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Sodium in PDB 5a71: Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native

Enzymatic activity of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native

All present enzymatic activity of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native:
3.1.1.3;

Protein crystallography data

The structure of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native, PDB code: 5a71 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) 71.04 / 0.91
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.670, 48.940, 71.610, 88.74, 97.15, 108.44
R / Rfree (%) 11.2 / 13.2

Other elements in 5a71:

The structure of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native also contains other interesting chemical elements:

Potassium (K) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native (pdb code 5a71). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native, PDB code: 5a71:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5a71

Go back to Sodium Binding Sites List in 5a71
Sodium binding site 1 out of 5 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1323

b:29.4
occ:1.00
 O A:PRO218 1.8 17.8 1.0
O A:HOH2404 2.5 17.3 1.0
O A:HOH2405 2.6 27.9 1.0
O A:PHE220 2.8 12.0 1.0
C A:PRO218 2.8 14.4 1.0
CG A:GLN213 3.2 10.4 1.0
C A:LEU219 3.6 10.0 1.0
N A:LEU219 3.7 12.6 1.0
N A:PHE220 3.7 12.5 1.0
CA A:PRO218 3.7 17.9 1.0
CA A:LEU219 3.8 14.2 1.0
CG2 A:THR186 3.8 9.0 1.0
C A:PHE220 3.9 10.9 1.0
NE2 A:GLN213 3.9 9.3 1.0
CD A:GLN213 3.9 9.4 1.0
O A:HOH2217 4.0 18.9 1.0
O A:LEU219 4.2 13.6 1.0
O A:HOH2181 4.3 17.5 1.0
CA A:PHE220 4.3 11.1 1.0
O A:GLY217 4.3 16.1 1.0
CB A:GLN213 4.3 11.4 1.0
O A:HOH2198 4.5 26.8 1.0
O A:HOH2407 4.7 17.0 1.0
CB A:PRO218 4.7 21.7 1.0
CB A:ALA185 4.8 8.7 1.0
N A:VAL221 4.9 10.3 1.0
N A:PRO218 5.0 22.6 1.0

Sodium binding site 2 out of 5 in 5a71

Go back to Sodium Binding Sites List in 5a71
Sodium binding site 2 out of 5 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1322

b:29.9
occ:0.92
 OG1 B:THR267 2.6 16.0 0.1
O B:HOH2418 2.8 20.8 1.0
OG1 B:THR267 2.8 15.2 0.9
CG2 B:THR267 3.6 18.6 0.9
CB B:THR267 3.6 16.3 0.9
CB B:THR267 3.6 11.3 0.1
CG2 B:THR267 3.8 11.8 0.1
CG B:GLN270 3.8 11.9 1.0
CD B:GLN270 3.9 10.9 1.0
NE2 B:GLN270 4.0 11.4 1.0
O B:HOH2417 4.2 30.0 1.0
OE1 B:GLU269 4.2 20.3 1.0
CB B:GLU269 4.3 17.1 1.0
OE1 B:GLN270 4.5 12.4 1.0
N B:GLN270 4.6 12.2 1.0
CA B:THR267 4.9 13.3 0.9
CA B:THR267 4.9 12.2 0.1
CB B:GLN270 4.9 10.5 1.0
CD B:GLU269 5.0 27.0 1.0

Sodium binding site 3 out of 5 in 5a71

Go back to Sodium Binding Sites List in 5a71
Sodium binding site 3 out of 5 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1323

b:33.9
occ:1.00
 O B:ARG309 2.3 19.2 1.0
O B:HOH2284 2.5 33.6 1.0
OE1 B:GLU294 2.6 12.3 1.0
C B:ARG309 3.5 14.7 1.0
O B:HOH2277 3.6 15.8 1.0
CD B:GLU294 3.7 10.1 1.0
N B:ALA162 3.8 9.5 1.0
CB B:GLU294 3.8 10.3 1.0
O B:HOH2448 4.0 19.1 1.0
O B:HOH2463 4.1 23.5 1.0
N B:ARG309 4.2 15.5 1.0
CA B:SER161 4.2 9.0 1.0
CA B:ARG309 4.3 15.9 1.0
O B:HOH2147 4.3 27.4 1.0
CG B:GLU294 4.3 10.5 1.0
CB B:ARG309 4.4 21.3 1.0
C B:SER161 4.5 8.8 1.0
CB B:ALA162 4.5 10.5 1.0
N B:THR310 4.5 13.2 1.0
CA B:ALA162 4.7 9.5 1.0
O B:GLY160 4.7 12.2 1.0
CG2 B:THR310 4.7 13.7 1.0
OE2 B:GLU294 4.7 10.3 1.0
CA B:THR310 4.7 12.6 1.0
CB B:SER161 4.9 8.6 1.0

Sodium binding site 4 out of 5 in 5a71

Go back to Sodium Binding Sites List in 5a71
Sodium binding site 4 out of 5 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1324

b:34.8
occ:0.96
 O B:HOH2432 2.3 26.0 1.0
OE1 B:GLN46 2.7 9.4 1.0
O B:GLY41 2.8 9.2 1.0
O B:HOH2120 3.0 28.5 1.0
O B:HOH2481 3.1 21.2 1.0
CD B:GLN46 3.3 9.2 1.0
NE2 B:GLN46 3.4 12.3 1.0
CD1 B:PHE71 3.5 12.3 1.0
CB B:ALA284 3.6 8.8 1.0
CE1 B:PHE71 3.8 15.2 1.0
C B:GLY41 3.9 8.1 1.0
CA B:THR42 4.1 7.6 1.0
CG B:PHE71 4.1 11.4 1.0
O B:PRO280 4.2 9.5 1.0
O B:HOH2062 4.3 29.1 1.0
N B:THR42 4.4 7.5 1.0
O B:HOH2119 4.4 24.2 1.0
CG B:GLN46 4.5 8.5 1.0
CB B:PHE71 4.6 10.9 1.0
CZ B:PHE71 4.6 17.4 1.0
CA B:ALA281 4.7 8.9 1.0
C B:PRO280 4.7 8.7 1.0
CB B:GLN46 4.9 7.8 1.0
O B:HOH2430 4.9 21.9 1.0
N B:THR43 4.9 7.8 1.0
C B:THR42 4.9 7.6 1.0
CG2 B:THR42 4.9 8.5 1.0
CB B:THR42 4.9 7.8 1.0
CD2 B:PHE71 4.9 14.3 1.0
N B:ALA281 4.9 8.3 1.0
CA B:GLY41 5.0 8.9 1.0

Sodium binding site 5 out of 5 in 5a71

Go back to Sodium Binding Sites List in 5a71
Sodium binding site 5 out of 5 in the Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Open and Closed Conformations and Protonation States of Candida Antarctica Lipase B: Atomic Resolution Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1325

b:20.4
occ:0.50
 O A:HOH2494 2.8 17.6 1.0
ND2 A:ASN292 3.4 16.4 1.0
OD1 A:ASN292 4.1 12.6 1.0
CG A:ASN292 4.2 11.6 1.0
O A:HOH2496 4.2 33.8 1.0
O A:HOH2522 4.3 17.0 1.0
O A:HOH2519 4.4 16.0 1.0
O A:HOH2493 4.6 33.7 1.0
O A:HOH2286 4.6 20.0 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: Tue Dec 15 10:11:23 2020

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