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Xenon in PDB 4guv: Tetx Derivatized with Xenon

Protein crystallography data

The structure of Tetx Derivatized with Xenon, PDB code: 4guv was solved by G.Volkers, G.J.Palm, S.Panjikar, W.Hinrichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.27 / 2.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 68.710, 80.140, 87.500, 111.04, 90.06, 93.29
R / Rfree (%) 18.1 / 22.1

Xenon Binding Sites:

The binding sites of Xenon atom in the Tetx Derivatized with Xenon (pdb code 4guv). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 8 binding sites of Xenon where determined in the Tetx Derivatized with Xenon, PDB code: 4guv:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Xenon binding site 1 out of 8 in 4guv

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Xenon binding site 1 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe404

b:89.0
occ:0.71
CE1 A:PHE267 3.5 47.2 1.0
O A:TYR274 3.5 49.7 1.0
CD1 A:PHE267 3.6 51.4 1.0
CD1 A:ILE237 3.6 41.4 1.0
CD1 A:LEU223 3.7 44.4 1.0
CG1 A:ILE278 3.9 51.9 1.0
CD1 A:ILE278 3.9 53.3 1.0
CZ A:PHE267 4.0 44.2 1.0
CG A:PHE267 4.2 52.0 1.0
CB A:TYR274 4.2 45.0 1.0
CG1 A:ILE237 4.2 36.6 1.0
C A:TYR274 4.2 50.9 1.0
CE2 A:PHE267 4.6 47.0 1.0
CB A:LEU277 4.6 50.1 1.0
CA A:TYR274 4.6 48.6 1.0
CD2 A:PHE267 4.6 48.3 1.0
CD2 A:LEU277 4.7 46.5 1.0
CG A:LEU223 4.9 43.4 1.0
CB A:PHE267 5.0 52.2 1.0

Xenon binding site 2 out of 8 in 4guv

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Xenon binding site 2 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe405

b:84.9
occ:0.32
ND2 A:ASN221 3.4 54.3 1.0
CD2 A:PHE239 3.4 39.6 1.0
CB A:GLU266 3.5 61.3 1.0
CE2 A:PHE267 3.7 47.0 1.0
CG A:PHE239 3.8 42.2 1.0
CG A:ASN221 3.8 56.2 1.0
CE2 A:PHE239 3.8 41.4 1.0
CG A:GLU266 3.9 71.5 1.0
CG2 A:ILE237 3.9 39.5 1.0
OE2 A:GLU266 3.9 84.0 1.0
CE1 A:PHE262 3.9 48.9 1.0
CD2 A:LEU263 4.0 46.7 1.0
OD1 A:ASN221 4.0 57.6 1.0
CD2 A:PHE267 4.2 48.3 1.0
CB A:PHE239 4.3 42.1 1.0
CZ A:PHE262 4.3 52.1 1.0
CD1 A:PHE239 4.4 43.6 1.0
CZ A:PHE239 4.4 41.4 1.0
CD A:GLU266 4.4 76.0 1.0
CB A:ASN221 4.7 54.9 1.0
CE1 A:PHE239 4.7 43.1 1.0
CD1 A:PHE262 4.8 51.6 1.0
CZ A:PHE267 4.9 44.2 1.0
CA A:GLU266 5.0 61.7 1.0

Xenon binding site 3 out of 8 in 4guv

Go back to Xenon Binding Sites List in 4guv
Xenon binding site 3 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe405

b:94.0
occ:0.62
CD1 B:PHE267 3.3 66.5 1.0
CE1 B:PHE267 3.3 64.4 1.0
CD1 B:ILE237 3.6 37.8 1.0
O B:TYR274 3.6 58.6 1.0
CD1 B:ILE278 3.7 56.6 1.0
CD1 B:LEU223 3.7 37.3 1.0
CG1 B:ILE278 3.9 55.9 1.0
CG B:PHE267 3.9 68.3 1.0
CZ B:PHE267 3.9 62.5 1.0
CB B:TYR274 4.2 50.3 1.0
CG1 B:ILE237 4.2 35.8 1.0
C B:TYR274 4.2 57.0 1.0
CD2 B:PHE267 4.4 67.5 1.0
CE2 B:PHE267 4.4 63.6 1.0
CA B:TYR274 4.6 53.4 1.0
CB B:PHE267 4.7 67.5 1.0
CB B:LEU277 4.8 51.3 1.0

