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Xenon in PDB 6ayk: Crystal Structure of TEM1 Beta-Lactamase Mutant I263A in the Presence of 1.2 Mpa Xenon

Enzymatic activity of Crystal Structure of TEM1 Beta-Lactamase Mutant I263A in the Presence of 1.2 Mpa Xenon

All present enzymatic activity of Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon, PDB code: 6ayk 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) 95.97 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.645, 84.751, 95.971, 90.00, 90.23, 90.00
R / Rfree (%) 19.7 / 21.9

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 TEM1 Beta-Lactamase Mutant I263A in the Presence of 1.2 Mpa Xenon (pdb code 6ayk). 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 TEM1 Beta-Lactamase Mutant I263A in the Presence of 1.2 Mpa Xenon, PDB code: 6ayk:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 14 in 6ayk

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Xenon binding site 1 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe301

b:15.9
occ:0.36
 CD2 A:LEU221 2.4 28.0 1.0
CG A:LEU221 3.4 24.7 1.0
CD1 A:LEU221 3.6 25.7 1.0
O A:ILE279 3.9 13.8 1.0
CG1 A:VAL261 3.9 16.4 1.0
CG2 A:ILE279 4.0 13.7 1.0
N A:GLY283 4.1 13.8 1.0
CG2 A:ILE282 4.1 14.8 1.0
CB A:ALA263 4.2 11.1 1.0
CA A:GLY283 4.2 14.5 1.0
CE1 A:TYR46 4.4 12.8 1.0
CG2 A:ILE246 4.4 9.2 1.0
CB A:ILE282 4.5 13.9 1.0
C A:ILE282 4.7 14.9 1.0
C A:ILE279 4.8 11.5 1.0
CB A:LEU221 4.8 17.3 1.0
CD1 A:TYR46 5.0 11.8 1.0

Xenon binding site 2 out of 14 in 6ayk

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Xenon binding site 2 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe302

b:16.5
occ:0.32
 CG1 A:ILE279 3.6 16.5 1.0
CD1 A:LEU40 3.9 12.1 1.0
CG2 A:VAL44 4.0 12.6 1.0
CD1 A:ILE282 4.0 11.8 1.0
CG1 A:VAL44 4.0 15.1 1.0
CB A:GLN278 4.1 14.7 1.0
CB A:THR265 4.1 8.7 1.0
CG2 A:THR265 4.1 10.6 1.0
N A:ILE279 4.3 14.6 1.0
CB A:ALA36 4.4 10.7 1.0
CD1 A:ILE279 4.5 20.3 1.0
C A:GLN278 4.5 14.2 1.0
CA A:ILE279 4.6 12.2 1.0
CB A:VAL44 4.7 14.4 1.0
CB A:ILE279 4.7 14.1 1.0
O A:ARG275 4.8 10.8 1.0
OG1 A:THR265 4.8 10.8 1.0
O A:GLN278 4.9 16.2 1.0
CA A:GLN278 5.0 13.1 1.0

Xenon binding site 3 out of 14 in 6ayk

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Xenon binding site 3 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe303

b:15.0
occ:0.09
 CD1 A:ILE208 2.7 14.1 1.0
CG A:PRO257 3.5 12.7 1.0
CD2 A:LEU51 3.6 25.4 1.0
CG1 A:ILE208 3.9 13.2 1.0
CD1 A:LEU194 3.9 12.6 1.0
CB A:PRO257 3.9 11.2 1.0
CB A:ALA249 3.9 10.3 1.0
CB A:LEU194 4.1 12.0 1.0
O A:HOH501 4.1 26.0 1.0
O A:HOH667 4.3 57.1 1.0
CD1 A:LEU51 4.4 23.1 1.0
CG2 A:THR195 4.5 19.1 1.0
CG A:LEU194 4.6 12.0 1.0
CG A:LEU51 4.6 24.4 1.0
CB A:ILE208 4.9 11.2 1.0
CD A:PRO257 4.9 14.5 1.0

