Magnesium in PDB 5ldp: Crystal Structure of E.Coli Ligt Complexed with Atp

The structure of Crystal Structure of E.Coli Ligt Complexed with Atp, PDB code: 5ldp was solved by M.Myllykoski, P.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.150, 73.470, 77.610, 90.00, 128.34, 90.00
R / Rfree (%)	16.9 / 20.9

The structure of Crystal Structure of E.Coli Ligt Complexed with Atp also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Ligt Complexed with Atp (pdb code 5ldp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Ligt Complexed with Atp, PDB code: 5ldp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:68.7 occ:1.00 O2G A:ATP201 2.0 87.3 1.0 O A:HOH407 2.0 51.0 1.0 O2A A:ATP201 2.4 41.6 1.0 O2B A:ATP201 2.4 62.9 1.0 PG A:ATP201 3.3 99.0 1.0 PB A:ATP201 3.5 57.1 1.0 PA A:ATP201 3.6 35.9 1.0 O3B A:ATP201 3.9 73.5 1.0 O3G A:ATP201 3.9 0.4 1.0 O3A A:ATP201 3.9 38.8 1.0 O5' A:ATP201 4.1 37.2 1.0 C8 A:ATP201 4.2 45.4 1.0 O A:HOH373 4.3 54.6 1.0 NH1 A:ARG6 4.4 50.5 1.0 O1G A:ATP201 4.5 96.1 1.0 N7 A:ATP201 4.6 40.5 1.0 C2' A:ATP201 4.9 37.9 1.0 O1B A:ATP201 4.9 66.0 1.0 O1A A:ATP201 4.9 36.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:63.1 occ:1.00 O2G B:ATP201 1.9 62.3 1.0 O B:HOH359 2.1 49.2 1.0 O2B B:ATP201 2.3 51.0 1.0 O1A B:ATP201 2.4 50.6 1.0 HN61 B:ATP202 3.2 93.5 0.8 PG B:ATP201 3.4 72.6 1.0 PB B:ATP201 3.4 56.3 1.0 PA B:ATP201 3.6 50.9 1.0 HN62 B:ATP202 3.6 93.5 0.8 NH2 B:ARG130 3.7 46.8 0.5 O3A B:ATP201 3.7 41.7 1.0 N6 B:ATP202 3.8 78.0 0.8 O3B B:ATP201 3.8 73.5 1.0 NH1 B:ARG6 4.2 52.3 1.0 O B:HOH326 4.2 47.0 1.0 O1G B:ATP201 4.2 81.6 1.0 O5' B:ATP201 4.2 45.8 1.0 O3G B:ATP201 4.4 68.6 1.0 CZ B:ARG130 4.6 53.6 0.5 C8 B:ATP201 4.7 45.5 1.0 O1B B:ATP201 4.8 60.8 1.0 NH1 B:ARG130 4.8 57.1 0.5 O2A B:ATP201 4.9 42.8 1.0

M.Myllykoski, P.Kursula. Structural Aspects of Nucleotide Ligand Binding By A Bacterial 2H Phosphoesterase. Plos One V. 12 70355 2017.
ISSN: ESSN 1932-6203
PubMed: 28141848
DOI: 10.1371/JOURNAL.PONE.0170355