Calcium in PDB 3o82: Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine

The structure of Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine, PDB code: 3o82 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)	40.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.447, 145.259, 149.063, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.1

The binding sites of Calcium atom in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine (pdb code 3o82). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine, PDB code: 3o82:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)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 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca543 b:53.9 occ:1.00 O A:HOH558 2.3 63.9 1.0 O A:GLN53 2.4 58.3 1.0 OE2 A:GLU58 2.4 60.3 1.0 O A:HOH547 2.5 37.9 1.0 OE1 A:GLU58 2.6 57.9 1.0 CD A:GLU58 2.8 57.1 1.0 C A:GLN53 3.6 58.2 1.0 CG A:GLU58 4.3 52.8 1.0 CA A:LEU54 4.4 56.1 1.0 N A:LEU54 4.5 56.9 1.0 CA A:GLN53 4.6 59.4 1.0 CB A:GLN53 4.7 59.9 1.0 N A:SER55 4.7 53.6 1.0 N A:GLN53 4.9 59.9 1.0 CD2 A:LEU54 4.9 60.1 1.0 CB A:GLU58 4.9 50.2 1.0

Calcium binding site 2 out of 4 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)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 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca544 b:56.3 occ:1.00 O A:GLN305 2.3 57.8 1.0 O A:LEU307 2.4 55.7 1.0 O A:ASN330 2.5 54.8 1.0 C A:GLN305 3.4 57.6 1.0 C A:LEU307 3.5 55.0 1.0 C A:ASN330 3.7 54.1 1.0 CA A:GLN305 4.0 58.3 1.0 N A:LEU307 4.0 54.9 1.0 CB A:ASN330 4.2 54.1 1.0 CA A:LEU307 4.3 55.0 1.0 C A:SER306 4.4 55.8 1.0 N A:SER306 4.5 57.0 1.0 O A:ILE304 4.5 57.6 1.0 N A:LYS308 4.5 54.8 1.0 CB A:LEU307 4.6 54.8 1.0 O A:HOH555 4.6 45.9 1.0 CA A:ASN330 4.6 54.4 1.0 CB A:CYS331 4.6 52.9 1.0 N A:CYS331 4.6 53.9 1.0 CA A:CYS331 4.7 53.2 1.0 CA A:LYS308 4.7 54.4 1.0 O A:LEU329 4.8 54.0 1.0 CB A:GLN305 4.8 58.7 1.0 CA A:SER306 4.8 56.2 1.0 O A:SER306 4.8 56.7 1.0

Calcium binding site 3 out of 4 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)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 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca543 b:89.1 occ:1.00 O B:HOH566 2.4 57.6 1.0 O B:GLN53 2.8 64.5 1.0 O B:HOH565 3.0 61.3 1.0 OE1 B:GLU58 3.5 63.4 1.0 C B:GLN53 3.9 63.0 1.0 CB B:GLN53 4.1 64.0 1.0 CD B:GLU58 4.4 63.3 1.0 CA B:GLN53 4.5 64.0 1.0 OE2 B:GLU58 4.5 67.2 1.0 N B:GLN53 4.6 64.7 1.0

Calcium binding site 4 out of 4 in the Structure of Base N-Terminal Domain From Acinetobacter Baumannii Bound to 5'-O-[N-(2,3-Dihydroxybenzoyl)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 5'-O-[N-(2,3-Dihydroxybenzoyl)Sulfamoyl] Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca544 b:62.6 occ:1.00 O B:ASN330 2.2 58.5 1.0 O B:HOH568 2.2 48.3 1.0 O B:GLN305 2.3 57.6 1.0 O B:LEU307 2.6 58.5 1.0 C B:ASN330 3.4 57.9 1.0 C B:GLN305 3.4 57.9 1.0 C B:LEU307 3.7 56.9 1.0 CA B:GLN305 4.0 59.1 1.0 CB B:ASN330 4.0 57.7 1.0 O B:ILE304 4.2 58.1 1.0 CA B:ASN330 4.3 57.7 1.0 N B:LEU307 4.3 56.6 1.0 N B:CYS331 4.4 57.2 1.0 CA B:LEU307 4.5 56.7 1.0 C B:SER306 4.5 56.9 1.0 CA B:CYS331 4.5 56.9 1.0 N B:SER306 4.5 56.9 1.0 O B:LEU329 4.6 56.1 1.0 CB B:CYS331 4.6 56.2 1.0 CB B:LEU307 4.7 56.5 1.0 CB B:GLN305 4.7 59.5 1.0 N B:LYS308 4.7 56.7 1.0 O B:SER306 4.8 56.9 1.0 CA B:LYS308 4.9 56.2 1.0 CA B:SER306 4.9 56.6 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