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Sodium in PDB 2fbl: The Crystal Structure of the Hypothetical Protein NE1496

Protein crystallography data

The structure of The Crystal Structure of the Hypothetical Protein NE1496, PDB code: 2fbl was solved by V.V.Lunin, T.Skarina, O.Onopriyenko, T.A.Binkowski, A.Joachimiak, A.M.Edwards, A.Savchenko, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.60 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.282, 52.282, 252.484, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 28.2

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of the Hypothetical Protein NE1496 (pdb code 2fbl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Crystal Structure of the Hypothetical Protein NE1496, PDB code: 2fbl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2fbl

Go back to Sodium Binding Sites List in 2fbl
Sodium binding site 1 out of 6 in the The Crystal Structure of the Hypothetical Protein NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Hypothetical Protein NE1496 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:33.5
occ:1.00
 O A:PHE131 2.2 27.1 1.0
O A:HOH334 2.3 41.0 1.0
O A:HOH394 2.3 39.8 1.0
O A:HOH400 2.4 48.2 1.0
O A:PRO129 2.5 28.9 1.0
O A:HOH321 2.6 32.7 1.0
O A:HOH406 3.4 37.1 1.0
C A:PHE131 3.5 27.4 1.0
C A:PRO129 3.5 30.5 1.0
CA A:PRO129 4.1 30.8 1.0
O A:HOH346 4.2 35.1 1.0
N A:PHE131 4.2 24.8 1.0
CB A:ALA11 4.3 31.5 1.0
N A:GLY132 4.3 28.6 1.0
CA A:GLY132 4.4 28.1 1.0
O A:PRO128 4.4 29.4 1.0
CA A:PHE131 4.4 25.0 1.0
O A:HOH382 4.4 34.7 1.0
C A:TRP130 4.5 25.8 1.0
N A:TRP130 4.6 29.4 1.0
O A:HOH433 4.6 49.5 1.0
CA A:TRP130 4.9 26.9 1.0
CB A:PHE131 5.0 25.3 1.0
C A:GLY132 5.0 28.4 1.0
O A:TRP130 5.0 25.5 1.0

Sodium binding site 2 out of 6 in 2fbl

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Sodium binding site 2 out of 6 in the The Crystal Structure of the Hypothetical Protein NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Hypothetical Protein NE1496 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:31.4
occ:1.00
 O A:SER149 2.3 32.4 1.0
O A:ALA147 2.3 24.0 1.0
O A:HOH330 2.5 30.5 1.0
O A:HOH325 2.5 27.5 1.0
O A:GLY79 2.6 24.8 1.0
C A:GLY79 3.2 23.3 1.0
C A:ALA147 3.5 25.6 1.0
C A:SER149 3.5 34.5 1.0
O A:HOH424 3.7 60.6 1.0
NE2 A:HIS105 3.8 29.5 1.0
N A:ARG80 3.9 23.2 1.0
C A:LEU148 3.9 31.1 1.0
CA A:GLY79 4.0 25.8 1.0
N A:SER149 4.0 32.0 1.0
CA A:ARG80 4.1 22.4 1.0
N A:ARG81 4.1 22.0 1.0
CA A:LEU148 4.2 30.2 1.0
O A:LEU146 4.2 24.6 1.0
O A:LEU148 4.2 30.2 1.0
O A:ARG81 4.2 19.8 1.0
N A:LEU148 4.3 28.2 1.0
O A:HOH447 4.4 35.6 1.0
CA A:SER149 4.4 33.0 1.0
N A:ILE150 4.4 37.5 1.0
O A:HOH327 4.4 41.1 1.0
CA A:ALA147 4.5 24.8 1.0
C A:ARG80 4.6 22.4 1.0
CA A:ILE150 4.6 40.9 1.0
CE1 A:HIS105 4.6 31.0 1.0
CD2 A:HIS105 4.7 30.4 1.0
OG A:SER149 4.7 32.3 1.0
CG1 A:ILE150 4.8 44.0 1.0
N A:GLY79 5.0 26.2 1.0

Sodium binding site 3 out of 6 in 2fbl

Go back to Sodium Binding Sites List in 2fbl
Sodium binding site 3 out of 6 in the The Crystal Structure of the Hypothetical Protein NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of the Hypothetical Protein NE1496 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:40.1
occ:1.00
 O A:SER107 2.3 23.6 1.0
O A:HOH342 2.3 52.1 1.0
O A:HOH426 2.3 57.6 1.0
O A:HIS105 2.5 23.3 1.0
O A:HOH421 2.6 38.9 1.0
C A:HIS105 3.4 23.2 1.0
C A:SER107 3.5 22.7 1.0
CA A:HIS105 4.0 23.6 1.0
N A:SER107 4.2 22.7 1.0
CA A:SER107 4.3 22.6 1.0
C A:LEU106 4.4 22.7 1.0
O A:HOH403 4.4 39.0 1.0
CD A:PRO108 4.4 24.5 1.0
N A:LEU106 4.4 21.5 1.0
N A:PRO108 4.4 23.3 1.0
O A:GLY104 4.5 24.6 1.0
CB A:SER107 4.7 21.8 1.0
CA A:LEU106 4.7 21.6 1.0
CB A:HIS105 4.7 25.2 1.0
O A:LEU106 4.8 22.7 1.0
O A:HOH352 4.9 36.4 1.0

