Magnesium in PDB 4z8n: Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A)

The structure of Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A), PDB code: 4z8n was solved by J.Gruszczyk, W.H.Tham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.84 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.790, 93.450, 126.720, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.9

The structure of Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A) (pdb code 4z8n). 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 Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A), PDB code: 4z8n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A)


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 Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:62.1 occ:1.00 N B:ASN246 3.3 57.8 1.0 CB B:GLU245 3.4 62.2 1.0 OD1 B:ASN246 3.4 70.2 1.0 N B:GLU245 3.5 50.3 1.0 C B:TYR243 3.6 44.9 1.0 CA B:TYR243 3.6 43.1 1.0 CG B:ASN246 3.7 65.8 1.0 O B:HOH621 3.7 50.4 1.0 CB B:TYR243 3.8 44.5 1.0 CA B:GLU245 3.8 58.1 1.0 O B:TYR243 3.9 46.8 1.0 N B:PRO244 4.0 43.1 1.0 CB B:ASN246 4.0 60.4 1.0 C B:GLU245 4.0 58.0 1.0 CD1 B:TYR243 4.1 46.8 1.0 ND2 B:ASN246 4.3 65.0 1.0 CA B:ASN246 4.3 58.4 1.0 CD B:PRO244 4.4 40.1 1.0 C B:PRO244 4.4 48.1 1.0 CG B:TYR243 4.4 47.2 1.0 OE1 B:GLU245 4.5 74.8 1.0 CG B:GLU245 4.8 68.0 1.0 CA B:PRO244 4.8 47.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A)


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 Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2A (PVRBP2A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:53.9 occ:1.00 CD2 B:HIS258 2.9 48.9 1.0 O B:SER359 3.0 39.3 1.0 CB B:SER359 3.6 46.9 1.0 C B:SER359 3.7 42.8 1.0 CA B:SER359 3.7 44.6 1.0 CE1 B:TYR254 3.7 40.9 1.0 NE2 B:HIS258 3.8 51.7 1.0 CG B:HIS258 4.0 47.7 1.0 CD1 B:TYR254 4.0 39.8 1.0 N B:PHE363 4.2 40.5 1.0 O B:HOH624 4.2 52.4 1.0 CB B:ASN362 4.2 37.5 1.0 OG B:SER359 4.3 53.2 1.0 CB B:PHE363 4.4 38.4 1.0 CB B:HIS258 4.5 43.6 1.0 CA B:PHE363 4.6 38.7 1.0 N B:ALA360 4.8 44.0 1.0 C B:ASN362 4.9 43.4 1.0 CZ B:TYR254 4.9 38.5 1.0 CE1 B:HIS258 5.0 49.0 1.0

J.Gruszczyk, N.T.Lim, A.Arnott, W.Q.He, W.Nguitragool, W.Roobsoong, Y.F.Mok, J.M.Murphy, K.R.Smith, S.Lee, M.Bahlo, I.Mueller, A.E.Barry, W.H.Tham. Structurally Conserved Erythrocyte-Binding Domain in Plasmodium Provides A Versatile Scaffold For Alternate Receptor Engagement. Proc.Natl.Acad.Sci.Usa V. 113 E191 2016.
ISSN: ESSN 1091-6490
PubMed: 26715754
DOI: 10.1073/PNAS.1516512113