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Sodium in PDB 4x0o: Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa

Enzymatic activity of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa

All present enzymatic activity of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa:
2.3.1.180;

Protein crystallography data

The structure of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa, PDB code: 4x0o was solved by J.Hou, M.Chruszcz, H.Zheng, D.R.Cooper, M.D.Chordia, M.D.Zimmerman, W.F.Anderson, W.Minor, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.70 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.763, 86.980, 157.342, 90.06, 89.96, 90.08
R / Rfree (%) 17.4 / 20.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa (pdb code 4x0o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa, PDB code: 4x0o:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4x0o

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Sodium binding site 1 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:42.1
occ:1.00
 O A:HOH507 2.0 9.8 0.5
OD2 A:ASP305 2.3 44.9 1.0
O A:HOH508 2.3 38.3 1.0
O A:GLU244 2.5 43.2 1.0
O A:HOH507 3.0 15.1 0.5
OD2 A:ASP246 3.1 37.9 1.0
CG A:ASP305 3.4 40.1 1.0
C A:GLU244 3.5 44.5 1.0
CB A:ASP305 3.9 37.7 1.0
CB A:GLU244 3.9 54.6 1.0
CA A:GLU244 3.9 49.5 1.0
O A:HOH580 3.9 39.6 1.0
CG A:ASP246 4.0 40.5 1.0
OD1 A:ASP246 4.1 40.5 1.0
NH1 A:ARG323 4.3 65.0 1.0
N A:ASP305 4.4 36.6 1.0
OD1 A:ASP305 4.5 41.1 1.0
CG A:GLU244 4.6 61.4 1.0
N A:ILE245 4.7 42.1 1.0
CA A:ASP305 4.8 36.9 1.0

Sodium binding site 2 out of 7 in 4x0o

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Sodium binding site 2 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:32.4
occ:1.00
 OD2 B:ASP305 2.2 39.2 1.0
OD2 B:ASP246 2.3 35.4 1.0
O B:GLU244 2.4 36.5 1.0
O B:HOH506 2.4 29.0 1.0
CG B:ASP305 3.1 36.0 1.0
CG B:ASP246 3.3 39.8 1.0
CB B:ASP305 3.4 33.3 1.0
O B:HOH507 3.6 47.4 1.0
C B:GLU244 3.6 38.4 1.0
OD1 B:ASP246 3.6 36.9 1.0
N B:ASP305 3.6 33.8 1.0
CA B:ASP305 4.1 33.1 1.0
CA B:GLU244 4.2 41.0 1.0
OD1 B:ASP305 4.3 37.5 1.0
CB B:GLU244 4.4 42.8 1.0
C B:ASP304 4.5 31.8 1.0
O B:HIS303 4.6 38.4 1.0
CB B:ASP246 4.6 39.9 1.0
N B:ASP246 4.6 37.2 1.0
N B:ILE245 4.6 37.3 1.0
NH2 B:ARG323 4.7 58.8 1.0
CA B:ASP304 4.7 32.7 1.0
CA B:ILE245 4.9 35.3 1.0
C B:ILE245 4.9 36.2 1.0

Sodium binding site 3 out of 7 in 4x0o

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Sodium binding site 3 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:39.3
occ:1.00
 O C:HOH507 2.3 42.2 1.0
O C:HOH508 2.3 24.4 1.0
OD2 C:ASP305 2.4 33.6 1.0
O C:GLU244 2.8 38.8 1.0
OD2 C:ASP246 3.0 39.2 1.0
O C:HOH594 3.0 27.8 1.0
CG C:ASP305 3.5 33.3 1.0
C C:GLU244 3.8 40.3 1.0
CG C:ASP246 3.8 41.4 1.0
OD1 C:ASP246 4.0 39.3 1.0
CB C:ASP305 4.1 34.6 1.0
CA C:GLU244 4.1 44.5 1.0
CB C:GLU244 4.2 45.3 1.0
N C:ASP305 4.3 37.4 1.0
O C:HOH564 4.6 40.1 1.0
OD1 C:ASP305 4.6 32.0 1.0
NH2 C:ARG323 4.7 64.0 1.0
O C:HIS303 4.8 38.8 1.0
CG C:GLU244 4.8 48.8 1.0
CA C:ASP305 4.9 34.6 1.0
N C:ILE245 5.0 39.7 1.0

Sodium binding site 4 out of 7 in 4x0o

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Sodium binding site 4 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:36.5
occ:1.00
 O D:HOH505 2.0 20.7 1.0
O D:HOH504 2.2 30.8 1.0
OD2 D:ASP305 2.5 33.7 1.0
OD2 D:ASP246 2.6 29.2 1.0
O D:GLU244 2.8 38.2 1.0
O D:HOH605 3.2 34.4 1.0
CG D:ASP246 3.5 33.5 1.0
CG D:ASP305 3.5 32.0 1.0
OD1 D:ASP246 3.7 32.0 1.0
C D:GLU244 3.8 39.8 1.0
CB D:ASP305 3.9 31.7 1.0
N D:ASP305 4.0 32.5 1.0
CA D:GLU244 4.3 44.1 1.0
CB D:GLU244 4.5 45.8 1.0
O D:HIS303 4.6 36.4 1.0
OD1 D:ASP305 4.6 30.5 1.0
CA D:ASP305 4.6 31.2 1.0
O D:HOH529 4.7 24.7 1.0
NH2 D:ARG323 4.8 51.5 1.0
C D:ASP304 4.8 31.3 1.0
CA D:ASP304 4.9 31.2 1.0
CB D:ASP246 4.9 32.9 1.0
N D:ILE245 5.0 38.1 1.0

