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Calcium in PDB 9my6: Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid

Enzymatic activity of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid

All present enzymatic activity of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid:
2.7.7.58;

Protein crystallography data

The structure of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid, PDB code: 9my6 was solved by S.F.Ahmed, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.78 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.424, 141.246, 148.464, 90, 90, 90
R / Rfree (%) 19.1 / 21.8

Other elements in 9my6:

The structure of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid (pdb code 9my6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid, PDB code: 9my6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 1 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:44.3
occ:1.00
 O B:ASN330 2.3 48.9 1.0
O B:GLN305 2.3 42.7 1.0
O B:HOH708 2.3 41.9 1.0
O B:LEU307 2.4 43.3 1.0
C B:GLN305 3.4 48.6 1.0
C B:ASN330 3.5 48.2 1.0
C B:LEU307 3.5 45.8 1.0
N B:LEU307 4.0 44.4 1.0
CA B:GLN305 4.1 49.7 1.0
CB B:ASN330 4.2 49.6 1.0
C B:SER306 4.2 45.5 1.0
CA B:LEU307 4.2 42.9 1.0
O B:ILE304 4.3 47.3 1.0
CB B:CYS331 4.3 44.4 1.0
CA B:CYS331 4.3 48.3 1.0
N B:CYS331 4.4 47.2 1.0
N B:SER306 4.4 44.5 1.0
CA B:ASN330 4.5 50.7 1.0
O B:LEU329 4.5 46.3 1.0
N B:LYS308 4.5 43.1 1.0
CB B:LEU307 4.6 40.7 1.0
CA B:SER306 4.6 46.3 1.0
CA B:LYS308 4.6 44.5 1.0
OE1 B:GLN305 4.7 61.1 1.0
O B:SER306 4.7 45.1 1.0

Calcium binding site 2 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 2 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:74.7
occ:1.00
 O B:HOH777 2.7 51.6 1.0
O B:HOH780 3.4 44.3 1.0
NH2 B:ARG219 3.5 39.7 1.0
O B:HOH808 3.7 49.7 1.0
NE B:ARG219 3.9 41.1 1.0
CE1 B:TYR216 4.0 39.7 1.0
O B:GLY23 4.1 42.3 1.0
CD1 B:TYR216 4.1 38.6 1.0
CZ B:ARG219 4.2 39.7 1.0
CB B:ARG219 4.6 37.7 1.0
O B:HOH722 4.9 42.5 1.0
C B:GLY23 5.0 43.1 1.0
CA B:TYR24 5.0 40.6 1.0

Calcium binding site 3 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 3 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:63.8
occ:1.00
 O B:HOH702 2.3 42.5 1.0
O B:GLY198 2.8 53.4 1.0
O B:HOH750 2.8 36.7 1.0
O B:HOH762 2.9 43.9 1.0
O B:HOH705 3.0 43.6 1.0
O B:HOH727 3.2 46.2 1.0
O B:HOH801 3.2 44.4 1.0
O B:HOH793 3.4 51.3 1.0
C B:GLY198 3.9 52.1 1.0
O B:HOH798 4.1 56.4 1.0
OE1 B:GLU341 4.4 39.8 1.0
N B:GLY198 4.4 46.1 1.0
CA B:GLY198 4.5 44.6 1.0
O B:SER418 4.6 46.9 1.0
OE2 B:GLU341 4.7 41.1 1.0
O B:HOH714 4.8 35.2 1.0
CB B:MET339 4.9 39.5 1.0
CD B:GLU341 4.9 42.5 1.0
N B:GLY199 5.0 56.8 1.0

Calcium binding site 4 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 4 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:74.7
occ:1.00
 O A:HOH801 2.3 68.3 1.0
O A:HOH737 2.5 64.6 1.0
O A:HOH778 2.6 66.9 1.0
O A:GLN53 2.7 65.3 1.0
O A:HOH794 2.9 62.7 1.0
C A:GLN53 3.9 63.3 1.0
OE1 A:GLU58 3.9 71.1 1.0
N A:GLN53 4.3 64.5 1.0
CB A:GLN53 4.3 64.0 1.0
CA A:GLN53 4.4 63.3 1.0
OE2 A:GLU58 4.6 73.8 1.0
CD A:GLU58 4.7 70.9 1.0
N A:LEU54 5.0 62.1 1.0