Xenon binding site 4 out of 8 in 4guv

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Xenon binding site 4 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe406

b:91.5
occ:0.26
ND2 B:ASN221 3.3 59.5 1.0
CD2 B:PHE239 3.4 45.0 1.0
CB B:GLU266 3.4 59.9 1.0
CG B:GLU266 3.6 65.9 1.0
CG B:PHE239 3.7 48.3 1.0
CG B:ASN221 3.7 62.0 1.0
CE2 B:PHE239 3.8 43.1 1.0
OE2 B:GLU266 3.8 72.1 1.0
CE2 B:PHE267 3.9 63.6 1.0
CE1 B:PHE262 3.9 54.5 1.0
OD1 B:ASN221 3.9 61.6 1.0
CG2 B:ILE237 4.0 42.7 1.0
CB B:PHE239 4.1 48.1 1.0
CD2 B:LEU263 4.2 46.8 1.0
CZ B:PHE262 4.2 58.2 1.0
CD B:GLU266 4.2 71.0 1.0
CD2 B:PHE267 4.3 67.5 1.0
CD1 B:PHE239 4.4 50.0 1.0
CZ B:PHE239 4.4 43.7 1.0
CB B:ASN221 4.7 62.0 1.0
CE1 B:PHE239 4.7 47.1 1.0
CA B:GLU266 4.8 65.5 1.0
CD1 B:PHE262 4.8 57.5 1.0

Xenon binding site 5 out of 8 in 4guv

Go back to Xenon Binding Sites List in 4guv
Xenon binding site 5 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe405

b:0.0
occ:0.53
CD1 C:PHE267 3.4 96.2 1.0
CE1 C:PHE267 3.4 97.0 1.0
O C:TYR274 3.6 86.8 1.0
CD1 C:ILE237 3.6 61.1 1.0
CD1 C:LEU223 3.7 71.2 1.0
CD1 C:ILE278 3.8 79.5 1.0
CG1 C:ILE278 3.9 81.2 1.0
CG C:PHE267 4.0 95.3 1.0
CZ C:PHE267 4.0 97.4 1.0
CB C:TYR274 4.0 83.5 1.0
C C:TYR274 4.2 85.8 1.0
CG1 C:ILE237 4.3 60.2 1.0
CD2 C:PHE267 4.5 94.8 1.0
CE2 C:PHE267 4.6 94.2 1.0
CA C:TYR274 4.6 85.4 1.0
CB C:PHE267 4.7 94.6 1.0
CB C:LEU277 4.8 68.4 1.0
CD2 C:LEU277 5.0 65.5 1.0
CG C:TYR274 5.0 81.9 1.0

Xenon binding site 6 out of 8 in 4guv

Go back to Xenon Binding Sites List in 4guv
Xenon binding site 6 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe406

b:0.5
occ:0.18
CB C:GLU266 3.2 94.2 1.0
CE2 C:PHE267 3.5 94.2 1.0
CG C:GLU266 3.6 0.7 1.0
CD2 C:PHE239 3.7 66.0 1.0
ND2 C:ASN221 3.7 84.8 1.0
CE1 C:PHE262 3.7 78.2 1.0
CD2 C:LEU263 3.8 74.4 1.0
CD2 C:PHE267 3.9 94.8 1.0
CE2 C:PHE239 3.9 65.5 1.0
CG2 C:ILE237 3.9 65.3 1.0
OE2 C:GLU266 4.0 0.7 1.0
CG C:ASN221 4.0 82.4 1.0
OD1 C:ASN221 4.1 82.8 1.0
CG C:PHE239 4.1 72.8 1.0
CZ C:PHE262 4.2 83.2 1.0
CD C:GLU266 4.3 0.2 1.0
CZ C:PHE239 4.5 68.9 1.0
CD1 C:PHE262 4.6 77.2 1.0
CB C:PHE239 4.6 73.9 1.0
CA C:GLU266 4.7 94.3 1.0
CD1 C:PHE239 4.7 74.2 1.0
CZ C:PHE267 4.7 97.4 1.0
CB C:ASN221 4.9 79.7 1.0
CE1 C:PHE239 4.9 72.5 1.0

