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Calcium 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:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 7 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4nhd

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Calcium binding site 1 out of 7 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 Calcium with other atoms in the Ca 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:Ca402

b:35.5
occ:1.00
 O A:HOH819 2.1 31.7 1.0
O A:HOH821 2.3 39.5 1.0
O A:ASN48 2.3 28.1 1.0
O A:HOH818 2.4 40.3 1.0
OD2 A:ASP53 2.4 17.7 1.0
O A:HOH822 2.5 35.7 1.0
O A:HOH717 2.5 42.0 1.0
CG A:ASP53 3.4 19.0 1.0
C A:ASN48 3.5 30.6 1.0
OD1 A:ASP53 3.7 20.0 1.0
CA A:GLU49 4.1 19.4 1.0
N A:GLU49 4.2 20.7 1.0
CB A:ASN48 4.4 38.9 1.0
N A:THR50 4.5 17.2 1.0
CA A:ASN48 4.5 34.3 1.0
O A:HOH669 4.6 38.4 1.0
CB A:ASP53 4.6 17.7 1.0
O A:HOH820 4.7 37.0 1.0
O A:HOH667 4.7 34.7 1.0
C A:GLU49 4.8 19.2 1.0
CG2 A:THR50 4.9 18.3 1.0
O A:HOH838 4.9 41.5 1.0

Calcium binding site 2 out of 7 in 4nhd

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Calcium binding site 2 out of 7 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 Calcium with other atoms in the Ca 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
B:Ca402

b:36.0
occ:1.00
 O B:HOH697 2.2 36.1 1.0
O B:HOH699 2.3 43.8 1.0
O B:HOH698 2.4 38.9 1.0
OD2 B:ASP53 2.4 21.1 1.0
O B:ASN48 2.4 26.1 1.0
O B:HOH552 2.5 33.8 1.0
CG B:ASP53 3.3 21.2 1.0
C B:ASN48 3.6 25.4 1.0
OD1 B:ASP53 3.7 22.5 1.0
O B:HOH834 3.9 55.5 1.0
CA B:GLU49 4.2 22.0 1.0
N B:GLU49 4.3 23.3 1.0
CB B:ASN48 4.5 28.0 1.0
N B:THR50 4.5 19.4 1.0
O B:HOH825 4.6 41.2 1.0
CB B:ASP53 4.6 19.3 1.0
O B:HOH564 4.6 27.8 1.0
CA B:ASN48 4.7 26.4 1.0
O A:HOH716 4.8 32.4 1.0
C B:GLU49 4.9 21.3 1.0
CG2 B:THR50 4.9 19.4 1.0

Calcium binding site 3 out of 7 in 4nhd

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Calcium binding site 3 out of 7 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 Calcium with other atoms in the Ca 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
B:Ca403

b:46.1
occ:1.00
 O B:HOH822 2.1 43.5 1.0
O B:HOH823 2.4 47.4 1.0
O B:HOH824 2.4 40.5 1.0
OD1 B:ASP74 2.5 25.8 1.0
O B:ASP72 2.6 21.7 1.0
OD2 B:ASP74 2.7 25.7 1.0
CG B:ASP74 2.9 25.0 1.0
O B:HOH835 2.9 51.4 1.0
C B:ASP72 3.6 21.7 1.0
CA B:ASP72 3.9 23.5 1.0
CB B:ASP72 4.2 26.0 1.0
O B:HOH816 4.2 44.4 1.0
O B:HOH821 4.3 46.3 1.0
CB B:ASP74 4.3 22.6 1.0
ND1 B:HIS133 4.4 26.2 1.0
CB B:LYS132 4.5 28.9 1.0
N B:ASP74 4.7 18.9 1.0
N B:ILE73 4.8 20.3 1.0
OD1 B:ASP72 4.8 29.9 1.0
CG B:ASP72 4.8 27.7 1.0
C B:ILE73 4.8 19.1 1.0
CA B:ASP74 4.9 20.2 1.0
N B:HIS133 5.0 21.9 1.0

Calcium binding site 4 out of 7 in 4nhd

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Calcium binding site 4 out of 7 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 Calcium with other atoms in the Ca binding site number 4 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
C:Ca402

b:25.8
occ:1.00
 O C:HOH829 2.2 21.4 1.0
O C:HOH832 2.3 19.1 1.0
OD1 C:ASP74 2.4 17.6 1.0
O C:HOH831 2.4 24.6 1.0
O C:HOH830 2.5 28.2 1.0
O C:ASP72 2.6 17.2 1.0
OD2 C:ASP74 2.7 18.9 1.0
CG C:ASP74 2.9 18.1 1.0
C C:ASP72 3.5 17.6 1.0
CA C:ASP72 3.9 19.4 1.0
CB C:ASP72 4.2 20.9 1.0
CB C:ASP74 4.3 16.6 1.0
O C:HOH698 4.3 33.8 1.0
O C:HOH525 4.4 21.9 1.0
O C:HOH833 4.4 40.3 1.0
O C:HOH540 4.5 32.5 1.0
ND1 C:HIS133 4.6 19.8 1.0
CB C:LYS132 4.6 21.6 1.0
N C:ASP74 4.6 14.7 1.0
N C:ILE73 4.7 15.9 1.0
C C:ILE73 4.7 15.0 1.0
CA C:ASP74 4.8 15.2 1.0
CG C:ASP72 4.9 24.9 1.0
OD1 C:ASP72 4.9 25.6 1.0
O C:ILE73 4.9 14.5 1.0

