Magnesium in PDB 6yxt: Crystal Structure of the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum

All present enzymatic activity of Crystal Structure of the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum:
2.7.1.32;

The structure of Crystal Structure of the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum, PDB code: 6yxt was solved by A.Torretta, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.17 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.450, 68.000, 105.110, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25.5

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum (pdb code 6yxt). 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 the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum, PDB code: 6yxt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum


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 the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:42.9 occ:1.00 OE2 A:GLU307 2.0 44.2 1.0 OD2 A:ASP305 2.0 41.3 1.0 O A:HOH677 2.1 38.1 1.0 O A:HOH613 2.2 39.5 1.0 O2B A:ADP503 2.2 71.0 1.0 OD1 A:ASP305 2.4 43.9 1.0 CG A:ASP305 2.5 41.3 1.0 O3B A:ADP503 2.9 50.1 1.0 PB A:ADP503 3.0 48.8 1.0 CD A:GLU307 3.1 45.7 1.0 CG A:GLU307 3.7 42.8 1.0 MG A:MG502 3.8 44.9 1.0 O3A A:ADP503 3.9 47.1 1.0 CB A:ASP305 4.0 33.9 1.0 O A:HOH605 4.1 75.1 1.0 OD2 A:ASP288 4.1 39.9 1.0 OE1 A:GLU307 4.2 52.5 1.0 O1B A:ADP503 4.3 66.5 1.0 O2A A:ADP503 4.5 53.7 1.0 O A:HOH695 4.5 53.7 1.0 CE2 A:TYR308 4.6 45.1 1.0 PA A:ADP503 4.6 45.9 1.0 O A:HOH642 4.7 50.1 1.0 O A:HOH693 4.9 47.4 1.0 CA A:ASP305 4.9 37.6 1.0 O A:HOH683 4.9 51.3 1.0 ND2 A:ASN117 4.9 71.0 1.0 CD2 A:TYR308 5.0 40.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum


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 the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.9 occ:1.00 O3B A:ADP503 2.0 50.1 1.0 OD1 A:ASN293 2.0 36.9 1.0 O A:HOH642 2.1 50.1 1.0 O A:HOH614 2.1 40.6 1.0 O2A A:ADP503 2.2 53.7 1.0 OD2 A:ASP305 2.4 41.3 1.0 CG A:ASN293 2.9 36.6 1.0 ND2 A:ASN293 3.1 37.5 1.0 CG A:ASP305 3.3 41.3 1.0 PB A:ADP503 3.4 48.8 1.0 PA A:ADP503 3.5 45.9 1.0 CB A:ASP305 3.6 33.9 1.0 ND2 A:ASN292 3.8 44.8 0.4 MG A:MG501 3.8 42.9 1.0 O3A A:ADP503 3.9 47.1 1.0 OD1 A:ASN292 3.9 44.1 0.4 CG A:ASN292 4.1 43.6 0.4 O A:HOH677 4.2 38.1 1.0 O A:HOH693 4.2 47.4 1.0 O A:ASN292 4.2 46.7 1.0 O2B A:ADP503 4.3 71.0 1.0 CB A:ASN293 4.3 33.1 1.0 O A:HOH658 4.3 59.9 1.0 C5' A:ADP503 4.4 47.6 1.0 O1B A:ADP503 4.4 66.5 1.0 OD1 A:ASP305 4.4 43.9 1.0 O5' A:ADP503 4.5 46.7 1.0 O1A A:ADP503 4.6 46.2 1.0 O A:HOH613 4.6 39.5 1.0 C A:ASN292 4.7 46.6 1.0 CA A:ASN293 4.7 34.7 1.0 OD2 A:ASP288 4.7 39.9 1.0 N A:ASN293 4.9 39.4 1.0

A.Torretta, L.C.Lopez-Cara, E.Parisini. Crystal Structure of the Apo and the Adp-Bound Form of Choline Kinase From Plasmodium Falciparum Crystals 2020.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST10070613