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Sodium in PDB 4fkb: An Organic Solvent Tolerant Lipase 42

Enzymatic activity of An Organic Solvent Tolerant Lipase 42

All present enzymatic activity of An Organic Solvent Tolerant Lipase 42:
3.1.1.3;

Protein crystallography data

The structure of An Organic Solvent Tolerant Lipase 42, PDB code: 4fkb was solved by R.N.Zaliha, R.A.Rahman, M.S.Khusaini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.824, 81.001, 99.529, 90.00, 96.69, 90.00
R / Rfree (%) 12.7 / 16.5

Other elements in 4fkb:

The structure of An Organic Solvent Tolerant Lipase 42 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the An Organic Solvent Tolerant Lipase 42 (pdb code 4fkb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the An Organic Solvent Tolerant Lipase 42, PDB code: 4fkb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 4fkb

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Sodium binding site 1 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.2
occ:1.00
 O A:HOH693 2.0 21.2 1.0
O A:LYS329 2.3 10.6 1.0
O A:HOH766 2.5 38.0 1.0
O A:SER332 2.5 15.6 1.0
O A:HOH861 2.7 80.6 1.0
O A:HOH826 2.9 1.0 1.0
C A:LYS329 3.5 8.7 1.0
C A:SER332 3.6 13.2 1.0
N A:SER332 3.8 11.0 1.0
O A:HOH639 3.9 27.9 1.0
CA A:LYS329 4.1 8.5 1.0
CA A:SER332 4.1 11.3 1.0
O A:HOH859 4.2 47.2 1.0
O A:HOH531 4.3 16.7 1.0
N A:GLY331 4.5 10.6 1.0
O A:HOH860 4.5 89.0 1.0
CB A:SER332 4.5 10.6 1.0
N A:ARG330 4.6 9.1 1.0
O A:HOH827 4.6 40.8 1.0
N A:SER333 4.7 13.7 1.0
CA A:ARG330 4.8 8.7 0.5
CB A:LYS329 4.8 8.9 1.0
C A:GLY331 4.8 10.0 1.0
CA A:ARG330 4.9 8.6 0.5
C A:ARG330 4.9 9.7 1.0

Sodium binding site 2 out of 9 in 4fkb

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Sodium binding site 2 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:25.9
occ:1.00
 O A:HOH578 2.1 21.5 1.0
O A:THR272 2.2 9.6 1.0
O A:HOH760 2.3 35.9 1.0
OE1 A:GLU270 2.4 9.5 1.0
OE2 A:GLU284 2.8 12.8 1.0
O A:HOH577 3.0 22.6 1.0
O A:HOH684 3.0 26.2 1.0
NA A:NA406 3.2 64.9 1.0
CD A:GLU270 3.2 9.7 1.0
OE2 A:GLU270 3.4 11.7 1.0
C A:THR272 3.4 8.0 1.0
O A:HOH743 3.4 34.9 1.0
CD A:GLU284 3.6 9.6 1.0
N A:THR272 3.7 6.9 1.0
O A:HOH742 4.0 33.0 1.0
ND2 A:ASN355 4.2 9.8 1.0
CA A:THR272 4.2 7.4 1.0
OE1 A:GLU284 4.3 8.6 1.0
N A:TYR273 4.3 6.9 1.0
CG A:GLU284 4.4 7.4 1.0
CA A:TYR273 4.4 7.7 1.0
CG A:GLU270 4.6 9.1 1.0
C A:ARG271 4.6 5.7 1.0
O A:HOH586 4.6 20.5 1.0
CA A:ARG271 4.9 5.8 1.0
OE2 A:GLU315 4.9 16.4 1.0
CG A:ASN355 5.0 9.5 1.0

Sodium binding site 3 out of 9 in 4fkb

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Sodium binding site 3 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:64.9
occ:1.00
 O A:HOH742 2.1 33.0 1.0
O A:HOH743 2.2 34.9 1.0
O A:HOH760 2.4 35.9 1.0
O A:HOH578 2.4 21.5 1.0
O A:HOH967 2.8 45.7 1.0
NA A:NA405 3.2 25.9 1.0
O A:HOH684 3.9 26.2 1.0
OE2 A:GLU270 4.1 11.7 1.0
O A:HOH577 4.4 22.6 1.0
O A:HOH942 4.7 34.2 1.0
OE1 A:GLU270 4.7 9.5 1.0
CD A:GLU270 4.7 9.7 1.0
OE2 A:GLU284 4.7 12.8 1.0
O A:HOH749 4.9 29.2 1.0
O A:THR272 5.0 9.6 1.0

Sodium binding site 4 out of 9 in 4fkb

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Sodium binding site 4 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:37.7
occ:1.00
 OE1 A:GLU202 2.0 20.0 1.0
CL A:CL417 2.2 14.6 1.0
CD A:GLU202 2.6 20.0 1.0
CG A:ARG214 2.8 18.8 1.0
N A:ARG215 3.2 11.2 1.0
OE2 A:GLU202 3.2 20.0 1.0
O A:HOH525 3.3 12.7 1.0
CG A:GLU202 3.6 20.0 1.0
CD A:ARG214 3.7 30.3 1.0
CB A:ARG215 3.8 11.7 1.0
O A:ARG215 3.8 20.4 1.0
CB A:ARG214 3.9 13.8 1.0
CA A:ARG214 3.9 11.3 1.0
C A:ARG214 4.0 12.0 1.0
CA A:ARG215 4.0 11.8 1.0
O A:HOH753 4.1 28.9 1.0
O A:HOH538 4.3 13.4 1.0
C A:ARG215 4.4 15.4 1.0
OD1 A:ASP205 4.4 11.5 1.0
CA A:ASP205 4.7 10.3 1.0
OH A:TYR224 4.7 10.6 1.0
NE A:ARG214 4.8 53.1 1.0
O A:TYR204 4.9 12.6 1.0
CG A:ASP205 4.9 11.8 1.0
N A:PHE206 5.0 9.5 1.0

