 4.9 26.7 1.0
CB A:ILE450 4.9 26.8 1.0
CB A:VAL381 4.9 17.3 1.0

Xenon binding site 5 out of 14 in 1e9v

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Xenon binding site 5 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe704

b:29.6
occ:0.50
CD2 A:LEU530 3.7 26.9 1.0
CD2 A:LEU147 4.1 14.5 1.0
CD2 A:LEU150 4.1 12.8 1.0
CG1 A:VAL196 4.2 15.4 1.0
CG1 A:VAL199 4.2 11.3 1.0
CG A:LEU530 4.2 25.9 1.0
CG2 A:VAL196 4.3 15.6 1.0
CG1 A:VAL526 4.5 18.3 1.0
CB A:VAL199 4.5 10.0 1.0
CB A:VAL196 4.6 15.6 1.0
CD1 A:LEU530 4.7 26.1 1.0
CG1 A:VAL529 4.8 30.6 1.0
CA A:VAL196 4.8 14.7 1.0
CG2 A:VAL199 4.8 10.5 1.0

Xenon binding site 6 out of 14 in 1e9v

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Xenon binding site 6 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe705

b:39.2
occ:0.30
CD2 A:LEU501 2.9 20.8 1.0
CG A:LEU501 4.0 19.0 1.0
CD1 A:LEU530 4.1 26.1 1.0
CD1 A:LEU150 4.2 12.9 1.0
CD2 A:LEU502 4.4 14.8 1.0
CD2 A:LEU522 4.6 17.6 1.0
CD1 A:LEU505 4.7 16.5 1.0
CD1 A:LEU522 4.7 18.8 1.0
CD1 A:ILE536 4.8 23.9 1.0
CD2 A:LEU150 4.8 12.8 1.0
CB A:LEU501 4.9 15.1 1.0
CG1 A:VAL498 5.0 12.4 1.0
CD2 A:LEU530 5.0 26.9 1.0

Xenon binding site 7 out of 14 in 1e9v

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Xenon binding site 7 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe706

b:30.0
occ:0.30
CE1 A:PHE400 3.5 20.6 1.0
CZ A:PHE400 3.8 21.3 1.0
CG1 A:VAL381 3.9 18.9 1.0
CG2 A:ILE468 4.0 16.4 1.0
CD2 A:LEU430 4.0 17.9 1.0
CD1 A:LEU454 4.0 15.9 1.0
CG1 A:VAL388 4.1 24.8 1.0
CD1 A:PHE400 4.2 20.4 1.0
CG2 A:VAL388 4.5 25.0 1.0
CD1 A:LEU430 4.7 17.5 1.0
CE2 A:PHE400 4.8 20.5 1.0
CG2 A:VAL381 4.9 16.8 1.0
CB A:VAL388 5.0 25.4 1.0
CG A:LEU430 5.0 16.7 1.0

Xenon binding site 8 out of 14 in 1e9v

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Xenon binding site 8 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe707

b:25.5
occ:0.20
CD1 A:LEU430 3.3 17.5 1.0
CB A:ALA469 3.7 16.7 1.0
N A:ALA469 3.8 17.3 1.0
CA A:ALA469 3.8 18.6 1.0
O A:LEU465 3.9 16.6 1.0
CG2 A:ILE468 3.9 16.4 1.0
CG2 A:VAL486 4.1 20.6 1.0
CD1 A:LEU472 4.4 24.4 1.0
CG1 A:VAL486 4.4 19.4 1.0
C A:ILE468 4.5 19.1 1.0
CB A:ILE468 4.5 17.0 1.0
CG2 A:VAL402 4.8 17.9 1.0
CG A:LEU430 4.8 16.7 1.0
C A:LEU465 4.9 16.7 1.0
CB A:VAL486 4.9 19.2 1.0
O A:ILE468 5.0 18.6 1.0

Xenon binding site 9 out of 14 in 1e9v

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Xenon binding site 9 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe708

b:25.2
occ:0.50
CB A:ASN525 4.0 20.8 1.0
CG1 A:VAL192 4.0 18.6 1.0
CG2 A:VAL526 4.0 17.4 1.0
C A:ASN525 4.2 19.4 1.0
OD2 A:ASP143 4.2 17.8 1.0
O A:ASN525 4.2 19.0 1.0
CG A:ASP143 4.2 17.5 1.0
N A:VAL526 4.3 18.2 1.0
CB A:ASP143 4.3 15.6 1.0
CG2 A:VAL192 4.4 18.6 1.0
CA A:VAL526 4.4 18.1 1.0
CD1 A:LEU147 4.5 14.2 1.0
CG2 A:VAL529 4.5 31.5 1.0
OD1 A:ASP143 4.7 17.7 1.0
O A:HOH2113 4.7 42.8 1.0
CA A:ASN525 4.8 19.5 1.0
CB A:VAL526 4.9 18.2 1.0
O A:HOH2330 4.9 43.7 1.0
CB A:VAL192 4.9 17.8 1.0

Xenon binding site 10 out of 14 in 1e9v

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Xenon binding site 10 out of 14 in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe709

b:23.8
occ:0.09
CG2 A:ILE490 3.3 19.8 1.0
O A:ALA497 3.5 13.2 1.0
CG1 A:VAL500 3.7 13.9 1.0
CB A:ALA497 3.8 14.2 1.0
CB A:VAL500 3.8 12.1 1.0
CA A:GLY405 3.8 15.4 1.0
CA A:ALA497 3.8 13.8 1.0
C A:ALA497 4.1 12.4 1.0
O A:ALA491 4.2 15.5 1.0
N A:LEU501 4.5 11.1 1.0
N A:GLY405 4.6 16.3 1.0
CG2 A:VAL500 4.6 12.2 1.0
O A:ALA404 4.7 16.1 1.0
CB A:ILE490 4.7 18.9 1.0
C A:ALA404 4.9 16.8 1.0
CA A:VAL500 4.9 12.1 1.0
C A:GLY405 5.0 15.8 1.0
C A:VAL500 5.0 11.4 1.0
CD1 A:ILE490 5.0 22.0 1.0

Reference:

S.J.Cooper, C.D.Garner, W.R.Hagen, P.F.Lindley, S.Bailey. Ferricyanide Soaked Hybrid Cluster Protein at 1.2A and Xenon Mapping of the Hydrophobic Cavity at 1.8A To Be Published.
Page generated: Wed Dec 16 02:39:19 2020

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