Calcium in PDB 5d2a: Bifunctional Dendrimers

The structure of Bifunctional Dendrimers, PDB code: 5d2a was solved by G.Michaud, R.Visini, A.Stocker, T.Darbre, J.L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.51 / 2.13
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.107, 105.107, 111.092, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.6

The binding sites of Calcium atom in the Bifunctional Dendrimers (pdb code 5d2a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Bifunctional Dendrimers, PDB code: 5d2a:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Bifunctional Dendrimers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bifunctional Dendrimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:47.5 occ:1.00 OE2 A:GLU95 2.3 49.5 1.0 OD2 A:ASP104 2.4 48.4 1.0 OD1 A:ASP101 2.5 47.9 1.0 OD1 A:ASP99 2.5 50.2 1.0 OE1 A:GLU95 2.5 47.5 1.0 O4 E:ZDC101 2.5 51.7 1.0 O3 E:ZDC101 2.5 50.0 1.0 OD1 A:ASP104 2.7 46.5 1.0 CD A:GLU95 2.7 49.0 1.0 CG A:ASP104 2.9 47.6 1.0 C4 E:ZDC101 3.2 51.6 1.0 C3 E:ZDC101 3.3 50.8 1.0 CG A:ASP99 3.4 50.8 1.0 CG A:ASP101 3.6 48.5 1.0 OD2 A:ASP99 3.7 49.1 1.0 CA A:CA202 3.9 48.6 1.0 N A:ASP101 4.0 48.1 1.0 OD1 A:ASP96 4.1 51.5 1.0 OD2 A:ASP101 4.2 45.0 1.0 CG A:GLU95 4.2 48.1 1.0 CB A:ASP104 4.4 47.4 1.0 N A:TYR102 4.4 46.6 1.0 N A:ASN100 4.5 50.8 1.0 N A:ASP96 4.5 51.0 1.0 N A:GLY97 4.5 53.1 1.0 CB A:ASP101 4.7 46.2 1.0 C5 E:ZDC101 4.7 54.0 1.0 CA A:GLU95 4.7 49.9 1.0 CA A:ASP101 4.7 47.6 1.0 C2 E:ZDC101 4.8 50.4 1.0 CB A:ASP99 4.8 51.5 1.0 N A:ASP99 4.8 53.6 1.0 OD1 A:ASN103 4.9 45.9 1.0 CA A:GLY97 4.9 53.3 1.0 CB A:GLU95 4.9 49.5 1.0 CA A:ASN100 4.9 49.6 1.0 C A:ASP101 5.0 47.4 1.0 C A:ASN100 5.0 48.4 1.0 CG A:ASP96 5.0 53.3 1.0

Calcium binding site 2 out of 4 in the Bifunctional Dendrimers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bifunctional Dendrimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:48.6 occ:1.00 OD1 A:ASN103 2.3 45.9 1.0 O3 E:ZDC101 2.3 50.0 1.0 OD1 A:ASP104 2.3 46.5 1.0 O A:ASN21 2.4 46.0 1.0 O B:GLY114 2.4 43.6 1.0 OD2 A:ASP101 2.5 45.0 1.0 O2 E:ZDC101 2.6 47.9 1.0 OD1 A:ASP101 3.0 47.9 1.0 CG A:ASP101 3.1 48.5 1.0 C3 E:ZDC101 3.2 50.8 1.0 CG A:ASN103 3.4 46.2 1.0 C B:GLY114 3.4 47.9 1.0 C2 E:ZDC101 3.4 50.4 1.0 OXT B:GLY114 3.5 46.7 1.0 C A:ASN21 3.5 47.5 1.0 CG A:ASP104 3.6 47.6 1.0 C4 E:ZDC101 3.7 51.6 1.0 ND2 A:ASN103 3.8 45.6 1.0 CA A:CA201 3.9 47.5 1.0 CB A:ASN21 4.1 44.4 1.0 CA A:ASP104 4.1 46.5 1.0 N A:ASP104 4.3 46.1 1.0 N A:SER22 4.4 45.8 1.0 O4 E:ZDC101 4.4 51.7 1.0 CB A:ASP104 4.4 47.4 1.0 CA A:SER22 4.5 47.6 1.0 OD2 A:ASP104 4.5 48.4 1.0 CA A:ASN21 4.5 46.9 1.0 C A:ASN103 4.5 45.8 1.0 O B:HOH308 4.6 49.3 1.0 CB A:ASP101 4.6 46.2 1.0 CB A:SER22 4.6 47.8 1.0 OD2 A:ASP99 4.7 49.1 1.0 C1 E:ZDC101 4.7 53.5 1.0 CB A:ASN103 4.7 43.1 1.0 CA B:GLY114 4.8 47.6 1.0 O5 E:ZDC101 4.8 53.9 1.0 O A:ASN103 4.8 44.5 1.0 N A:ASN103 4.8 46.0 1.0 C5 E:ZDC101 4.8 54.0 1.0 CA A:ASN103 4.9 45.2 1.0

