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Xenon in PDB 5i63: Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon

Enzymatic activity of Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon

All present enzymatic activity of Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon, PDB code: 5i63 was solved by B.W.Roose, I.J.Dmochowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.07 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.070, 84.200, 96.220, 90.00, 89.97, 90.00
R / Rfree (%) 18.4 / 22.2

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon (pdb code 5i63). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 8 binding sites of Xenon where determined in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon, PDB code: 5i63:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Xenon binding site 1 out of 8 in 5i63

Go back to Xenon Binding Sites List in 5i63
Xenon binding site 1 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe301

b:29.4
occ:0.47
 CB A:THR265 3.6 11.9 1.0
CD1 A:LEU40 3.6 8.6 1.0
CG2 A:THR265 3.7 11.4 1.0
CG2 A:VAL44 3.8 8.1 1.0
CG1 A:VAL44 3.9 12.3 1.0
CG1 A:ILE279 3.9 9.4 1.0
OG1 A:THR265 4.1 13.2 1.0
CB A:GLN278 4.2 12.8 1.0
OD1 A:ASN263 4.3 15.5 1.0
CB A:ALA36 4.4 7.0 1.0
ND2 A:ASN263 4.5 13.7 1.0
CB A:VAL44 4.5 10.6 1.0
N A:ILE279 4.5 13.2 1.0
O A:TYR264 4.6 10.9 1.0
CD1 A:ILE282 4.7 13.4 0.8
CD1 A:ILE279 4.7 9.4 1.0
CG A:ASN263 4.8 13.5 1.0
O A:ARG275 4.8 6.7 1.0
CA A:THR265 4.9 10.2 1.0
C A:GLN278 4.9 12.8 1.0
CA A:ILE279 4.9 12.2 1.0

Xenon binding site 2 out of 8 in 5i63

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Xenon binding site 2 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe302

b:11.7
occ:0.24
 CD1 A:ILE282 2.9 13.7 0.2
OD1 A:ASN263 3.6 15.5 1.0
CG2 A:ILE279 3.7 9.5 1.0
O A:ILE279 3.7 11.4 1.0
CB A:ASN263 3.7 11.5 1.0
CD2 A:LEU221 3.8 12.5 1.0
CG1 A:ILE282 3.8 14.0 0.2
CG A:LEU221 3.9 10.8 1.0
CG A:ASN263 4.0 13.5 1.0
CG2 A:ILE246 4.2 4.9 1.0
CD1 A:LEU221 4.3 5.4 1.0
CE1 A:TYR46 4.3 6.7 1.0
CG1 A:VAL261 4.4 14.1 1.0
N A:GLY283 4.5 11.7 1.0
C A:ILE279 4.6 10.7 1.0
CA A:GLY283 4.6 10.4 1.0
CG2 A:ILE282 4.7 14.3 0.8
CB A:ILE282 4.7 14.1 0.8
CA A:ILE279 4.8 12.2 1.0
CD1 A:TYR46 4.8 9.3 1.0
CB A:ILE279 4.8 10.8 1.0
CB A:ILE282 4.8 14.0 0.2
C A:ILE282 4.9 13.7 1.0

Xenon binding site 3 out of 8 in 5i63

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Xenon binding site 3 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe301

b:13.9
occ:0.22
 CG1 B:ILE279 3.5 9.3 1.0
OD1 B:ASN263 3.6 10.9 1.0
CG2 B:THR265 3.8 6.8 1.0
CD1 B:LEU40 3.9 10.1 1.0
CB B:THR265 3.9 10.1 1.0
CG1 B:VAL44 4.0 6.5 1.0
CG2 B:VAL44 4.2 10.2 1.0
CD1 B:ILE279 4.3 10.7 1.0
CB B:GLN278 4.3 13.3 1.0
ND2 B:ASN263 4.4 6.2 1.0
CG B:ASN263 4.4 8.2 1.0
N B:ILE279 4.5 10.1 1.0
CD1 B:ILE282 4.5 8.1 1.0
CA B:ILE279 4.6 10.3 1.0
OG1 B:THR265 4.7 11.7 1.0
CB B:ALA36 4.7 10.3 1.0
O B:ARG275 4.7 12.6 1.0
CB B:ILE279 4.7 9.2 1.0
C B:GLN278 4.7 12.1 1.0
O B:TYR264 4.7 9.8 1.0
CB B:VAL44 4.7 13.2 1.0

Xenon binding site 4 out of 8 in 5i63

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Xenon binding site 4 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe302

b:15.0
occ:0.32
 CD2 B:LEU221 3.6 14.8 1.0
CG2 B:ILE279 3.6 9.5 1.0
CG B:LEU221 3.7 13.8 1.0
CG1 B:VAL261 3.8 4.9 1.0
CB B:ASN263 3.8 8.1 1.0
O B:ILE279 4.0 9.8 1.0
OD1 B:ASN263 4.0 10.9 1.0
CG2 B:ILE246 4.1 11.2 1.0
CD1 B:LEU221 4.2 13.2 1.0
CG B:ASN263 4.2 8.2 1.0
CG2 B:ILE282 4.4 12.4 1.0
CE1 B:TYR46 4.5 8.8 1.0
N B:GLY283 4.6 9.1 1.0
CA B:GLY283 4.8 9.8 1.0
CB B:ILE282 4.8 12.5 1.0
C B:ILE279 4.8 9.1 1.0
CB B:ILE279 4.9 9.2 1.0
CD1 B:TYR46 4.9 6.3 1.0