Sodium binding site 4 out of 6 in 2fbl

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Sodium binding site 4 out of 6 in the The Crystal Structure of the Hypothetical Protein NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of the Hypothetical Protein NE1496 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:32.9
occ:1.00
 O B:HOH330 2.2 30.4 1.0
O B:PHE131 2.2 27.6 1.0
O B:HOH332 2.2 41.0 1.0
O B:HOH446 2.3 47.1 1.0
O B:HOH398 2.3 39.1 1.0
O B:PRO129 2.6 31.3 1.0
C B:PHE131 3.5 28.7 1.0
C B:PRO129 3.6 30.5 1.0
O B:HOH334 4.0 32.5 1.0
CA B:PRO129 4.1 30.8 1.0
N B:PHE131 4.2 25.7 1.0
O B:HOH386 4.3 35.2 1.0
O B:PRO128 4.3 31.7 1.0
CB B:ALA11 4.4 31.6 1.0
N B:GLY132 4.4 29.6 1.0
CA B:GLY132 4.4 30.2 1.0
CA B:PHE131 4.4 26.4 1.0
O B:HOH408 4.5 48.9 1.0
C B:TRP130 4.6 26.3 1.0
N B:TRP130 4.7 29.4 1.0
CB B:PHE131 4.9 26.3 1.0
C B:GLY132 5.0 31.0 1.0

Sodium binding site 5 out of 6 in 2fbl

Go back to Sodium Binding Sites List in 2fbl
Sodium binding site 5 out of 6 in the The Crystal Structure of the Hypothetical Protein NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of the Hypothetical Protein NE1496 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:30.8
occ:1.00
 O B:ALA147 2.2 24.5 1.0
O B:SER149 2.3 31.1 1.0
O B:HOH319 2.3 28.5 1.0
O B:HOH323 2.5 26.2 1.0
O B:GLY79 2.6 24.5 1.0
C B:GLY79 3.2 23.6 1.0
C B:ALA147 3.4 25.2 1.0
C B:SER149 3.6 33.7 1.0
NE2 B:HIS105 3.8 29.7 1.0
N B:ARG80 3.9 23.9 1.0
N B:ARG81 3.9 22.1 1.0
CA B:ARG80 4.0 22.7 1.0
CA B:GLY79 4.0 25.4 1.0
C B:LEU148 4.0 29.8 1.0
N B:SER149 4.1 30.9 1.0
O B:ARG81 4.1 19.0 1.0
O B:LEU146 4.2 25.4 1.0
CA B:LEU148 4.2 29.6 1.0
N B:LEU148 4.2 27.3 1.0
O B:LEU148 4.3 28.7 1.0
CA B:ALA147 4.4 24.9 1.0
C B:ARG80 4.4 22.8 1.0
CA B:SER149 4.5 32.0 1.0
O B:HOH349 4.5 38.8 1.0
N B:ILE150 4.5 36.5 1.0
CE1 B:HIS105 4.6 30.0 1.0
CA B:ILE150 4.7 40.2 1.0
CD2 B:HIS105 4.7 27.6 1.0
OG B:SER149 4.8 30.0 1.0
N B:GLY79 5.0 25.3 1.0
C B:ARG81 5.0 19.8 1.0

Sodium binding site 6 out of 6 in 2fbl

Go back to Sodium Binding Sites List in 2fbl
Sodium binding site 6 out of 6 in the The Crystal Structure of the Hypothetical Protein NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of the Hypothetical Protein NE1496 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:37.3
occ:1.00
 O B:SER107 2.3 23.2 1.0
O B:HOH352 2.4 54.7 1.0
O B:HOH415 2.5 49.4 1.0
O B:HIS105 2.5 22.3 1.0
O B:HOH444 2.8 36.8 1.0
C B:HIS105 3.4 23.8 1.0
C B:SER107 3.5 22.0 1.0
CA B:HIS105 4.0 24.1 1.0
N B:SER107 4.1 22.9 1.0
CA B:SER107 4.3 21.8 1.0
C B:LEU106 4.3 22.6 1.0
CD B:PRO108 4.3 23.7 1.0
N B:LEU106 4.4 20.9 1.0
O B:HOH454 4.4 38.7 1.0
N B:PRO108 4.4 22.7 1.0
O B:GLY104 4.5 25.6 1.0
CA B:LEU106 4.6 21.8 1.0
CB B:SER107 4.7 23.0 1.0
O B:LEU106 4.7 21.9 1.0
CB B:HIS105 4.7 25.6 1.0
O B:HOH400 4.9 40.4 1.0

Reference:

V.V.Lunin, T.Skarina, O.Onopriyenko, T.A.Binkowski, A.Joachimiak, A.M.Edwards, A.Savchenko. The Crystal Structure of the Hypothetical Protein NE1496 To Be Published.
Page generated: Tue Dec 15 05:48:55 2020

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