Xenon binding site 4 out of 14 in 6ayk

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Xenon binding site 4 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe301

b:15.1
occ:0.32
 CD2 B:LEU221 2.4 22.1 1.0
CG B:LEU221 3.4 18.5 1.0
CD1 B:LEU221 3.7 18.4 1.0
CG2 B:ILE282 3.8 12.3 1.0
CG1 B:VAL261 3.9 12.8 1.0
O B:ILE279 3.9 11.4 1.0
CG2 B:ILE279 4.1 11.7 1.0
N B:GLY283 4.2 10.6 1.0
CB B:ALA263 4.2 8.9 1.0
CE1 B:TYR46 4.3 9.6 1.0
CA B:GLY283 4.4 10.7 1.0
CB B:ILE282 4.4 12.1 1.0
CG2 B:ILE246 4.4 7.4 1.0
C B:ILE282 4.7 11.1 1.0
CB B:LEU221 4.8 12.2 1.0
C B:ILE279 4.9 9.9 1.0
CD1 B:TYR46 4.9 12.0 1.0

Xenon binding site 5 out of 14 in 6ayk

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Xenon binding site 5 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe302

b:16.5
occ:0.37
 CG1 B:ILE279 3.8 13.8 1.0
CG1 B:VAL44 3.9 10.6 1.0
CD1 B:ILE282 4.0 12.9 1.0
CG2 B:VAL44 4.1 9.1 1.0
CD1 B:LEU40 4.1 10.2 1.0
CG2 B:THR265 4.1 8.4 1.0
CB B:THR265 4.1 12.7 1.0
CB B:GLN278 4.2 13.5 1.0
N B:ILE279 4.4 10.8 1.0
CB B:ALA36 4.5 11.8 1.0
CD1 B:ILE279 4.6 16.2 1.0
CA B:ILE279 4.6 11.5 1.0
CB B:VAL44 4.6 11.9 1.0
C B:GLN278 4.7 12.2 1.0
OG1 B:THR265 4.8 14.4 1.0
CB B:ILE279 4.9 12.0 1.0
O B:ARG275 4.9 13.3 1.0
O B:TYR264 5.0 9.6 1.0

Xenon binding site 6 out of 14 in 6ayk

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Xenon binding site 6 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe303

b:24.0
occ:0.05
 CD1 B:ILE208 2.6 13.9 1.0
CG B:PRO257 3.4 12.0 1.0
CD2 B:LEU51 3.5 19.5 1.0
CB B:PRO257 4.0 10.8 1.0
CG1 B:ILE208 4.0 13.1 1.0
CD1 B:LEU194 4.0 12.0 1.0
CB B:ALA249 4.1 8.4 1.0
CB B:LEU194 4.2 10.8 1.0
O B:HOH505 4.2 21.4 1.0
CG2 B:THR195 4.3 16.8 1.0
O B:HOH663 4.4 24.3 1.0
CG B:LEU51 4.6 17.0 1.0
CG B:LEU194 4.7 11.0 1.0
CD1 B:LEU51 4.8 15.4 1.0
CB B:ILE208 4.8 9.8 1.0
CD B:PRO257 4.8 15.0 1.0

Xenon binding site 7 out of 14 in 6ayk

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Xenon binding site 7 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe301

b:15.8
occ:0.41
 CD2 C:LEU221 2.4 11.2 0.4
CG C:LEU221 3.4 10.9 0.4
CD1 C:LEU221 3.7 12.0 0.4
O C:ILE279 3.8 14.5 1.0
CG1 C:VAL261 3.9 14.5 1.0
CG2 C:ILE282 4.0 13.9 1.0
CG2 C:ILE279 4.0 13.7 1.0
N C:GLY283 4.1 14.2 1.0
CB C:ALA263 4.1 8.4 1.0
CA C:GLY283 4.3 13.2 1.0
CG2 C:ILE246 4.4 9.3 1.0
CB C:ILE282 4.4 16.5 1.0
CD1 C:LEU221 4.4 13.3 0.6
CE1 C:TYR46 4.5 13.3 1.0
C C:ILE282 4.6 14.1 1.0
C C:ILE279 4.8 13.0 1.0
CD2 C:LEU221 4.8 10.8 0.6
CB C:LEU221 4.8 10.5 0.4
CB C:LEU221 4.8 10.4 0.6
CG C:LEU221 4.9 11.7 0.6