Xenon binding site 5 out of 8 in 5i63

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Xenon binding site 5 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe301

b:29.6
occ:0.31
 CG1 C:ILE279 3.7 12.8 1.0
OD1 C:ASN263 3.7 8.8 1.0
CD1 C:ILE282 3.7 7.9 1.0
CG1 C:VAL44 3.9 8.1 1.0
CB C:GLN278 3.9 9.9 1.0
N C:ILE279 4.0 11.3 1.0
CD1 C:LEU40 4.1 5.6 1.0
C C:GLN278 4.1 8.8 1.0
CG2 C:VAL44 4.1 4.9 1.0
CB C:ALA36 4.2 7.6 1.0
CA C:ILE279 4.2 11.2 1.0
O C:GLN278 4.4 7.8 1.0
CG2 C:THR265 4.4 8.4 1.0
CB C:THR265 4.4 8.2 1.0
CG C:ASN263 4.5 5.6 1.0
ND2 C:ASN263 4.6 5.9 1.0
CB C:ILE279 4.6 11.7 1.0
CB C:VAL44 4.7 8.1 1.0
CA C:GLN278 4.7 8.6 1.0
CD1 C:ILE279 4.8 14.0 1.0
O C:ARG275 4.8 8.0 1.0
CG1 C:ILE282 4.8 7.6 1.0

Xenon binding site 6 out of 8 in 5i63

Go back to Xenon Binding Sites List in 5i63
Xenon binding site 6 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe302

b:22.3
occ:0.31
 CD2 C:LEU221 3.0 18.1 1.0
CG C:LEU221 3.6 17.1 1.0
CG2 C:ILE282 3.7 9.4 1.0
O C:ILE279 3.8 9.0 1.0
N C:GLY283 3.8 7.0 1.0
CD1 C:LEU221 3.8 18.2 1.0
CA C:GLY283 4.0 6.6 1.0
CG1 C:VAL261 4.1 9.2 1.0
CB C:ILE282 4.2 7.8 1.0
OD1 C:ASN263 4.2 8.8 1.0
CB C:ASN263 4.3 2.6 1.0
C C:ILE282 4.3 7.5 1.0
CG2 C:ILE279 4.4 11.0 1.0
CG C:ASN263 4.4 5.6 1.0
CD2 C:LEU286 4.5 16.4 1.0
CE1 C:TYR46 4.7 10.0 1.0
O C:ILE282 4.8 6.8 1.0
C C:ILE279 4.8 9.3 1.0
CA C:ILE282 4.9 9.5 1.0

Xenon binding site 7 out of 8 in 5i63

Go back to Xenon Binding Sites List in 5i63
Xenon binding site 7 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe301

b:20.1
occ:0.33
 OD1 D:ASN263 3.5 12.0 1.0
CD1 D:ILE282 3.6 6.9 1.0
CG1 D:ILE279 3.6 11.3 1.0
CG1 D:VAL44 3.8 5.0 1.0
CG2 D:VAL44 4.1 8.7 1.0
CB D:GLN278 4.1 11.8 1.0
N D:ILE279 4.2 11.3 1.0
CG2 D:THR265 4.2 6.6 1.0
CD1 D:LEU40 4.2 8.1 1.0
CG D:ASN263 4.2 10.0 1.0
CB D:THR265 4.3 6.6 1.0
ND2 D:ASN263 4.3 9.3 1.0
CB D:ALA36 4.3 7.6 1.0
C D:GLN278 4.4 11.5 1.0
CA D:ILE279 4.4 10.4 1.0
CB D:VAL44 4.6 10.2 1.0
CD1 D:ILE279 4.6 13.8 1.0
O D:GLN278 4.6 11.6 1.0
CB D:ILE279 4.7 9.8 1.0
O D:ARG275 4.8 7.2 1.0
OG1 D:THR265 4.8 7.7 1.0
CG1 D:ILE282 4.9 8.2 1.0
CA D:GLN278 4.9 10.9 1.0

Xenon binding site 8 out of 8 in 5i63

Go back to Xenon Binding Sites List in 5i63
Xenon binding site 8 out of 8 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon


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 TEM1 Beta-Lactamase Mutant I263N in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe302

b:23.7
occ:0.26
 CD2 D:LEU221 2.8 11.9 1.0
CG D:LEU221 3.4 11.6 1.0
O D:ILE279 3.9 9.7 1.0
N D:GLY283 3.9 12.5 1.0
CD1 D:LEU221 3.9 9.9 1.0
CA D:GLY283 3.9 12.1 1.0
CG1 D:VAL261 3.9 9.8 1.0
CG2 D:ILE282 4.2 12.4 1.0
CG2 D:ILE279 4.2 10.5 1.0
CB D:ASN263 4.4 8.2 1.0
CB D:ILE282 4.5 10.9 1.0
OD1 D:ASN263 4.5 12.0 1.0
C D:ILE282 4.6 13.4 1.0
CE1 D:TYR46 4.7 5.5 1.0
CB D:LEU221 4.8 9.5 1.0
CG D:ASN263 4.8 10.0 1.0
CD2 D:LEU286 4.9 7.2 1.0
CG2 D:ILE246 4.9 20.6 1.0
C D:ILE279 4.9 8.7 1.0
CB D:VAL261 4.9 7.8 1.0

Reference:

B.W.Roose, S.D.Zemerov, Y.Wang, M.A.Kasimova, V.Carnevale, I.J.Dmochowski. A Structural Basis FOR129XE Hyper-Cest Signal in Tem-1 Beta-Lactamase. Chemphyschem 2018.
ISSN: ISSN 1439-7641
PubMed: 30151973
DOI: 10.1002/CPHC.201800624
Page generated: Sat Oct 12 19:37:43 2024

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