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Sodium in PDB 4ls8: Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin

Enzymatic activity of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin

All present enzymatic activity of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin:
2.3.1.179;

Protein crystallography data

The structure of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin, PDB code: 4ls8 was solved by F.Trajtenberg, N.Larrieux, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.11 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.440, 87.560, 116.440, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.6

Other elements in 4ls8:

The structure of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin (pdb code 4ls8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin, PDB code: 4ls8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4ls8

Go back to Sodium Binding Sites List in 4ls8
Sodium binding site 1 out of 3 in the Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:35.6
occ:1.00
 OE1 A:GLU233 2.6 25.8 1.0
O A:HOH611 2.8 24.7 1.0
N A:LEU195 3.0 27.3 1.0
C A:ALA193 3.0 30.7 1.0
CA A:ALA193 3.1 26.2 1.0
N A:PRO194 3.3 25.4 1.0
CB A:LEU195 3.3 26.9 1.0
CG A:LEU195 3.4 29.4 1.0
NH1 A:ARG40 3.4 26.5 1.0
CB A:ALA193 3.5 26.4 1.0
CB A:GLU233 3.6 21.3 1.0
O A:ALA193 3.6 32.6 1.0
CD A:GLU233 3.6 34.0 1.0
CD A:PRO194 3.6 25.8 1.0
CA A:LEU195 3.7 27.0 1.0
CD1 A:LEU195 4.0 29.0 1.0
C A:PRO194 4.1 30.7 1.0
CG A:GLU233 4.1 22.7 1.0
O A:HOH618 4.2 36.9 1.0
O A:LEU195 4.2 30.6 1.0
CA A:PRO194 4.2 25.1 1.0
C A:LEU195 4.3 32.3 1.0
OH A:TYR77 4.5 28.5 1.0
N A:ALA193 4.5 24.8 1.0
OE2 A:GLU233 4.6 27.0 1.0
CE2 A:TYR77 4.7 25.7 1.0
CZ A:ARG40 4.7 42.4 1.0
CD2 A:LEU195 4.7 29.5 1.0
CD A:ARG73 4.8 35.1 1.0
O A:GLU192 4.8 25.1 1.0
CG A:PRO194 4.9 29.4 1.0
CA A:GLU233 4.9 20.4 1.0

Sodium binding site 2 out of 3 in 4ls8

Go back to Sodium Binding Sites List in 4ls8
Sodium binding site 2 out of 3 in the Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:36.6
occ:1.00
 O A:HOH656 3.0 36.2 1.0
N A:VAL21 3.1 25.9 1.0
SD A:MET84 3.1 38.9 1.0
N A:ALA13 3.1 24.2 1.0
CA A:ASP20 3.3 24.7 1.0
CB A:ASP20 3.4 26.2 1.0
CG2 A:VAL21 3.6 27.4 1.0
CA A:GLY12 3.6 20.4 1.0
CB A:MET84 3.6 25.9 1.0
C A:ASP20 3.6 29.5 1.0
CE A:MET84 3.6 33.7 1.0
O A:ALA13 3.6 24.6 1.0
C A:GLY12 3.8 25.9 1.0
CG A:MET84 3.9 32.5 1.0
CB A:VAL21 4.0 28.8 1.0
O A:HOH773 4.1 38.1 1.0
CA A:VAL21 4.1 25.7 1.0
CA A:ALA13 4.2 23.4 1.0
C A:ALA13 4.3 26.5 1.0
O A:LEU11 4.4 22.2 1.0
N A:ASP20 4.5 24.3 1.0
N A:GLY12 4.7 20.3 1.0
O A:ASN19 4.7 29.0 1.0
O A:HOH770 4.8 46.5 1.0
O A:ASP20 4.8 29.0 1.0
CB A:ALA13 4.8 23.7 1.0
CG A:ASP20 4.9 34.6 1.0
C A:LEU11 4.9 24.6 1.0
CA A:MET84 4.9 23.3 1.0
O A:HOH679 5.0 40.1 1.0

Sodium binding site 3 out of 3 in 4ls8

Go back to Sodium Binding Sites List in 4ls8
Sodium binding site 3 out of 3 in the Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Bacillus Subtilis Beta-Ketoacyl-Acp Synthase II (Fabf) in A Covalent Complex with Cerulenin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:40.8
occ:1.00
 O B:GLY108 2.7 31.4 1.0
OD1 A:ASP141 2.7 34.2 1.0
N B:ALA163 3.1 29.9 1.0
CA B:ALA163 3.2 30.6 1.0
CG1 B:VAL161 3.5 29.4 1.0
C B:GLY108 3.5 32.8 1.0
CB A:ILE139 3.6 28.3 1.0
CG A:ASP141 3.6 33.2 1.0
CA B:GLY108 3.7 28.4 1.0
CG2 A:ILE139 3.8 29.0 1.0
CB B:ALA163 3.9 31.6 1.0
OD2 A:ASP141 4.0 33.4 1.0
CD1 A:ILE139 4.0 31.3 1.0
C7 B:1XG501 4.1 44.8 1.0
CG1 A:ILE139 4.3 28.4 1.0
C B:THR162 4.3 31.4 1.0
C6 B:1XG501 4.4 44.7 1.0
C B:ALA163 4.5 34.4 1.0
N B:THR162 4.5 27.6 1.0
CD A:PRO140 4.6 26.0 1.0
C B:VAL161 4.6 31.1 1.0
CA A:ILE139 4.7 24.6 1.0
O B:ALA163 4.7 32.2 1.0
CA B:THR162 4.7 26.8 1.0
N B:ILE109 4.8 30.5 1.0
CB B:VAL161 4.8 29.1 1.0
CB A:ASP141 4.8 26.4 1.0
OG1 B:THR166 4.9 27.8 1.0
O B:VAL161 4.9 29.8 1.0

Reference:

F.Trajtenberg, S.Altabe, N.Larrieux, F.Ficarra, D.De Mendoza, A.Buschiazzo, G.E.Schujman. Structural Insights Into Bacterial Resistance to Cerulenin. Febs J. V. 281 2324 2014.
ISSN: ISSN 1742-464X
PubMed: 24641521
DOI: 10.1111/FEBS.12785
Page generated: Tue Dec 15 06:52:12 2020

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