Magnesium in PDB 6su9: Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl:
2.7.1.35;

The structure of Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl, PDB code: 6su9 was solved by M.R.Groves, K.Gao, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.33 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.703, 62.004, 93.712, 90.00, 94.99, 90.00
R / Rfree (%)	20.9 / 27.2

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl (pdb code 6su9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl, PDB code: 6su9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl


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 Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:80.6 occ:1.00 OD1 A:ASP318 2.0 60.8 1.0 O A:HOH830 2.1 60.0 1.0 O A:HOH805 2.2 42.3 1.0 OD2 A:ASP318 2.4 44.7 1.0 CG A:ASP318 2.5 47.9 1.0 O A:HOH822 2.7 34.3 1.0 O A:HOH808 3.0 34.6 1.0 O2B A:ANP701 3.2 45.5 1.0 O A:HOH803 3.6 40.5 1.0 O A:THR348 3.8 32.7 1.0 CB A:ASP318 4.0 37.8 1.0 CG2 A:VAL320 4.0 37.5 1.0 C A:GLY428 4.4 32.6 1.0 O A:GLY428 4.4 25.9 1.0 PB A:ANP701 4.5 60.7 1.0 CA A:GLY428 4.5 26.6 1.0 OG A:SER432 4.5 65.7 1.0 OG1 A:THR348 4.6 35.8 1.0 OE1 A:GLU353 4.6 31.8 1.0 OD1 A:ASP429 4.7 39.3 1.0 CA A:ASP318 4.7 29.0 1.0 O A:HOH814 4.8 35.3 1.0 C A:ASP318 4.8 43.0 1.0 N3B A:ANP701 4.8 71.4 1.0 O3A A:ANP701 4.8 51.7 1.0 N A:ASP429 4.9 25.2 1.0 O A:ASP318 4.9 59.6 1.0 C A:THR348 5.0 36.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl


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 Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:28.9 occ:1.00 NH1 A:ARG28 3.3 41.8 1.0 NH1 B:ARG28 3.3 33.0 1.0 CA B:PHE25 3.6 33.6 1.0 CB B:PHE25 3.7 42.9 1.0 CA A:PHE25 3.7 42.2 1.0 N B:PHE25 3.8 50.0 1.0 CB A:PHE25 3.8 42.4 1.0 N A:PHE25 3.9 34.3 1.0 CD A:ARG28 3.9 34.8 1.0 CD B:ARG28 3.9 31.9 1.0 CD1 A:PHE25 3.9 36.2 1.0 C B:ALA24 4.1 35.2 1.0 CD1 B:PHE25 4.1 37.0 1.0 C A:ALA24 4.3 27.6 1.0 O B:ALA24 4.3 43.5 1.0 CG A:PHE25 4.3 40.0 1.0 CB B:ALA24 4.4 30.6 1.0 CG B:PHE25 4.4 41.8 1.0 CZ A:ARG28 4.4 37.5 1.0 CZ B:ARG28 4.4 37.7 1.0 CB A:ALA24 4.4 25.6 1.0 O A:ALA24 4.6 43.6 1.0 NE A:ARG28 4.6 36.2 1.0 NE B:ARG28 4.6 44.2 1.0 CA B:ALA24 4.9 42.3 1.0 C B:PHE25 5.0 44.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:75.9 occ:1.00 O B:THR348 2.5 55.0 1.0 OG1 B:THR386 2.8 74.7 1.0 CG2 B:THR386 2.9 71.1 1.0 N3B B:ANP501 3.1 86.9 1.0 CB B:THR386 3.4 68.6 1.0 C B:PRO349 3.5 54.9 1.0 N B:ASN350 3.6 56.9 1.0 C B:THR348 3.6 53.0 1.0 OD1 B:ASP318 3.6 70.0 1.0 O B:PRO349 3.7 54.0 1.0 CA B:PRO349 4.1 49.7 1.0 PG B:ANP501 4.1 98.1 1.0 O2G B:ANP501 4.1 68.2 1.0 O2A B:ANP501 4.1 98.9 1.0 OD2 B:ASP318 4.1 61.1 1.0 CA B:ASN350 4.1 65.6 1.0 CG B:ASP318 4.2 59.3 1.0 O3A B:ANP501 4.2 97.1 1.0 OG1 B:THR348 4.3 50.8 1.0 N B:PRO349 4.3 49.1 1.0 CB B:ASN350 4.3 56.0 1.0 PB B:ANP501 4.3 91.6 1.0 CB B:THR348 4.4 59.2 1.0 O1G B:ANP501 4.4 85.8 1.0 CA B:THR348 4.6 55.1 1.0 CA B:THR386 4.6 74.2 1.0 OE1 B:GLU353 4.7 47.9 1.0 N B:THR386 4.7 68.5 1.0 CA B:GLY428 4.7 49.8 1.0 PA B:ANP501 4.9 0.8 1.0 OG B:SER432 5.0 72.4 1.0

K.Gao, W.Wang, M.R.Groves. Crystal Structure of Plasmodium Falciparum Pdxk with Ligands Amp-Pnp and Pl. Crystals 2019.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST9100534