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Xenon in PDB 1o75: TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum

Protein crystallography data

The structure of TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum, PDB code: 1o75 was solved by R.K.Deka, M.Machius, M.V.Norgard, D.R.Tomchick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.20 / 1.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.931, 128.931, 151.161, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 22.8

Xenon Binding Sites:

The binding sites of Xenon atom in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum (pdb code 1o75). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 5 binding sites of Xenon where determined in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum, PDB code: 1o75:
Jump to Xenon binding site number: 1; 2; 3; 4; 5;

Xenon binding site 1 out of 5 in 1o75

Go back to Xenon Binding Sites List in 1o75
Xenon binding site 1 out of 5 in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1415

b:35.9
occ:0.70
O A:CYS296 3.5 30.9 1.0
CZ A:TYR260 3.5 29.7 1.0
CZ A:PHE331 3.6 31.6 1.0
OH A:TYR260 3.6 32.1 1.0
CE2 A:PHE331 3.6 33.0 1.0
CE2 A:TYR260 3.8 28.0 1.0
C A:CYS296 3.9 28.5 1.0
CB A:CYS296 4.0 28.5 1.0
C A:GLY297 4.0 30.4 1.0
CE1 A:TYR260 4.0 29.6 1.0
CB A:ILE298 4.1 29.9 1.0
CD2 A:LEU315 4.2 26.4 1.0
N A:ILE298 4.2 28.9 1.0
O A:GLY297 4.2 30.0 1.0
N A:GLY297 4.3 27.8 1.0
CA A:GLY297 4.3 27.3 1.0
CG2 A:ILE298 4.3 28.1 1.0
CD2 A:TYR260 4.4 27.9 1.0
CD1 A:LEU315 4.4 30.2 1.0
CB A:ALA231 4.6 28.1 1.0
CA A:CYS296 4.6 29.3 1.0
CD1 A:TYR260 4.6 27.7 1.0
CA A:ILE298 4.7 28.8 1.0
N A:ALA231 4.7 29.3 1.0
CG A:TYR260 4.8 27.0 1.0
O A:ALA229 4.9 31.2 1.0
CE1 A:PHE331 4.9 31.7 1.0
CD2 A:PHE331 5.0 28.8 1.0
CG A:LEU315 5.0 26.6 1.0

Xenon binding site 2 out of 5 in 1o75

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Xenon binding site 2 out of 5 in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1416

b:56.8
occ:0.50
O A:GLU72 3.7 34.8 1.0
CB A:LYS151 3.7 43.1 1.0
CE A:MET104 3.8 49.8 0.6
N A:LEU74 3.9 34.8 1.0
O A:ASN149 3.9 36.0 1.0
N A:LYS151 3.9 34.9 1.0
CB A:LEU74 3.9 37.1 1.0
C A:ASN149 4.1 36.1 1.0
C A:VAL150 4.1 33.9 1.0
C A:VAL73 4.2 36.0 1.0
C A:GLU72 4.2 35.5 1.0
CB A:ASN149 4.2 39.4 1.0
N A:VAL150 4.3 33.4 1.0
CA A:VAL73 4.3 34.7 1.0
CA A:VAL150 4.3 32.7 1.0
SD A:MET104 4.3 50.1 0.6
CG A:MET104 4.3 47.2 0.6
CA A:LYS151 4.5 37.0 1.0
N A:VAL73 4.5 36.1 1.0
CA A:LEU74 4.5 37.0 1.0
CG A:MET104 4.6 45.2 0.4
CB A:GLU72 4.6 37.3 1.0
O A:VAL150 4.6 33.0 1.0
CD A:LYS151 4.7 50.2 1.0
CA A:ASN149 4.8 37.2 1.0
O A:VAL73 4.8 36.1 1.0
CG A:LYS151 4.9 47.1 1.0

Xenon binding site 3 out of 5 in 1o75

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Xenon binding site 3 out of 5 in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe1415