Calcium binding site 3 out of 4 in the Bifunctional Dendrimers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bifunctional Dendrimers within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:53.4 occ:1.00 OE2 B:GLU95 2.3 56.2 1.0 OD1 B:ASP101 2.4 49.3 1.0 OD1 B:ASP99 2.4 54.8 1.0 OE1 B:GLU95 2.5 53.7 1.0 O3 D:ZDC101 2.5 55.5 1.0 OD2 B:ASP104 2.5 54.5 1.0 O4 D:ZDC101 2.5 54.8 1.0 OD1 B:ASP104 2.6 53.9 1.0 CD B:GLU95 2.7 54.8 1.0 CG B:ASP104 2.9 53.5 1.0 C4 D:ZDC101 3.3 58.0 1.0 C3 D:ZDC101 3.4 56.1 1.0 CG B:ASP99 3.4 55.3 1.0 CG B:ASP101 3.4 50.6 1.0 CA B:CA202 3.7 52.0 1.0 OD2 B:ASP99 3.7 56.8 1.0 OD2 B:ASP101 4.0 49.9 1.0 N B:ASP101 4.0 51.1 1.0 CG B:GLU95 4.2 52.7 1.0 OD1 B:ASP96 4.2 57.4 1.0 CB B:ASP104 4.4 53.0 1.0 N B:ASN100 4.5 53.9 1.0 N B:TYR102 4.5 48.3 1.0 N B:GLY97 4.6 55.6 1.0 N B:ASP96 4.6 55.9 1.0 CB B:ASP101 4.6 49.0 1.0 C2 D:ZDC101 4.7 57.9 1.0 CA B:ASP101 4.7 49.0 1.0 CB B:ASP99 4.7 53.2 1.0 N B:ASP99 4.8 54.8 1.0 O2 D:ZDC101 4.8 55.2 1.0 C5 D:ZDC101 4.8 59.3 1.0 CA B:GLU95 4.8 53.9 1.0 OD1 B:ASN103 4.9 50.2 1.0 CB B:GLU95 4.9 51.9 1.0 C B:ASN100 5.0 53.1 1.0 CA B:ASN100 5.0 54.3 1.0 C B:ASP99 5.0 54.8 1.0 CA B:GLY97 5.0 57.8 1.0 CG B:ASP96 5.0 57.2 1.0

Calcium binding site 4 out of 4 in the Bifunctional Dendrimers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bifunctional Dendrimers within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:52.0 occ:1.00 O B:ASN21 2.4 51.9 1.0 OD1 B:ASP104 2.4 53.9 1.0 O2 D:ZDC101 2.4 55.2 1.0 O3 D:ZDC101 2.5 55.5 1.0 OD2 B:ASP101 2.5 49.9 1.0 O A:GLY114 2.6 52.1 1.0 OD1 B:ASN103 2.6 50.2 1.0 OD1 B:ASP101 3.0 49.3 1.0 CG B:ASP101 3.1 50.6 1.0 C2 D:ZDC101 3.3 57.9 1.0 C3 D:ZDC101 3.3 56.1 1.0 C A:GLY114 3.4 54.6 1.0 OXT A:GLY114 3.4 54.0 1.0 C B:ASN21 3.6 53.5 1.0 CA B:CA201 3.7 53.4 1.0 CG B:ASP104 3.7 53.5 1.0 CG B:ASN103 3.7 50.1 1.0 C4 D:ZDC101 3.8 58.0 1.0 ND2 B:ASN103 4.2 48.3 1.0 CA B:ASP104 4.3 52.0 1.0 CA B:SER22 4.3 56.3 1.0 CB B:ASN21 4.3 51.2 1.0 N B:SER22 4.4 54.3 1.0 O4 D:ZDC101 4.4 54.8 1.0 OD2 B:ASP99 4.4 56.8 1.0 N B:ASP104 4.4 52.8 1.0 OD2 B:ASP104 4.5 54.5 1.0 CB B:ASP104 4.5 53.0 1.0 C B:ASN103 4.6 52.1 1.0 O A:HOH318 4.6 55.6 1.0 CB B:ASP101 4.6 49.0 1.0 CA B:ASN21 4.6 51.5 1.0 CB B:SER22 4.6 55.6 1.0 C1 D:ZDC101 4.7 61.1 1.0 O B:ASN103 4.8 51.4 1.0 CA A:GLY114 4.9 52.0 1.0 N B:ASN103 5.0 48.8 1.0 CB B:ASN103 5.0 48.2 1.0 OD1 B:ASP99 5.0 54.8 1.0

G.Michaud, R.Visini, M.Bergmann, G.Salerno, R.Bosco, E.Gillon, B.Richichi, C.Nativi, A.Imberty, A.Stocker, T.Darbre, J.L.Reymond. Overcoming Antibiotic Resistance Inpseudomonas Aeruginosabiofilms Using Glycopeptide Dendrimers. Chem Sci V. 7 166 2016.
ISSN: ISSN 2041-6520
PubMed: 29896342
DOI: 10.1039/C5SC03635F