Atomistry » Cadmium » PDB 5gu2-5qrf » 5mvv
Atomistry »
  Cadmium »
    PDB 5gu2-5qrf »
      5mvv »

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

Protein crystallography data

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

Other elements in 5mvv:

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

Cadmium Binding Sites:

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 5mvv

Go back to Cadmium Binding Sites List in 5mvv
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 5mvv

Go back to Cadmium Binding Sites List in 5mvv
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 5mvv

Go back to Cadmium Binding Sites List in 5mvv
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

Reference:

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
Page generated: Sat Dec 12 08:27:10 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy