Magnesium in PDB 4f1j: Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein

The structure of Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein, PDB code: 4f1j was solved by T.Pihlajamaa, J.Knuuti, T.Kajander, A.Sharma, P.Permi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.73
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.313, 89.313, 104.192, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

The structure of Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein (pdb code 4f1j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein, PDB code: 4f1j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein


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 MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:11.3 occ:1.00 O A:HOH412 2.0 9.7 1.0 O A:HOH409 2.0 9.8 1.0 OD1 A:ASP162 2.1 6.8 1.0 OG A:SER58 2.1 12.2 1.0 O A:HOH415 2.1 8.6 1.0 OG A:SER56 2.2 10.8 1.0 CG A:ASP162 3.0 10.4 1.0 CB A:SER58 3.2 12.3 1.0 CB A:SER56 3.2 10.5 1.0 OD2 A:ASP162 3.4 11.1 1.0 OG1 A:THR131 3.9 11.2 1.0 O A:ASP162 4.0 10.4 1.0 C A:ASP162 4.0 9.9 1.0 OD2 A:ASP54 4.0 8.2 1.0 OD1 A:ASP54 4.1 10.6 1.0 O A:HOH524 4.1 28.3 1.0 N A:GLY163 4.1 9.7 1.0 CA A:GLY163 4.2 9.8 1.0 O A:HOH420 4.2 13.0 1.0 CA A:SER58 4.4 11.9 1.0 CB A:ASP162 4.4 9.3 1.0 N A:SER58 4.4 12.6 1.0 CG A:ASP54 4.5 9.4 1.0 O A:HOH575 4.5 25.5 1.0 CA A:SER56 4.5 9.7 1.0 CA A:ASP162 4.7 9.1 1.0 C A:SER56 4.8 10.6 1.0 N A:ILE59 4.8 10.9 1.0 C A:SER58 4.9 11.8 1.0 O A:SER56 4.9 10.3 1.0 N A:ASP162 4.9 8.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein


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 MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:15.5 occ:0.50 O A:HOH588 2.0 37.9 1.0 O A:HOH423 2.0 17.5 1.0 OD2 A:ASP170 2.1 17.3 0.5 O A:HOH587 2.1 25.2 1.0 OG A:SER134 2.1 11.5 1.0 O A:HOH458 2.2 25.6 1.0 CB A:SER134 3.1 9.6 1.0 CG A:ASP170 3.1 18.7 0.5 OD2 A:ASP170 3.2 21.6 0.5 CB A:ASP170 3.5 18.0 0.5 CB A:ASP170 3.6 17.7 0.5 CG A:ASP170 3.8 19.6 0.5 O A:HOH454 3.9 21.9 1.0 O A:HOH445 4.1 15.7 1.0 OD1 A:ASN132 4.2 9.6 1.0 OD1 A:ASP170 4.2 20.6 0.5 CA A:SER134 4.2 8.9 1.0 C A:SER134 4.3 8.7 1.0 N A:ASP135 4.4 8.3 1.0 O A:HOH450 4.5 23.6 1.0 O A:HOH578 4.6 38.9 1.0 O A:HOH426 4.8 22.0 1.0 O A:SER134 4.9 8.4 1.0 CL A:CL314 4.9 11.1 1.0 OD1 A:ASP170 4.9 22.8 0.5 CA A:ASP170 4.9 17.8 0.5 CA A:ASP170 5.0 17.6 0.5

Magnesium binding site 3 out of 4 in the Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein


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 the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:11.0 occ:1.00 O B:HOH425 2.0 11.0 1.0 OG B:SER58 2.0 13.1 1.0 OD1 B:ASP162 2.1 9.4 1.0 O B:HOH426 2.1 9.6 1.0 O B:HOH435 2.1 10.3 1.0 OG B:SER56 2.2 11.9 1.0 CG B:ASP162 3.0 9.1 1.0 CB B:SER58 3.1 12.8 1.0 CB B:SER56 3.2 10.5 1.0 OD2 B:ASP162 3.4 11.9 1.0 OG1 B:THR131 4.0 13.1 1.0 OD1 B:ASP54 4.1 8.9 1.0 OD2 B:ASP54 4.1 9.1 1.0 C B:ASP162 4.1 10.1 1.0 O B:HOH522 4.1 24.1 1.0 O B:HOH436 4.2 14.4 1.0 O B:ASP162 4.2 11.4 1.0 N B:GLY163 4.2 9.8 1.0 CA B:GLY163 4.2 10.7 1.0 CA B:SER58 4.3 12.4 1.0 N B:SER58 4.4 12.8 1.0 CB B:ASP162 4.4 8.3 1.0 O B:HOH537 4.4 20.7 1.0 CA B:SER56 4.5 10.0 1.0 CG B:ASP54 4.5 9.5 1.0 C B:SER56 4.7 10.7 1.0 CA B:ASP162 4.7 9.2 1.0 N B:ILE59 4.8 12.5 1.0 C B:SER58 4.8 12.6 1.0 O B:SER56 4.8 10.2 1.0 CG1 B:ILE59 4.9 13.1 1.0 N B:ASP162 5.0 9.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the MG2+ Loaded Vwa Domain of Plasmodium Falciparum Trap Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:15.7 occ:0.50 O B:HOH595 1.9 25.8 1.0 O B:HOH509 2.0 21.0 1.0 O B:HOH479 2.1 18.1 1.0 O B:HOH594 2.1 33.2 1.0 OD2 B:ASP170 2.1 18.6 0.5 OG B:SER134 2.2 10.8 1.0 CG B:ASP170 3.2 17.8 0.5 OD2 B:ASP170 3.2 19.4 0.5 CB B:SER134 3.2 9.7 1.0 CB B:ASP170 3.6 17.1 0.5 CB B:ASP170 3.7 17.1 0.5 CG B:ASP170 3.8 17.6 0.5 O B:HOH459 3.9 20.9 1.0 O B:HOH455 3.9 16.3 1.0 OD1 B:ASN132 4.1 12.3 1.0 OD1 B:ASP170 4.3 18.9 0.5 C B:SER134 4.4 8.7 1.0 CA B:SER134 4.4 8.8 1.0 N B:ASP135 4.4 8.6 1.0 O B:HOH444 4.4 21.6 1.0 O B:HOH511 4.5 29.1 1.0 O B:SER134 4.9 8.6 1.0 OD1 B:ASP170 5.0 16.2 0.5 CL B:CL311 5.0 11.4 1.0

T.Pihlajamaa, T.Kajander, J.Knuuti, K.Horkka, A.Sharma, P.Permi. Structure of Plasmodium Falciparum Trap (Thrombospondin-Related Anonymous Protein) A Domain Highlights Distinct Features in Apicomplexan Von Willebrand Factor A Homologues. Biochem.J. V. 450 469 2013.
ISSN: ISSN 0264-6021
PubMed: 23317521
DOI: 10.1042/BJ20121058