Calcium in PDB 5zdm: The Ligand-Free Structure of Fomd

The structure of The Ligand-Free Structure of Fomd, PDB code: 5zdm was solved by S.Sato, A.Miyanaga, F.Kudo, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.474, 46.215, 52.504, 90.00, 110.27, 90.00
R / Rfree (%)	16.4 / 19.2

The binding sites of Calcium atom in the The Ligand-Free Structure of Fomd (pdb code 5zdm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Ligand-Free Structure of Fomd, PDB code: 5zdm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Ligand-Free Structure of Fomd


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Ligand-Free Structure of Fomd within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:13.0 occ:1.00 OD1 A:ASN109 2.2 12.9 1.0 OD1 A:ASP129 2.4 15.8 1.0 OD1 A:ASP125 2.4 11.6 1.0 O A:HOH459 2.4 12.8 1.0 O A:HOH442 2.4 14.2 1.0 CG A:ASN109 3.2 12.1 1.0 CG A:ASP125 3.4 11.0 1.0 OD2 A:ASP125 3.6 13.1 1.0 CG A:ASP129 3.6 15.1 1.0 ND2 A:ASN109 3.7 12.4 1.0 CA A:CA302 3.8 14.0 1.0 O A:GLU127 4.2 12.6 1.0 OH A:TYR107 4.3 13.7 1.0 OD2 A:ASP129 4.3 15.7 1.0 CE2 A:TYR107 4.4 12.2 1.0 CB A:ASN109 4.5 11.7 1.0 O A:ILE128 4.6 12.6 1.0 CB A:ASP129 4.6 13.2 1.0 CA A:ASN109 4.6 11.4 1.0 C A:GLU127 4.7 12.2 1.0 CB A:ASP125 4.7 11.2 1.0 CA A:GLU127 4.8 12.8 1.0 O A:VAL110 4.8 11.3 1.0 O3 A:GOL303 4.8 34.0 1.0 CZ A:TYR107 4.8 12.4 1.0 N A:GLU127 4.8 12.1 1.0

Calcium binding site 2 out of 2 in the The Ligand-Free Structure of Fomd


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Ligand-Free Structure of Fomd within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:14.0 occ:1.00 O A:GLU127 2.3 12.6 1.0 OE1 A:GLU127 2.3 13.6 1.0 OD2 A:ASP143 2.4 15.0 1.0 OD2 A:ASP129 2.4 15.7 1.0 O A:HOH442 2.5 14.2 1.0 OD1 A:ASP129 2.9 15.8 1.0 CG A:ASP129 3.0 15.1 1.0 CG A:ASP143 3.3 15.4 1.0 C A:GLU127 3.4 12.2 1.0 CD A:GLU127 3.4 14.4 1.0 CB A:ASP143 3.5 14.1 1.0 CA A:CA301 3.8 13.0 1.0 CA A:GLU127 3.9 12.8 1.0 NZ A:LYS142 3.9 14.9 1.0 CG A:GLU127 4.1 13.4 1.0 CB A:ASP129 4.4 13.2 1.0 OE2 A:GLU127 4.4 16.2 1.0 OD1 A:ASP143 4.5 17.2 1.0 O A:HOH459 4.5 12.8 1.0 N A:ILE128 4.5 12.4 1.0 OH A:TYR107 4.5 13.7 1.0 NZ A:LYS146 4.5 25.9 1.0 N A:ASP129 4.5 12.5 1.0 C A:ILE128 4.6 11.9 1.0 CB A:GLU127 4.6 13.0 1.0 O A:HOH408 4.7 27.8 1.0 CA A:ILE128 4.8 12.6 1.0 OD2 A:ASP125 4.9 13.1 1.0 O A:ILE128 5.0 12.6 1.0 CA A:ASP143 5.0 15.2 1.0

S.Sato, A.Miyanaga, S.Y.Kim, T.Kuzuyama, F.Kudo, T.Eguchi. Biochemical and Structural Analysis of Fomd That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis. Biochemistry V. 57 4858 2018.
ISSN: ISSN 1520-4995
PubMed: 30010320
DOI: 10.1021/ACS.BIOCHEM.8B00690