Sodium binding site 5 out of 7 in 4x0o

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Sodium binding site 5 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:34.9
occ:1.00
 O F:GLU244 2.3 40.8 1.0
OD2 F:ASP305 2.4 38.1 1.0
OD2 F:ASP246 2.6 39.1 1.0
O F:HOH564 2.9 38.7 1.0
C F:GLU244 3.4 43.0 1.0
CG F:ASP305 3.4 35.9 1.0
CG F:ASP246 3.4 39.9 1.0
OD1 F:ASP246 3.6 38.1 1.0
CB F:ASP305 3.7 34.1 1.0
CA F:GLU244 3.9 45.7 1.0
N F:ASP305 4.0 33.2 1.0
CB F:GLU244 4.1 48.0 1.0
O F:HOH573 4.4 21.8 1.0
N F:ILE245 4.5 42.2 1.0
CA F:ASP305 4.5 32.7 1.0
OD1 F:ASP305 4.5 37.0 1.0
NH2 F:ARG323 4.7 53.3 1.0
N F:ASP246 4.7 39.1 1.0
CB F:ASP246 4.8 38.7 1.0
CG F:GLU244 4.9 52.1 1.0
CA F:ILE245 4.9 41.1 1.0
C F:ASP304 4.9 32.5 1.0
O F:HIS303 4.9 33.1 1.0
C F:ILE245 5.0 40.8 1.0

Sodium binding site 6 out of 7 in 4x0o

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Sodium binding site 6 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na402

b:51.2
occ:1.00
 O G:HOH509 2.0 34.4 1.0
O G:HOH510 2.3 31.5 1.0
OD2 G:ASP305 2.5 39.5 1.0
O G:GLU244 2.5 44.4 1.0
OD2 G:ASP246 2.6 39.3 1.0
O G:HOH530 3.3 49.9 1.0
CG G:ASP246 3.5 42.2 1.0
CG G:ASP305 3.6 37.7 1.0
C G:GLU244 3.6 42.9 1.0
OD1 G:ASP246 3.6 43.2 1.0
CB G:ASP305 3.9 35.8 1.0
CA G:GLU244 4.0 45.5 1.0
N G:ASP305 4.1 37.2 1.0
CB G:GLU244 4.2 48.4 1.0
OD1 G:ASP305 4.7 36.8 1.0
CA G:ASP305 4.7 35.7 1.0
NH2 G:ARG323 4.7 64.8 1.0
N G:ILE245 4.7 41.3 1.0
O G:HIS303 4.8 39.7 1.0
CB G:ASP246 4.9 43.4 1.0
CG G:GLU244 4.9 52.7 1.0
N G:ASP246 4.9 42.8 1.0
C G:ASP304 5.0 37.9 1.0

Sodium binding site 7 out of 7 in 4x0o

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Sodium binding site 7 out of 7 in the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Beta-Ketoacyl-(Acyl Carrier Protein) Synthase III-2 (FABH2) From Vibrio Cholerae Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na402

b:45.9
occ:1.00
 OD2 H:ASP305 2.3 36.1 1.0
O H:GLU244 2.5 47.0 1.0
OD2 H:ASP246 2.6 38.1 1.0
CG H:ASP305 3.4 34.4 1.0
CG H:ASP246 3.6 39.6 1.0
C H:GLU244 3.6 40.8 1.0
OD1 H:ASP246 3.8 39.7 1.0
CB H:ASP305 3.8 32.5 1.0
N H:ASP305 4.0 33.7 1.0
CA H:GLU244 4.1 46.0 1.0
O H:HOH572 4.1 44.4 1.0
CB H:GLU244 4.2 48.2 1.0
OD1 H:ASP305 4.5 32.1 1.0
NH2 H:ARG323 4.5 64.7 1.0
CA H:ASP305 4.6 32.1 1.0
O H:HIS303 4.7 41.2 1.0
N H:ILE245 4.8 39.5 1.0
C H:ASP304 4.9 35.7 1.0
CB H:ASP246 4.9 39.6 1.0
CG H:GLU244 4.9 52.3 1.0

Reference:

J.Hou, J.Hou, M.Chruszcz, H.Zheng, D.R.Cooper, M.D.Chordia, M.D.Zimmerman, W.F.Anderson, W.Minor, Center For Structural Genomics Of Infectiousdiseases (Csgid). N/A N/A.
Page generated: Mon Oct 7 18:57:08 2024

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