Calcium in PDB 3o83: Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine

The structure of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine, PDB code: 3o83 was solved by E.J.Drake, B.P.Duckworth, J.Neres, C.C.Aldrich, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.95 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.460, 144.238, 148.469, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.7

The binding sites of Calcium atom in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine (pdb code 3o83). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine, PDB code: 3o83:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca543 b:34.2 occ:1.00 O A:GLU327 2.3 24.2 1.0 ND2 A:ASN330 2.4 14.6 1.0 O A:HOH661 2.4 31.6 1.0 O A:HOH772 2.4 35.8 1.0 O A:HOH662 3.0 45.6 1.0 C A:GLU327 3.4 24.7 1.0 CG A:ASN330 3.5 20.5 1.0 OD1 A:ASN330 3.9 23.9 1.0 O A:PRO326 4.0 24.2 1.0 CA A:GLU327 4.0 25.9 1.0 N A:VAL328 4.4 23.5 1.0 CB A:ASN330 4.6 19.5 1.0 OE2 A:GLU327 4.7 42.9 1.0 CA A:VAL328 4.8 22.9 1.0 CA A:ASN330 4.8 20.1 1.0 C A:PRO326 4.9 24.9 1.0 CD A:GLU327 4.9 39.6 1.0 CG A:GLU327 4.9 32.9 1.0 N A:GLU327 4.9 25.2 1.0

Calcium binding site 2 out of 6 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca544 b:25.5 occ:1.00 O A:HOH665 1.7 19.6 1.0 O A:HOH663 2.2 30.0 1.0 O A:GLN53 2.4 24.5 1.0 OE1 A:GLU58 2.4 25.1 1.0 O A:HOH664 2.4 27.2 1.0 OE2 A:GLU58 2.6 27.2 1.0 CD A:GLU58 2.9 26.1 1.0 O A:HOH666 3.6 32.5 1.0 C A:GLN53 3.6 24.8 1.0 O A:HOH601 4.1 21.6 1.0 CA A:LEU54 4.4 23.4 1.0 CG A:GLU58 4.4 22.9 1.0 N A:LEU54 4.4 23.9 1.0 N A:SER55 4.5 21.6 1.0 CB A:GLN53 4.6 25.3 1.0 CA A:GLN53 4.6 24.7 1.0 O A:HOH699 4.8 39.3 1.0 N A:GLN53 4.9 24.1 1.0 C A:LEU54 4.9 22.6 1.0

Calcium binding site 3 out of 6 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca545 b:20.6 occ:1.00 O A:GLN305 2.3 20.5 1.0 O A:HOH660 2.3 21.7 1.0 O A:ASN330 2.3 19.9 1.0 O A:LEU307 2.3 19.6 1.0 O A:HOH659 2.5 17.1 1.0 C A:GLN305 3.4 21.0 1.0 C A:ASN330 3.5 20.0 1.0 C A:LEU307 3.5 20.2 1.0 N A:LEU307 4.0 20.0 1.0 CA A:GLN305 4.1 22.6 1.0 CB A:ASN330 4.2 19.5 1.0 OE1 A:GLN305 4.3 33.1 1.0 CA A:LEU307 4.3 20.5 1.0 C A:SER306 4.3 20.5 1.0 O A:ILE304 4.3 22.6 1.0 CA A:CYS331 4.4 21.0 1.0 N A:CYS331 4.4 20.6 1.0 CB A:CYS331 4.4 20.3 1.0 N A:SER306 4.4 20.6 1.0 CA A:ASN330 4.5 20.1 1.0 N A:LYS308 4.5 19.5 1.0 O A:LEU329 4.6 20.9 1.0 CB A:LEU307 4.6 20.9 1.0 O A:HOH724 4.7 33.0 1.0 CA A:SER306 4.7 20.3 1.0 CA A:LYS308 4.7 19.7 1.0 O A:SER306 4.7 20.3 1.0 O A:HOH773 4.8 34.0 1.0 O A:HOH725 4.8 34.5 1.0 CB A:GLN305 4.9 22.9 1.0

