Magnesium in PDB 5zdn: The Complex Structure of Fomd with Cdp

The structure of The Complex Structure of Fomd with Cdp, PDB code: 5zdn 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)	48.28 / 2.02
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	56.165, 77.452, 96.566, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.8

The binding sites of Magnesium atom in the The Complex Structure of Fomd with Cdp (pdb code 5zdn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Complex Structure of Fomd with Cdp, PDB code: 5zdn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Complex Structure of Fomd with Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Complex Structure of Fomd with Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:15.1 occ:1.00 OE1 A:GLU127 1.9 17.0 1.0 OD2 A:ASP143 2.1 22.4 1.0 O A:GLU127 2.1 22.7 1.0 OD2 A:ASP129 2.1 22.2 1.0 O A:HOH438 2.1 20.6 1.0 CG A:ASP143 2.9 24.2 1.0 O A:HOH421 3.0 19.5 1.0 C A:GLU127 3.0 23.2 1.0 CD A:GLU127 3.0 17.2 1.0 CG A:ASP129 3.1 23.7 1.0 CB A:ASP143 3.2 23.4 1.0 CA A:GLU127 3.4 20.9 1.0 OD1 A:ASP129 3.4 22.4 1.0 CG A:GLU127 3.6 19.1 1.0 O A:HOH450 3.7 16.8 1.0 MG A:MG303 3.8 17.8 1.0 NZ A:LYS142 4.0 23.6 1.0 OE2 A:GLU127 4.0 16.3 1.0 CB A:GLU127 4.1 20.3 1.0 OD1 A:ASP143 4.1 22.2 1.0 N A:ILE128 4.2 23.1 1.0 CB A:ASP129 4.4 23.7 1.0 N A:ASP129 4.4 23.9 1.0 O A:HOH419 4.5 31.4 1.0 C A:ILE128 4.5 25.7 1.0 O A:HOH402 4.5 22.6 1.0 CA A:ILE128 4.6 23.2 1.0 OH A:TYR107 4.7 26.6 1.0 N A:GLU127 4.7 21.9 1.0 CA A:ASP143 4.7 24.5 1.0 O A:LYS142 4.8 23.5 1.0 OD1 A:ASP125 4.8 21.1 1.0 CG A:LYS142 4.9 25.0 1.0 O A:ILE128 4.9 25.2 1.0 MG A:MG304 4.9 38.2 1.0

Magnesium binding site 2 out of 4 in the The Complex Structure of Fomd with Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Complex Structure of Fomd with Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:17.8 occ:1.00 OD1 A:ASN109 2.0 22.9 1.0 OD1 A:ASP129 2.0 22.4 1.0 OD2 A:ASP125 2.0 24.1 1.0 O A:HOH438 2.2 20.6 1.0 O A:HOH450 2.2 16.8 1.0 O A:HOH402 2.2 22.6 1.0 CG A:ASN109 3.0 23.7 1.0 CG A:ASP125 3.1 21.3 1.0 CG A:ASP129 3.2 23.7 1.0 ND2 A:ASN109 3.5 21.6 1.0 OD1 A:ASP125 3.5 21.1 1.0 OD2 A:ASP129 3.7 22.2 1.0 MG A:MG302 3.8 15.1 1.0 O A:HOH421 3.8 19.5 1.0 O A:GLU127 4.0 22.7 1.0 O A:ILE128 4.1 25.2 1.0 CB A:ASN109 4.2 24.0 1.0 OH A:TYR107 4.2 26.6 1.0 C A:GLU127 4.3 23.2 1.0 CA A:ASN109 4.3 23.3 1.0 CA A:GLU127 4.3 20.9 1.0 CB A:ASP125 4.4 22.1 1.0 O A:VAL110 4.4 20.6 1.0 CB A:ASP129 4.4 23.7 1.0 N A:GLU127 4.5 21.9 1.0 CE1 A:TYR107 4.5 29.3 1.0 C1 A:GOL306 4.6 40.3 1.0 N A:VAL110 4.6 25.6 1.0 C A:ILE128 4.7 25.7 1.0 C A:ASN109 4.8 24.9 1.0 CZ A:TYR107 4.8 26.6 1.0 OE1 A:GLU127 4.9 17.0 1.0 O A:HOH412 5.0 31.9 1.0 N A:HIS126 5.0 20.5 1.0 N A:ILE128 5.0 23.1 1.0 O A:HOH409 5.0 42.1 1.0

Magnesium binding site 3 out of 4 in the The Complex Structure of Fomd with Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Complex Structure of Fomd with Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:38.2 occ:1.00 O A:HOH412 1.8 31.9 1.0 O A:HOH421 2.0 19.5 1.0 O3B A:CDP301 2.0 20.4 1.0 O A:HOH409 2.1 42.1 1.0 O2A A:CDP301 2.2 24.0 1.0 O A:HOH444 2.3 28.3 1.0 O A:HOH450 3.1 16.8 1.0 PB A:CDP301 3.4 22.4 1.0 PA A:CDP301 3.5 28.8 1.0 O3A A:CDP301 3.6 24.2 1.0 O A:HOH438 3.9 20.6 1.0 NZ A:LYS142 4.0 23.6 1.0 NE1 A:TRP68 4.1 27.6 1.0 O A:HOH427 4.2 27.3 1.0 O1B A:CDP301 4.3 23.2 1.0 O2B A:CDP301 4.3 23.9 1.0 O1A A:CDP301 4.3 28.3 1.0 OH A:TYR107 4.3 26.6 1.0 O A:HOH419 4.4 31.4 1.0 O5' A:CDP301 4.6 25.4 1.0 C5' A:CDP301 4.6 26.2 1.0 O1 A:GOL306 4.6 38.8 1.0 CD1 A:TRP68 4.8 27.1 1.0 MG A:MG302 4.9 15.1 1.0 OD2 A:ASP143 5.0 22.4 1.0

Magnesium binding site 4 out of 4 in the The Complex Structure of Fomd with Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Complex Structure of Fomd with Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:22.1 occ:0.50 O A:HOH441 1.9 34.4 0.5 O A:HOH419 2.0 31.4 1.0 O1B A:CDP301 2.0 23.2 1.0 O A:HOH426 2.1 26.3 0.5 PB A:CDP301 3.4 22.4 1.0 NZ A:LYS146 3.8 23.4 1.0 O3B A:CDP301 3.8 20.4 1.0 OD1 A:ASP143 4.2 22.2 1.0 O2B A:CDP301 4.3 23.9 1.0 O A:HOH427 4.3 27.3 1.0 O3A A:CDP301 4.4 24.2 1.0 O A:HOH444 4.6 28.3 1.0 OD2 A:ASP143 4.7 22.4 1.0 NZ A:LYS142 4.8 23.6 1.0 O A:HOH410 4.9 23.2 1.0 CG A:ASP143 4.9 24.2 1.0 O A:HOH463 4.9 24.4 0.5 CE A:LYS142 4.9 25.0 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