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Xenon in PDB 5a6v: Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex

Enzymatic activity of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex

All present enzymatic activity of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex:
3.1.1.3;

Protein crystallography data

The structure of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex, PDB code: 5a6v was solved by B.Stauch, S.J.Fisher, M.Cianci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.97 / 2.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.656, 48.890, 71.680, 87.80, 98.07, 108.17
R / Rfree (%) 13.9 / 19.5

Xenon Binding Sites:

The binding sites of Xenon atom in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex (pdb code 5a6v). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 6 binding sites of Xenon where determined in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex, PDB code: 5a6v:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 5a6v

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Xenon binding site 1 out of 6 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1321

b:30.6
occ:0.14
 XE A:XE1323 3.2 38.4 0.2
CD2 B:LEU219 3.2 40.5 1.0
CD2 A:LEU278 3.7 19.4 1.0
CD1 A:LEU278 3.8 17.5 1.0
CG B:LEU219 3.9 38.8 1.0
CB A:LEU278 4.1 18.0 1.0
CG A:LEU278 4.1 19.4 1.0
O A:LEU278 4.2 20.2 1.0
CB B:LEU219 4.4 33.9 1.0
CD1 A:ILE189 4.5 9.4 1.0
CB A:ALA281 4.5 15.9 1.0
N A:ALA282 4.7 19.3 1.0
CA A:LEU278 4.8 19.6 1.0
CA A:ALA282 4.8 20.6 1.0
C A:ALA281 4.9 18.7 1.0
C A:LEU278 4.9 20.8 1.0

Xenon binding site 2 out of 6 in 5a6v

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Xenon binding site 2 out of 6 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1322

b:33.9
occ:0.18
 CD1 A:ILE285 3.7 16.8 1.0
CD1 A:LEU144 3.9 15.4 1.0
O A:HOH2119 4.1 21.7 1.0
CG2 A:VAL154 4.2 7.2 1.0
CD1 B:LEU219 4.2 33.7 1.0
XE A:XE1323 4.2 38.4 0.2
CG2 A:ILE285 4.3 17.3 1.0
CG1 A:VAL154 4.4 7.5 1.0
CG1 A:ILE285 4.5 16.5 1.0
O2 A:IPA1320 4.5 17.6 1.0
CD2 B:LEU219 4.7 40.5 1.0
CG B:LEU219 4.8 38.8 1.0
C3 A:IPA1320 4.9 17.2 1.0
CB A:VAL154 5.0 8.1 1.0
CB A:ILE285 5.0 16.3 1.0

Xenon binding site 3 out of 6 in 5a6v

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Xenon binding site 3 out of 6 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1323

b:38.4
occ:0.16
 XE A:XE1321 3.2 30.6 0.1
O A:HOH2101 3.5 16.1 1.0
C3 A:IPA1320 3.5 17.2 1.0
CD1 A:ILE285 3.7 16.8 1.0
XE A:XE1322 4.2 33.9 0.2
O A:THR40 4.2 12.7 1.0
CD2 B:LEU219 4.4 40.5 1.0
CG2 A:ILE189 4.4 9.9 1.0
CB A:THR40 4.6 11.7 1.0
CB A:ALA281 4.8 15.9 1.0
CD2 A:LEU278 4.9 19.4 1.0
CD1 A:ILE189 4.9 9.4 1.0
CG2 A:THR40 4.9 10.0 1.0
C2 A:IPA1320 5.0 18.1 1.0

Xenon binding site 4 out of 6 in 5a6v

Go back to Xenon Binding Sites List in 5a6v
Xenon binding site 4 out of 6 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1324

b:26.8
occ:0.18
 CB A:ALA111 3.7 6.7 1.0
CG2 A:VAL101 3.7 7.3 1.0
CD1 A:LEU115 3.7 8.0 1.0
CG2 A:VAL125 3.8 11.1 1.0
O A:ALA111 3.8 7.4 1.0
CG1 A:VAL101 3.8 7.5 1.0
CG A:LEU115 3.9 8.7 1.0
CB A:VAL101 3.9 7.9 1.0
CG1 A:VAL125 4.0 10.3 1.0
SD A:MET83 4.0 18.1 1.0
CA A:ALA111 4.1 7.6 1.0
CD1 A:ILE87 4.1 10.7 1.0
C A:ALA111 4.2 7.5 1.0
CE A:MET83 4.2 13.0 1.0
CD2 A:LEU115 4.2 8.4 1.0
CB A:VAL125 4.4 11.3 1.0
CD1 A:ILE121 4.6 11.0 1.0
CD1 A:LEU128 4.7 6.8 1.0

Xenon binding site 5 out of 6 in 5a6v

Go back to Xenon Binding Sites List in 5a6v
Xenon binding site 5 out of 6 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe1320

b:34.0
occ:0.21
 O B:ALA111 3.5 9.7 1.0
CD1 B:LEU115 3.6 10.4 1.0
CG B:LEU115 3.6 11.5 1.0
CB B:ALA111 3.8 9.4 1.0
CG2 B:VAL125 3.9 11.9 1.0
SD B:MET83 3.9 12.8 1.0
CA B:ALA111 4.0 10.1 1.0
CD1 B:ILE87 4.0 10.4 1.0
CE B:MET83 4.1 10.7 1.0
C B:ALA111 4.1 10.5 1.0
CG1 B:VAL125 4.1 11.4 1.0
CD2 B:LEU115 4.2 11.1 1.0
CG2 B:VAL101 4.2 8.8 1.0
CG1 B:VAL101 4.3 8.9 1.0
CB B:VAL101 4.4 9.0 1.0
CB B:VAL125 4.5 12.3 1.0
CD1 B:ILE121 4.5 12.5 1.0
CD1 B:LEU128 4.7 9.6 1.0
CB B:LEU115 4.9 11.4 1.0

Xenon binding site 6 out of 6 in 5a6v

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Xenon binding site 6 out of 6 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Xenon Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe1321

b:21.4
occ:0.17
 CA B:SER161 4.0 11.2 1.0
N B:SER161 4.0 11.7 1.0
CG2 B:THR158 4.1 11.2 1.0
C B:GLY160 4.3 13.0 1.0
CZ3 B:TRP155 4.3 11.7 1.0
CE3 B:TRP155 4.3 12.2 1.0
O B:GLY160 4.3 15.1 1.0
CB B:THR158 4.4 12.7 1.0
CB B:SER161 4.5 11.1 1.0
O B:THR158 4.6 14.0 1.0
O B:THR159 4.6 13.9 1.0
OE1 B:GLU294 4.8 16.9 1.0
O B:TRP155 4.8 12.3 1.0

Reference:

B.Stauch, S.J.Fisher, M.Cianci. Open and Closed States of Candida Antarctica Lipase B: Protonation and the Mechanism of Interfacial Activation. J.Lipid Res. V. 56 2348 2015.
ISSN: ISSN 0022-2275
PubMed: 26447231
DOI: 10.1194/JLR.M063388
Page generated: Sat Oct 12 19:30:42 2024

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