Xenon binding site 7 out of 8 in 4guv

Go back to Xenon Binding Sites List in 4guv
Xenon binding site 7 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe405

b:0.9
occ:0.51
CE1 D:PHE267 3.3 94.0 1.0
CD1 D:PHE267 3.4 93.0 1.0
CD1 D:LEU223 3.4 73.1 1.0
CD1 D:ILE237 3.5 65.7 1.0
O D:TYR274 3.8 81.7 1.0
CZ D:PHE267 3.9 96.3 1.0
CG D:PHE267 4.1 93.8 1.0
CG1 D:ILE237 4.1 64.0 1.0
CD1 D:ILE278 4.1 84.8 1.0
CB D:TYR274 4.1 77.0 1.0
CG1 D:ILE278 4.1 79.8 1.0
C D:TYR274 4.4 78.9 1.0
CE2 D:PHE267 4.5 96.4 1.0
CD2 D:PHE267 4.6 94.7 1.0
CA D:TYR274 4.7 78.4 1.0
CG D:LEU223 4.8 71.2 1.0
CB D:LEU277 4.8 70.7 1.0
CD2 D:LEU277 4.8 68.5 1.0
CB D:PHE267 4.9 95.2 1.0
CD1 D:TYR274 5.0 74.8 1.0
CG D:TYR274 5.0 77.6 1.0

Xenon binding site 8 out of 8 in 4guv

Go back to Xenon Binding Sites List in 4guv
Xenon binding site 8 out of 8 in the Tetx Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Tetx Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe406

b:0.7
occ:0.27
ND2 D:ASN221 3.2 95.9 1.0
CD2 D:PHE239 3.4 76.2 1.0
CB D:GLU266 3.5 93.4 1.0
CG D:ASN221 3.6 93.4 1.0
CE2 D:PHE267 3.6 96.4 1.0
CG D:PHE239 3.7 82.2 1.0
OD1 D:ASN221 3.8 95.3 1.0
CG D:GLU266 3.8 0.1 1.0
CE2 D:PHE239 3.8 77.2 1.0
OE2 D:GLU266 3.9 0.6 1.0
CG2 D:ILE237 3.9 70.3 1.0
CD2 D:PHE267 4.1 94.7 1.0
CE1 D:PHE262 4.1 82.1 1.0
CB D:PHE239 4.1 82.3 1.0
CD2 D:LEU263 4.2 79.8 1.0
CD D:GLU266 4.4 1.0 1.0
CD1 D:PHE239 4.4 84.4 1.0
CZ D:PHE262 4.4 84.9 1.0
CB D:ASN221 4.5 88.0 1.0
CZ D:PHE239 4.5 78.8 1.0
CZ D:PHE267 4.7 96.3 1.0
CE1 D:PHE239 4.8 83.8 1.0
CA D:GLU266 4.9 93.8 1.0

Reference:

G.Volkers, J.M.Damas, G.J.Palm, S.Panjikar, C.M.Soares, W.Hinrichs. Putative Dioxygen-Binding Sites and Recognition of Tigecycline and Minocycline in the Tetracycline-Degrading Monooxygenase Tetx. Acta Crystallogr.,Sect.D V. 69 1758 2013.
ISSN: ISSN 0907-4449
PubMed: 23999299
DOI: 10.1107/S0907444913013802
Page generated: Wed Dec 16 02:40:08 2020

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