Xenon binding site 8 out of 14 in 6ayk

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Xenon binding site 8 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe302

b:17.9
occ:0.31
 CG1 C:ILE279 3.6 15.4 1.0
CD1 C:ILE282 3.9 17.3 1.0
CD1 C:LEU40 4.0 16.4 1.0
CG2 C:THR265 4.0 9.6 1.0
CG2 C:VAL44 4.0 12.2 1.0
CG1 C:VAL44 4.1 13.0 1.0
CB C:GLN278 4.1 18.4 1.0
CB C:THR265 4.1 10.4 1.0
N C:ILE279 4.2 14.3 1.0
CA C:ILE279 4.5 13.3 1.0
C C:GLN278 4.5 16.6 1.0
CD1 C:ILE279 4.5 17.9 1.0
CB C:ALA36 4.6 15.3 1.0
CB C:VAL44 4.7 12.3 1.0
CB C:ILE279 4.7 13.7 1.0
O C:ARG275 4.8 13.1 1.0
OG1 C:THR265 4.9 13.7 1.0
O C:GLN278 4.9 18.7 1.0
O C:TYR264 5.0 10.4 1.0

Xenon binding site 9 out of 14 in 6ayk

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Xenon binding site 9 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 9 of Crystal Structure of TEM1 Beta-Lactamase Mutant I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe303

b:17.2
occ:0.13
 CD1 C:ILE208 2.6 16.8 1.0
CG C:PRO257 3.5 15.6 1.0
CD2 C:LEU51 3.6 22.5 1.0
CB C:PRO257 3.8 15.8 1.0
CB C:ALA249 3.8 10.0 1.0
CG1 C:ILE208 3.9 14.8 1.0
CD1 C:LEU194 4.0 13.5 1.0
O C:HOH486 4.2 24.1 1.0
CB C:LEU194 4.3 9.0 1.0
O C:HOH627 4.4 27.0 1.0
CD1 C:LEU51 4.5 22.2 1.0
CG2 C:THR195 4.6 20.4 1.0
CG C:LEU51 4.6 22.5 1.0
CG C:LEU194 4.7 12.3 1.0
CB C:ILE208 4.8 12.4 1.0
CD C:PRO257 4.9 15.2 1.0

Xenon binding site 10 out of 14 in 6ayk

Go back to Xenon Binding Sites List in 6ayk
Xenon binding site 10 out of 14 in the Crystal Structure of TEM1 Beta-Lactamase Mutant I263A 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 10 of Crystal Structure of TEM1 Beta-Lactamase Mutant I263A in the Presence of 1.2 Mpa Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe301

b:17.1
occ:0.32
 CD2 D:LEU221 2.7 9.8 0.6
CG D:LEU221 3.4 10.9 0.6
CD1 D:LEU221 3.7 10.4 0.6
CG1 D:VAL261 3.8 18.4 1.0
O D:ILE279 3.8 14.2 1.0
CG2 D:ILE279 4.0 12.7 1.0
CG2 D:ILE282 4.0 12.8 1.0
N D:GLY283 4.1 9.8 1.0
CB D:ALA263 4.2 9.2 1.0
CA D:GLY283 4.3 9.9 1.0
CB D:ILE282 4.4 12.8 1.0
CG2 D:ILE246 4.4 8.8 1.0
CD1 D:LEU221 4.4 11.5 0.4
CE1 D:TYR46 4.5 10.2 1.0
C D:ILE282 4.7 11.6 1.0
CD2 D:LEU221 4.7 9.9 0.4
C D:ILE279 4.8 13.4 1.0
CB D:LEU221 4.9 10.2 0.4
CB D:LEU221 4.9 10.2 0.6
CG D:LEU221 4.9 11.0 0.4
CD1 D:TYR46 5.0 11.9 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 V. 20 260 2019.
ISSN: ISSN 1439-7641
PubMed: 30151973
DOI: 10.1002/CPHC.201800624
Page generated: Sat Oct 12 19:52:39 2024

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