Calcium in PDB 6i4d: Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State

The structure of Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State, PDB code: 6i4d was solved by E.-P.Kumpula, A.J.Lopez, L.Tajedin, H.Han, I.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.93 / 1.24
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.760, 71.450, 110.040, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15.5

The structure of Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State (pdb code 6i4d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State, PDB code: 6i4d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:17.0 occ:0.78 O G:HOH412 2.2 36.3 1.0 OD2 G:ASP85 2.4 17.6 1.0 O G:ALA92 2.4 21.4 1.0 O G:GLY90 2.6 20.6 1.0 OE1 A:GLU168 2.7 17.4 1.0 OD1 G:ASP85 3.0 15.4 1.0 CG G:ASP85 3.1 14.8 1.0 C G:GLY90 3.4 18.6 1.0 H G:ALA92 3.5 20.7 0.4 HA2 G:GLY90 3.6 22.0 1.0 C G:ALA92 3.6 18.1 1.0 O A:HOH682 3.7 26.8 1.0 CD A:GLU168 3.7 14.8 1.0 H G:ALA92 3.7 20.7 0.6 N G:ALA92 3.9 17.2 1.0 CA G:GLY90 4.0 18.3 1.0 HE21 G:GLN94 4.0 14.0 1.0 HA G:VAL93 4.1 18.5 1.0 O A:HOH771 4.1 22.2 0.5 OE2 A:GLU168 4.1 14.9 1.0 HG3 G:GLN94 4.1 13.5 1.0 O A:HOH644 4.2 28.8 1.0 N G:ARG91 4.3 18.4 0.4 N G:ARG91 4.3 18.2 0.6 HA3 G:GLY90 4.3 22.0 1.0 HB3 A:GLU168 4.3 13.5 1.0 C G:ARG91 4.3 18.0 0.6 CA G:ALA92 4.3 17.7 1.0 O G:HOH427 4.4 51.5 1.0 HB3 G:ALA92 4.4 21.1 1.0 HA G:ARG91 4.5 23.7 0.4 C G:ARG91 4.5 18.5 0.4 CB G:ASP85 4.5 13.0 1.0 N G:VAL93 4.6 16.1 1.0 HA G:ARG91 4.6 23.6 0.6 O G:HOH309 4.6 32.1 1.0 CA G:ARG91 4.6 19.7 0.6 CA G:ARG91 4.7 19.7 0.4 NE2 G:GLN94 4.7 11.6 1.0 CA G:VAL93 4.8 15.4 1.0 HB3 G:ASP85 4.8 15.6 1.0 CG A:GLU168 4.8 12.4 1.0 HB2 G:ASP85 4.9 15.6 1.0 O G:ARG91 4.9 17.5 0.6 CB A:GLU168 4.9 11.2 1.0 H G:GLN94 4.9 15.1 1.0 H G:ARG91 4.9 22.1 0.4 H G:ARG91 4.9 21.8 0.6 HB2 A:GLU168 4.9 13.5 1.0 O A:HOH771 4.9 19.7 0.5 CB G:ALA92 5.0 17.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Plasmodium Falciparum Actin I in the Mg-K-Atp/Adp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:9.6 occ:1.00 OD1 G:ASP42 2.3 10.8 1.0 O G:GLY41 2.4 9.9 1.0 O G:VAL121 2.4 11.0 1.0 O G:HOH394 2.4 12.0 1.0 O G:HOH410 2.4 12.9 1.0 OE2 G:GLU73 2.4 9.9 1.0 OE1 G:GLU73 2.5 9.7 1.0 CD G:GLU73 2.8 9.5 1.0 HA G:ASP42 3.3 10.2 1.0 C G:GLY41 3.4 9.1 1.0 CG G:ASP42 3.5 9.8 1.0 C G:VAL121 3.5 10.3 1.0 HG12 G:VAL121 3.6 14.4 1.0 HG13 G:VAL121 3.8 14.4 1.0 H G:VAL121 3.8 13.8 1.0 HA3 G:GLY120 3.8 16.1 1.0 N G:VAL121 3.9 11.5 1.0 HA G:CYS69 3.9 11.7 1.0 CA G:ASP42 4.0 8.5 1.0 H G:SER70 4.0 11.5 1.0 N G:ASP42 4.1 9.1 1.0 HA3 G:GLY41 4.1 11.2 1.0 CG1 G:VAL121 4.1 12.0 1.0 O G:HOH344 4.2 10.0 1.0 CA G:VAL121 4.3 11.1 1.0 CB G:ASP42 4.3 8.9 1.0 C G:GLY120 4.3 12.3 1.0 CG G:GLU73 4.3 8.9 1.0 CA G:GLY41 4.4 9.3 1.0 OD2 G:ASP42 4.4 9.9 1.0 O G:HOH349 4.4 19.3 1.0 C G:ALA122 4.5 11.2 1.0 HA G:SER123 4.5 13.6 0.2 HA G:SER123 4.5 13.0 0.8 N G:SER123 4.5 11.5 0.8 HA G:ALA122 4.6 13.5 1.0 N G:SER123 4.6 11.4 0.2 HB2 G:CYS69 4.6 12.0 1.0 CA G:GLY120 4.6 13.4 1.0 OG G:SER70 4.6 11.9 1.0 N G:ALA122 4.6 11.3 1.0 H G:SER123 4.6 13.8 0.8 H G:SER123 4.6 13.7 0.2 O G:HOH442 4.7 16.0 0.3 HG3 G:GLU73 4.7 10.7 1.0 HA2 G:GLY41 4.7 11.2 1.0 HG2 G:GLU73 4.7 10.7 1.0 O G:HOH441 4.7 15.7 0.6 O G:HOH441 4.8 22.4 0.4 HB3 G:ASP42 4.8 10.8 1.0 CA G:ALA122 4.8 11.3 1.0 N G:SER70 4.8 9.6 1.0 O G:ALA122 4.8 10.7 1.0 CA G:CYS69 4.8 9.7 1.0 CB G:VAL121 4.9 12.2 1.0 O G:HOH442 4.9 17.9 0.7 HG11 G:VAL121 4.9 14.4 1.0 O G:HOH356 4.9 10.5 1.0 H G:ASP42 5.0 10.9 1.0 HB3 G:SER123 5.0 13.9 0.2 O G:HOH407 5.0 22.1 0.3 O G:GLY120 5.0 14.5 1.0

E.P.Kumpula, A.J.Lopez, L.Tajedin, H.Han, I.Kursula. Atomic View Into Plasmodium Actin Polymerization, Atp Hydrolysis, and Fragmentation. Plos Biol. V. 17 00315 2019.
ISSN: ESSN 1545-7885
PubMed: 31199804
DOI: 10.1371/JOURNAL.PBIO.3000315