Calcium binding site 5 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 5 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:60.8
occ:1.00
 O A:HOH788 2.2 60.8 1.0
O A:ASN330 2.3 61.5 1.0
O A:LEU307 2.5 56.3 1.0
O A:GLN305 2.5 59.8 1.0
O A:HOH721 2.5 55.1 1.0
C A:ASN330 3.5 62.1 1.0
C A:GLN305 3.6 61.9 1.0
C A:LEU307 3.6 55.9 1.0
CB A:ASN330 4.1 60.9 1.0
N A:LEU307 4.1 56.1 1.0
N A:CYS331 4.4 62.6 1.0
CA A:GLN305 4.4 60.4 1.0
CA A:CYS331 4.4 59.3 1.0
CA A:LEU307 4.4 55.0 1.0
C A:SER306 4.4 56.8 1.0
CB A:CYS331 4.4 58.4 1.0
CA A:ASN330 4.4 62.0 1.0
O A:ILE304 4.5 59.6 1.0
N A:SER306 4.6 57.7 1.0
N A:LYS308 4.6 55.3 1.0
O A:LEU329 4.7 63.9 1.0
CA A:LYS308 4.7 57.3 1.0
CB A:LEU307 4.8 55.9 1.0
CA A:SER306 4.8 60.0 1.0
O A:SER306 4.9 58.3 1.0

Calcium binding site 6 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 6 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:54.3
occ:1.00
 OD1 A:ASP171 2.2 58.4 1.0
O A:HOH725 2.5 61.7 1.0
CG A:ASP171 3.1 58.2 1.0
OD2 A:ASP171 3.4 60.4 1.0
O A:HOH701 3.5 56.7 1.0
O A:ASP171 4.4 62.8 1.0
CB A:ASP171 4.5 58.5 1.0
NH2 A:ARG69 4.6 68.2 1.0
CA A:ASP171 4.9 58.8 1.0
C A:ASP171 5.0 58.5 1.0

Calcium binding site 7 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 7 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:88.6
occ:1.00
 O A:GLY74 2.6 60.8 1.0
OD1 A:ASP79 3.6 57.6 1.0
C A:GLY74 3.7 60.0 1.0
OD2 A:ASP79 4.0 56.6 1.0
CG A:ASP79 4.2 55.5 1.0
CA A:GLY74 4.4 57.5 1.0
CD A:LYS127 4.6 59.9 1.0
N A:LEU75 4.7 57.1 1.0
CE A:LYS127 4.7 63.4 1.0
CA A:LEU75 4.9 57.2 1.0

Calcium binding site 8 out of 8 in 9my6

Go back to Calcium Binding Sites List in 9my6
Calcium binding site 8 out of 8 in the Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca608

b:54.6
occ:1.00
 O A:HOH795 2.2 44.6 1.0
O A:HOH793 2.3 52.3 1.0
O A:HOH720 2.5 46.2 1.0
O A:SER418 2.5 45.7 1.0
O A:HOH800 2.5 57.0 1.0
C A:SER418 3.7 47.4 1.0
O A:HOH723 4.0 47.7 1.0
OD2 A:ASP420 4.1 52.7 1.0
CA A:SER418 4.3 43.9 1.0
OD1 A:ASP420 4.3 52.8 1.0
CB A:SER418 4.3 43.6 1.0
CG A:ASP420 4.5 50.3 1.0
O A:HOH740 4.5 40.2 1.0
OH A:TYR416 4.5 45.6 1.0
CA A:GLY199 4.7 58.1 1.0
N A:GLY419 4.7 47.1 1.0
N A:GLY199 4.8 47.8 1.0
CA A:GLY419 5.0 44.7 1.0

Reference:

S.F.Ahmed, A.M.Gulick. Structure of the Base Double Mutant V336A/S247C, An Nrps Adenylation Domain in the Acinetobactin Biosynthetic Pathway Bound to 4-Fluoro Salicylic Acid To Be Published.
Page generated: Thu Jul 10 10:18:45 2025

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