b:34.8
occ:0.50
CZ B:PHE331 3.4 30.4 1.0
O B:CYS296 3.4 30.4 1.0
CE2 B:PHE331 3.5 31.5 1.0
CZ B:TYR260 3.5 27.6 1.0
OH B:TYR260 3.6 25.8 1.0
C B:CYS296 3.7 28.4 1.0
C B:GLY297 3.8 25.1 1.0
CE2 B:TYR260 3.8 24.7 1.0
CA B:GLY297 3.9 25.7 1.0
N B:GLY297 3.9 26.9 1.0
CB B:CYS296 4.0 28.3 1.0
CE1 B:TYR260 4.0 24.2 1.0
O B:GLY297 4.0 24.5 1.0
CD2 B:LEU315 4.2 24.3 1.0
CB B:ILE298 4.2 25.6 1.0
N B:ILE298 4.2 22.9 1.0
CG2 B:ILE298 4.4 23.6 1.0
CD2 B:TYR260 4.5 23.7 1.0
CA B:CYS296 4.5 28.4 1.0
CD1 B:LEU315 4.6 26.5 1.0
CD1 B:TYR260 4.6 24.3 1.0
O B:ALA229 4.7 24.0 1.0
CE1 B:PHE331 4.7 30.6 1.0
N B:ALA231 4.7 26.6 1.0
CA B:ILE298 4.8 24.8 1.0
CD2 B:PHE331 4.8 28.2 1.0
CG B:TYR260 4.8 26.0 1.0
CB B:ALA231 4.9 28.5 1.0

Xenon binding site 4 out of 5 in 1o75

Go back to Xenon Binding Sites List in 1o75
Xenon binding site 4 out of 5 in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe1416

b:45.5
occ:0.50
CE B:MET104 3.6 48.5 0.6
O B:GLU72 3.7 35.5 1.0
CB B:LYS151 3.7 39.7 1.0
N B:LEU74 3.8 35.2 1.0
CB B:LEU74 3.9 38.9 1.0
N B:LYS151 3.9 35.6 1.0
O B:ASN149 4.0 32.6 1.0
C B:VAL73 4.0 35.5 1.0
C B:VAL150 4.1 36.0 1.0
C B:GLU72 4.1 35.4 1.0
C B:ASN149 4.2 35.5 1.0
CA B:VAL73 4.2 34.0 1.0
SD B:MET104 4.2 49.2 0.6
CA B:VAL150 4.2 34.4 1.0
CB B:ASN149 4.2 37.5 1.0
N B:VAL150 4.3 33.4 1.0
N B:VAL73 4.3 33.8 1.0
CG B:MET104 4.4 46.2 0.6
CA B:LEU74 4.4 37.5 1.0
CB B:GLU72 4.4 35.5 1.0
CA B:LYS151 4.5 37.4 1.0
CG B:MET104 4.5 44.0 0.4
O B:VAL73 4.6 36.4 1.0
OG B:SER54 4.6 61.1 1.0
O B:VAL150 4.6 34.4 1.0
CD B:LYS151 4.8 47.8 1.0
CG B:LYS151 4.9 45.1 1.0
CA B:ASN149 4.9 35.4 1.0
CA B:GLU72 5.0 34.7 1.0

Xenon binding site 5 out of 5 in 1o75

Go back to Xenon Binding Sites List in 1o75
Xenon binding site 5 out of 5 in the TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of TP47, the 47-Kilodalton Lipoprotein of Treponema Pallidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe1417

b:58.1
occ:0.40
CZ3 B:TRP93 3.2 44.9 0.2
NE1 B:TRP93 3.4 45.0 0.8
CD1 B:TRP93 3.4 40.0 0.8
CE3 B:TRP93 3.4 44.5 0.2
CE B:LYS81 3.8 41.8 1.0
CG B:LYS81 3.9 38.6 1.0
CH2 B:TRP93 4.1 45.2 0.2
CD B:LYS81 4.2 42.0 1.0
O B:LYS81 4.3 31.0 1.0
N B:GLU83 4.4 31.4 1.0
CD2 B:TRP93 4.5 43.3 0.2
C B:LYS81 4.6 36.4 1.0
CB B:GLU83 4.6 35.4 1.0
CE2 B:TRP93 4.7 44.7 0.8
C B:GLN82 4.7 33.4 1.0
CA B:GLN82 4.8 33.6 1.0
NZ B:LYS81 4.8 42.0 1.0
CG B:TRP93 4.8 41.0 0.8
N B:GLN82 4.8 32.9 1.0
CB B:LYS81 4.9 36.4 1.0
CA B:GLU83 5.0 33.6 1.0
CZ2 B:TRP93 5.0 45.4 0.2

Reference:

R.K.Deka, M.Machius, M.V.Norgard, D.R.Tomchick. Crystal Structure of the 47-kDa Lipoprotein of Treponema Pallidum Reveals A Novel Penicillin-Binding Protein. J. Biol. Chem. V. 277 41857 2002.
ISSN: ISSN 0021-9258
PubMed: 12196546
DOI: 10.1074/JBC.M207402200
Page generated: Wed Dec 16 02:39:23 2020

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