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Sodium in PDB 4nhd: Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A

Enzymatic activity of Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A

All present enzymatic activity of Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A:
2.3.1.180;

Protein crystallography data

The structure of Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A, PDB code: 4nhd was solved by J.Hou, H.Zheng, K.Langner, W.F.Anderson, W.Minor, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.449, 100.248, 132.763, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.6

Other elements in 4nhd:

The structure of Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A (pdb code 4nhd). 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 Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A, PDB code: 4nhd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4nhd

Go back to Sodium Binding Sites List in 4nhd
Sodium binding site 1 out of 3 in the Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A


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 Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:33.3
occ:1.00
O A:HOH606 2.2 44.4 1.0
O A:HOH719 2.3 36.5 1.0
O A:HOH800 2.3 46.2 1.0
O A:ASN231 2.4 28.1 1.0
C A:ASN231 3.6 28.1 1.0
O A:HOH801 3.9 49.1 1.0
CB A:ASN231 4.1 32.7 1.0
OE2 A:GLU236 4.4 26.7 1.0
CA A:MET232 4.4 25.3 1.0
N A:MET232 4.4 25.6 1.0
CA A:ASN231 4.5 29.8 1.0
O A:ASN230 4.6 25.0 1.0
OE1 A:GLU236 4.6 28.1 1.0
CD A:GLU236 4.9 26.9 1.0

Sodium binding site 2 out of 3 in 4nhd

Go back to Sodium Binding Sites List in 4nhd
Sodium binding site 2 out of 3 in the Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A


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 Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:40.0
occ:1.00
O D:HOH715 2.0 59.2 1.0
O D:HOH713 2.4 49.3 1.0
O D:ASN231 2.4 41.4 1.0
O D:HOH716 2.4 57.5 1.0
O D:HOH714 2.7 47.2 0.6
C D:ASN231 3.6 40.8 1.0
O D:HOH717 3.8 59.2 0.5
CB D:ASN231 4.2 44.1 1.0
OE2 D:GLU236 4.3 42.4 1.0
CA D:MET232 4.4 38.8 1.0
N D:MET232 4.5 39.0 1.0
OE1 D:GLU236 4.5 40.8 1.0
CA D:ASN231 4.6 41.2 1.0
O D:ASN230 4.6 34.3 1.0
CD D:GLU236 4.9 41.2 1.0

Sodium binding site 3 out of 3 in 4nhd

Go back to Sodium Binding Sites List in 4nhd
Sodium binding site 3 out of 3 in the Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A


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 Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:21.0
occ:1.00
O D:HOH734 2.1 50.0 1.0
O D:HOH731 2.2 37.8 1.0
O D:GLY67 2.2 25.1 1.0
O D:HOH733 2.3 40.4 1.0
O D:HOH732 2.4 34.7 1.0
O D:HOH735 2.6 53.2 1.0
C D:GLY67 3.4 25.2 1.0
CA D:GLY67 4.1 24.8 1.0
N D:ILE68 4.4 24.2 1.0
CA D:ILE68 4.6 24.9 1.0
C D:ILE68 4.8 25.6 1.0
O D:HOH517 4.9 26.6 1.0

Reference:

J.Hou, H.Zheng, K.Langner, W.F.Anderson, W.Minor, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Beta-Ketoacyl-Acp Synthase III (Fabh) From Vibrio Cholerae in Complex with Coenzyme A To Be Published.
Page generated: Sun Aug 17 20:47:08 2025

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