Cadmium in PDB 5mvv: Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex

The structure of Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex, PDB code: 5mvv was solved by S.Panneerselvam, E.-P.Kumpula, I.Kursula, A.Burkhardt, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.55 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.420, 68.920, 71.550, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 15.9

The structure of Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex (pdb code 5mvv). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex, PDB code: 5mvv:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:11.1 occ:0.55 O1B A:ATP401 2.2 8.0 0.8 O1G A:ATP401 2.2 10.0 1.0 O A:HOH661 2.2 10.5 1.0 O A:HOH567 2.2 11.2 1.0 O A:HOH547 2.2 12.0 1.0 O A:HOH517 2.2 10.5 1.0 O3B A:ATP401 2.4 9.4 0.2 PB A:ATP401 3.3 8.8 0.8 PG A:ATP401 3.4 11.4 1.0 O2B A:ATP401 3.5 8.8 0.2 PB A:ATP401 3.6 9.8 0.2 O3B A:ATP401 3.7 10.4 0.8 O2A A:ATP401 3.9 10.8 0.2 O3A A:ATP401 4.0 8.2 0.8 O A:HOH579 4.0 16.0 1.0 CD A:CD405 4.0 12.3 0.2 O A:HOH543 4.0 21.4 1.0 O1A A:ATP401 4.1 11.1 0.8 O3G A:ATP401 4.2 12.8 1.0 O A:HOH592 4.2 18.0 0.9 OE1 A:GLN138 4.3 9.9 1.0 OD2 A:ASP155 4.3 11.4 0.5 OD1 A:ASP155 4.3 10.8 0.5 OD1 A:ASP155 4.4 14.1 0.5 OD2 A:ASP12 4.4 10.1 1.0 O3A A:ATP401 4.4 10.3 0.2 OD2 A:ASP155 4.4 12.0 0.5 NZ A:LYS19 4.5 16.0 1.0 OD1 A:ASP12 4.5 10.2 1.0 PA A:ATP401 4.5 11.4 0.8 PA A:ATP401 4.6 11.2 0.2 O2G A:ATP401 4.6 13.1 1.0 CD A:GLN138 4.6 9.1 1.0 O2B A:ATP401 4.6 9.6 0.8 CA A:GLY14 4.6 13.5 1.0 O A:HOH611 4.6 16.7 1.0 O1B A:ATP401 4.7 9.7 0.2 CG A:ASP155 4.8 10.5 0.5 CG A:ASP155 4.9 11.6 0.5 O1A A:ATP401 4.9 12.0 0.2 CG A:ASP12 4.9 10.0 1.0 CA A:GLY157 5.0 10.1 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:25.8 occ:0.41 O A:HOH614 2.5 62.8 1.0 O A:ALA322 2.6 16.1 1.0 O A:HOH766 2.8 40.7 1.0 O A:THR319 2.8 16.5 1.0 O A:THR320 3.0 19.1 1.0 OG A:SER324 3.2 16.2 0.7 C A:THR320 3.6 16.4 1.0 C A:ALA322 3.8 15.0 1.0 O A:HOH666 3.8 17.6 0.9 C A:THR319 3.9 15.7 1.0 CA A:THR320 4.0 17.4 1.0 N A:SER324 4.0 15.8 0.7 N A:SER324 4.0 16.2 0.3 CA A:SER324 4.3 16.0 0.7 CB A:SER324 4.3 15.4 0.7 CA A:SER324 4.3 17.2 0.3 C A:PRO323 4.3 15.5 1.0 N A:ALA322 4.3 14.8 1.0 O A:HOH505 4.4 22.7 0.8 N A:THR320 4.4 15.7 1.0 CB A:SER324 4.5 17.6 0.3 C A:LEU321 4.5 15.1 1.0 N A:LEU321 4.6 15.2 1.0 O A:HOH789 4.7 52.5 1.0 CA A:PRO323 4.7 17.2 1.0 CA A:ALA322 4.7 14.6 1.0 N A:PRO323 4.7 16.5 1.0 O A:PRO323 4.8 16.0 1.0 O A:LEU321 4.9 16.4 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Plasmodium Falciparum Actin I- Gelsolin Segment 1 -Cdatp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:12.3 occ:0.24 OD1 A:ASP155 2.7 10.8 0.5 O A:HOH569 2.8 18.3 1.0 O1G A:ATP401 2.8 10.0 1.0 O A:VAL160 2.9 11.9 1.0 OD1 A:ASP155 3.1 14.1 0.5 CG A:ASP155 3.3 10.5 0.5 O A:ASP155 3.3 9.7 0.5 N A:GLY157 3.4 10.0 1.0 O A:HOH517 3.5 10.5 1.0 O2G A:ATP401 3.5 13.1 1.0 CG A:ASP155 3.5 11.6 0.5 O A:HOH547 3.5 12.0 1.0 O A:HOH611 3.6 16.7 1.0 PG A:ATP401 3.6 11.4 1.0 OD2 A:ASP155 3.7 11.4 0.5 CG1 A:VAL160 3.7 13.6 1.0 C A:VAL160 3.8 10.3 1.0 O A:ASP155 3.9 11.2 0.5 OD2 A:ASP155 3.9 12.0 0.5 CA A:GLY157 3.9 10.1 1.0 C A:ASP155 3.9 9.9 0.5 CD A:CD403 4.0 11.1 0.6 C A:ASP155 4.1 10.1 0.5 C A:SER156 4.2 8.9 1.0 CB A:ASP155 4.2 10.5 0.5 CB A:ASP155 4.3 10.7 0.5 CA A:SER156 4.4 10.1 1.0 N A:SER156 4.4 9.8 1.0 CA A:SER161 4.6 10.6 1.0 O3G A:ATP401 4.6 12.8 1.0 N A:SER161 4.6 10.4 1.0 CA A:VAL160 4.7 12.0 1.0 CA A:ASP155 4.7 9.7 0.5 CA A:ASP155 4.7 9.6 0.5 N A:VAL160 4.7 12.6 1.0 O A:HOH628 4.8 11.7 1.0 O3B A:ATP401 4.8 10.4 0.8 CB A:VAL160 4.8 13.0 1.0 O2B A:ATP401 4.8 8.8 0.2 ND1 A:HIS162 4.8 12.9 1.0 OE1 A:GLN138 5.0 9.9 1.0

S.Panneerselvam, E.P.Kumpula, I.Kursula, A.Burkhardt, A.Meents. Rapid Cadmium Sad Phasing at the Standard Wavelength (1 Angstrom ). Acta Crystallogr D Struct V. 73 581 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28695858
DOI: 10.1107/S2059798317006970