Calcium binding site 5 out of 7 in 4nhd

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Calcium binding site 5 out of 7 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 Calcium with other atoms in the Ca binding site number 5 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
C:Ca403

b:37.5
occ:1.00
 OD2 C:ASP53 2.4 18.3 1.0
O C:ASN48 2.4 21.8 1.0
O C:HOH838 2.5 41.5 1.0
O C:HOH837 2.5 45.0 1.0
O C:HOH835 2.5 38.6 1.0
O C:HOH707 2.9 45.4 1.0
O C:HOH836 3.2 51.2 1.0
CG C:ASP53 3.3 18.3 1.0
OD1 C:ASP53 3.6 20.7 1.0
C C:ASN48 3.6 23.6 1.0
CA C:GLU49 4.2 19.4 1.0
N C:GLU49 4.4 20.6 1.0
N C:THR50 4.5 16.6 1.0
CB C:ASN48 4.6 28.2 1.0
CG2 C:THR50 4.6 17.1 1.0
CA C:ASN48 4.6 25.8 1.0
CB C:ASP53 4.6 16.1 1.0
O C:HOH844 4.7 37.3 1.0
OG1 C:THR50 4.8 15.0 1.0
C C:GLU49 4.9 18.7 1.0

Calcium binding site 6 out of 7 in 4nhd

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Calcium binding site 6 out of 7 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 Calcium with other atoms in the Ca binding site number 6 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:Ca402

b:42.2
occ:1.00
 O D:HOH719 2.3 48.7 1.0
OD2 D:ASP53 2.4 27.5 1.0
O D:ASN48 2.4 33.6 1.0
O D:HOH720 2.4 39.5 1.0
O D:HOH721 2.5 45.4 1.0
O D:HOH718 2.5 44.8 1.0
CG D:ASP53 3.3 25.8 1.0
OD1 D:ASP53 3.6 26.1 1.0
C D:ASN48 3.6 34.9 1.0
CA D:GLU49 4.3 30.3 1.0
N D:GLU49 4.4 32.6 1.0
N D:THR50 4.5 26.4 1.0
CB D:ASN48 4.6 41.9 1.0
O D:HOH674 4.6 47.4 1.0
CB D:ASP53 4.7 23.5 1.0
CA D:ASN48 4.7 39.1 1.0
CG2 D:THR50 4.7 25.5 1.0
OG1 D:THR50 4.9 23.0 1.0
C D:GLU49 4.9 28.4 1.0

Calcium binding site 7 out of 7 in 4nhd

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Calcium binding site 7 out of 7 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 Calcium with other atoms in the Ca binding site number 7 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:Ca403

b:27.3
occ:1.00
 O D:HOH725 2.2 24.7 1.0
O D:HOH724 2.3 29.6 1.0
O D:HOH723 2.4 31.6 1.0
OD1 D:ASP74 2.4 21.6 1.0
O D:HOH726 2.5 32.7 1.0
O D:ASP72 2.5 21.2 1.0
OD2 D:ASP74 2.6 22.4 1.0
CG D:ASP74 2.8 21.0 1.0
C D:ASP72 3.5 22.4 1.0
CA D:ASP72 3.9 25.0 1.0
CB D:ASP72 4.1 27.7 1.0
CB D:ASP74 4.3 19.5 1.0
O D:HOH526 4.4 25.8 1.0
O D:HOH698 4.4 46.6 1.0
ND1 D:HIS133 4.4 22.1 1.0
O D:HOH728 4.5 46.1 1.0
CB D:LYS132 4.5 22.9 1.0
N D:ASP74 4.7 17.6 1.0
N D:ILE73 4.7 20.1 1.0
C D:ILE73 4.7 18.4 1.0
CG D:ASP72 4.8 31.5 1.0
CA D:ASP74 4.8 18.2 1.0
O D:HOH683 4.8 54.7 1.0
OD1 D:ASP72 4.9 35.0 1.0
O D:HOH727 4.9 36.6 1.0
N D:HIS133 4.9 19.5 1.0
O D:ILE73 5.0 18.1 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 Jul 14 11:05:29 2024

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