Calcium in PDB 5ecc: Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine

The structure of Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine, PDB code: 5ecc was solved by M.N.Lombardo, A.C.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.54 / 1.87
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.199, 76.199, 113.784, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.9

The binding sites of Calcium atom in the Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine (pdb code 5ecc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine, PDB code: 5ecc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:50.1 occ:1.00 N6A A:NAP201 3.3 40.5 1.0 N A:ILE79 3.3 41.2 1.0 N A:LYS80 3.3 39.3 1.0 CB A:ILE79 3.7 38.0 1.0 CB A:SER78 3.8 38.8 1.0 CA A:ILE79 3.9 43.3 1.0 CB A:LYS80 4.0 47.4 1.0 C A:ILE79 4.1 44.1 1.0 C6A A:NAP201 4.1 41.4 1.0 N1A A:NAP201 4.2 39.9 1.0 C A:SER78 4.2 46.4 1.0 CA A:LYS80 4.3 38.7 1.0 CA A:SER78 4.3 41.6 1.0 OG A:SER78 4.4 41.1 1.0 CG1 A:ILE79 4.4 37.4 1.0 O A:HOH303 4.7 55.5 1.0 CG2 A:ILE79 4.7 31.1 1.0 CD1 A:ILE79 5.0 44.0 1.0

Calcium binding site 2 out of 3 in the Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:67.3 occ:0.50 CE B:LYS103 3.6 53.1 1.0 CG B:GLU100 3.9 35.9 1.0 O B:HOH323 3.9 54.6 1.0 CD B:LYS103 4.0 47.0 1.0 CA B:GLU100 4.2 38.0 1.0 CB B:GLU100 4.4 31.1 1.0 O B:HOH353 4.5 39.6 1.0 N B:GLU100 4.8 30.0 1.0 CB B:LYS103 4.8 35.7 1.0 CD B:GLU100 4.9 43.6 1.0 NZ B:LYS103 4.9 56.0 1.0

Calcium binding site 3 out of 3 in the Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Klebsiella Pneumoniae DFRA1 Complexed with Nadph and 6-Ethyl-5-(3-(2- Methoxy-5-(Pyridin-4-Yl)Phenyl)Prop-1-Yn-1-Yl)Pyrimidine-2,4-Diamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca206 b:50.5 occ:1.00 N B:GLU129 3.2 36.3 1.0 CA B:PRO128 3.7 35.9 1.0 CG B:GLU129 3.7 37.9 1.0 CB B:PRO128 3.8 38.4 1.0 NZ B:LYS103 3.9 56.0 1.0 C B:PRO128 3.9 41.6 1.0 CB B:GLU129 4.0 35.6 1.0 CA B:GLU129 4.1 37.3 1.0 CD B:GLU129 4.3 36.4 1.0 OE2 B:GLU129 4.5 35.5 1.0 O B:GLU129 4.7 33.7 1.0 CG B:LYS103 4.8 45.7 1.0 C B:GLU129 5.0 36.2 1.0

M.N.Lombardo, N.G-Dayanandan, D.L.Wright, A.C.Anderson. Crystal Structures of Trimethoprim-Resistant DFRA1 Rationalize Potent Inhibition By Propargyl-Linked Antifolates. Acs Infect Dis V. 2 149 2016.
ISSN: ESSN 2373-8227
PubMed: 27624966
DOI: 10.1021/ACSINFECDIS.5B00129