Sodium binding site 5 out of 9 in 4fkb

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Sodium binding site 5 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:26.9
occ:1.00
 O B:HOH816 2.1 43.5 1.0
O B:HOH730 2.1 25.1 1.0
O B:LYS329 2.3 13.7 1.0
O B:HOH757 2.4 41.3 1.0
O B:SER332 2.4 14.7 1.0
C B:LYS329 3.5 10.8 1.0
C B:SER332 3.6 12.0 1.0
N B:SER332 3.8 10.9 1.0
O B:HOH791 4.0 34.9 1.0
CA B:LYS329 4.1 9.6 1.0
CA B:SER332 4.1 11.4 1.0
O B:HOH934 4.3 48.9 1.0
O B:HOH580 4.3 18.6 1.0
O B:HOH745 4.4 61.0 1.0
O B:HOH741 4.4 46.2 1.0
O B:HOH815 4.5 42.7 1.0
N B:GLY331 4.5 11.2 1.0
CB B:SER332 4.5 12.0 1.0
N B:ARG330 4.5 11.8 1.0
N B:SER333 4.7 14.3 1.0
C B:GLY331 4.8 9.8 1.0
CB B:LYS329 4.8 9.3 1.0
CA B:ARG330 4.8 11.8 1.0
C B:ARG330 4.9 10.1 1.0

Sodium binding site 6 out of 9 in 4fkb

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Sodium binding site 6 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:40.9
occ:1.00
 O B:HOH910 2.1 46.0 1.0
O B:HOH575 2.5 20.0 1.0
OG B:SER369 2.5 14.4 0.6
O B:HOH724 2.7 29.1 1.0
CB B:SER369 3.4 14.4 0.4
CB B:SER369 3.5 13.8 0.6
O B:SER369 4.0 15.6 1.0
O B:ASN355 4.1 8.9 1.0
C B:SER369 4.2 12.9 1.0
O A:HOH739 4.2 50.5 1.0
OD1 B:ASN355 4.3 11.6 1.0
OG B:SER369 4.4 19.1 0.4
O B:HOH662 4.4 39.4 1.0
CA B:SER369 4.4 12.7 0.4
CA B:SER369 4.5 12.2 0.6
ND2 B:ASN367 4.6 11.3 1.0
N B:PHE370 4.6 11.7 1.0
OD1 B:ASN367 4.6 10.7 1.0
CG B:ASN355 5.0 7.5 1.0

Sodium binding site 7 out of 9 in 4fkb

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Sodium binding site 7 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:31.9
occ:1.00
 O B:THR272 2.2 11.7 1.0
O B:HOH726 2.2 22.7 1.0
OE1 B:GLU270 2.4 12.8 1.0
O B:HOH621 2.6 25.6 1.0
O B:HOH653 2.7 21.7 1.0
O B:HOH900 2.8 52.8 1.0
OE2 B:GLU284 3.1 12.7 1.0
CD B:GLU270 3.2 9.6 1.0
C B:THR272 3.4 8.9 1.0
OE2 B:GLU270 3.4 14.3 1.0
N B:THR272 3.9 9.0 1.0
CD B:GLU284 3.9 9.9 1.0
O B:HOH899 4.0 36.5 1.0
CA B:THR272 4.3 8.4 1.0
N B:TYR273 4.4 7.9 1.0
ND2 B:ASN355 4.5 8.6 1.0
CG B:GLU270 4.5 10.3 1.0
CA B:TYR273 4.5 8.2 1.0
OE1 B:GLU284 4.6 10.0 1.0
OE2 B:GLU315 4.6 20.2 1.0
CG B:GLU284 4.6 8.1 1.0
C B:ARG271 4.8 7.5 1.0
OG1 B:THR272 4.9 19.3 1.0
O B:HOH657 4.9 23.7 1.0

Sodium binding site 8 out of 9 in 4fkb

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Sodium binding site 8 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:42.4
occ:1.00
 O B:HOH918 2.2 44.4 1.0
O B:HOH929 2.4 50.9 1.0
O A:HOH884 2.5 33.1 1.0
O A:HOH727 2.6 23.9 1.0
O B:HOH746 2.6 22.5 1.0
O A:HOH642 4.1 22.3 1.0
O B:HOH921 4.1 42.6 1.0
O A:ALA83 4.2 11.6 1.0
ND2 B:ASN280 4.2 16.8 1.0
O B:HOH919 4.2 34.3 1.0
OH B:TYR282 4.5 10.5 1.0
O A:HOH906 4.9 47.3 1.0

Sodium binding site 9 out of 9 in 4fkb

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Sodium binding site 9 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:12.7
occ:1.00
 O B:HOH733 2.3 25.1 1.0
O B:HOH519 2.3 8.6 1.0
O B:ALA192 2.3 7.8 1.0
O B:HOH543 2.4 9.2 1.0
CB B:ALA192 3.4 7.6 1.0
C B:ALA192 3.4 7.9 1.0
CA B:ALA192 4.0 7.1 1.0
O B:ALA191 4.4 7.7 1.0
N B:VAL193 4.6 6.7 1.0
O B:HOH566 4.7 8.7 1.0
CA B:VAL193 5.0 6.8 1.0

Reference:

R.N.Zaliha, R.N.Rahman, M.S.Khusaini. An Organic Solvent Tolerant Lipase 42 To Be Published.
Page generated: Tue Dec 15 06:40:35 2020

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