Calcium binding site 4 out of 6 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca543 b:29.9 occ:1.00 O B:HOH552 2.3 36.1 1.0 O B:LEU307 2.4 25.7 1.0 O B:HOH550 2.4 29.1 1.0 O B:GLN305 2.4 25.4 1.0 O B:ASN330 2.4 28.4 1.0 O B:HOH553 2.4 30.2 1.0 O B:HOH551 2.5 30.6 1.0 C B:GLN305 3.5 25.2 1.0 C B:LEU307 3.5 25.9 1.0 C B:ASN330 3.6 28.2 1.0 N B:LEU307 4.0 25.1 1.0 CB B:ASN330 4.2 29.4 1.0 CA B:GLN305 4.2 25.9 1.0 CA B:LEU307 4.3 25.8 1.0 C B:SER306 4.3 25.1 1.0 O B:ILE304 4.5 25.2 1.0 N B:CYS331 4.5 27.6 1.0 CA B:ASN330 4.5 28.7 1.0 N B:SER306 4.5 25.1 1.0 N B:LYS308 4.6 25.8 1.0 CA B:CYS331 4.6 27.0 1.0 CB B:CYS331 4.6 26.6 1.0 CB B:LEU307 4.7 25.6 1.0 O B:LEU329 4.7 28.0 1.0 O B:SER306 4.7 24.8 1.0 CA B:SER306 4.7 25.3 1.0 CA B:LYS308 4.8 25.8 1.0

Calcium binding site 5 out of 6 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca544 b:62.5 occ:1.00 O B:HOH728 2.1 43.9 1.0 O B:HOH730 2.3 43.4 1.0 O B:HOH729 2.4 53.4 1.0 O B:GLN53 2.5 33.3 1.0 OE1 B:GLU58 2.6 35.2 1.0 O B:HOH788 2.6 46.0 1.0 OE2 B:GLU58 3.1 36.9 1.0 CD B:GLU58 3.2 33.8 1.0 C B:GLN53 3.7 33.2 1.0 CA B:LEU54 4.3 29.7 1.0 N B:LEU54 4.5 31.1 1.0 N B:SER55 4.5 27.1 1.0 CG B:GLU58 4.7 29.0 1.0 CA B:GLN53 4.7 33.9 1.0 CB B:GLN53 4.7 34.5 1.0 C B:LEU54 4.9 28.5 1.0

Calcium binding site 6 out of 6 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 2-(4-N-Dodecyl-1,2,3-Triazol-1-Yl)-5'-O-[N-(2-Hydroxybenzoyl) Sulfamoyl]Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca545 b:61.1 occ:1.00 O B:HOH789 2.3 41.1 1.0 O B:HOH694 2.4 46.7 1.0 O B:HOH771 2.4 39.5 1.0 O B:HOH767 2.5 38.1 1.0 O B:HOH696 2.5 38.3 1.0 O B:HOH695 2.6 43.2 1.0 O B:GLY74 2.6 28.8 1.0 C B:GLY74 3.5 28.6 1.0 CA B:GLY74 3.9 28.8 1.0 OD2 B:ASP79 4.6 22.0 1.0 N B:LEU75 4.6 28.0 1.0 O B:LYS73 4.6 29.2 1.0 OE1 B:GLU155 4.7 31.5 1.0 O B:HOH589 4.7 39.9 1.0 OE2 B:GLU155 4.7 30.4 1.0 CD2 B:LEU75 4.9 29.8 1.0 CD B:LYS127 5.0 25.7 1.0

E.J.Drake, B.P.Duckworth, J.Neres, C.C.Aldrich, A.M.Gulick. Biochemical and Structural Characterization of Bisubstrate Inhibitors of Base, the Self-Standing Nonribosomal Peptide Synthetase Adenylate-Forming Enzyme of Acinetobactin Synthesis. Biochemistry V. 49 9292 2010.
ISSN: ISSN 0006-2960
PubMed: 20853905
DOI: 10.1021/BI101226N