Calcium in PDB 6i4e: Crystal Structure of Plasmodium Falciparum Actin I in the Mg-Adp State

The structure of Crystal Structure of Plasmodium Falciparum Actin I in the Mg-Adp State, PDB code: 6i4e 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)	49.39 / 1.22
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.520, 71.270, 109.980, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 15.7

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

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-Adp State (pdb code 6i4e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-Adp State, PDB code: 6i4e:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-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-Adp State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:18.2 occ:0.74 O A:ALA322 2.6 14.6 1.0 O A:HOH692 2.7 18.3 0.5 O A:HOH762 2.8 36.1 1.0 HG A:SER324 2.8 25.2 1.0 O A:THR319 2.8 16.5 1.0 O A:THR320 2.9 18.6 1.0 O A:HOH692 3.0 25.9 0.5 OG A:SER324 3.2 21.0 1.0 HA A:THR320 3.4 21.7 1.0 C A:THR320 3.6 17.0 1.0 HA A:SER324 3.7 21.1 1.0 C A:ALA322 3.8 14.2 1.0 O A:HOH655 3.8 19.0 1.0 C A:THR319 3.9 15.6 1.0 CA A:THR320 3.9 18.1 1.0 N A:SER324 4.1 15.4 1.0 H A:SER324 4.2 18.5 1.0 CA A:SER324 4.2 17.6 1.0 CB A:SER324 4.3 18.3 1.0 H A:ALA322 4.3 17.7 1.0 N A:ALA322 4.3 14.8 1.0 C A:PRO323 4.3 15.4 1.0 N A:THR320 4.4 15.3 1.0 HG22 A:THR319 4.5 19.6 1.0 HA A:PRO323 4.5 19.5 1.0 C A:LEU321 4.5 15.2 1.0 N A:LEU321 4.5 15.4 1.0 CA A:ALA322 4.7 15.5 1.0 CA A:PRO323 4.7 16.2 1.0 O A:PRO323 4.7 16.1 1.0 N A:PRO323 4.7 15.0 1.0 O A:LEU321 4.8 17.9 1.0 HB3 A:SER324 4.8 21.9 1.0 HB2 A:SER324 4.9 21.9 1.0 HB3 A:ALA322 4.9 18.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-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-Adp State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:24.1 occ:0.57 O G:ALA92 2.3 25.7 0.5 OD2 G:ASP85 2.6 21.9 0.7 OE1 A:GLU168 2.7 22.7 1.0 O G:GLY90 2.8 28.0 1.0 O G:ALA92 2.8 22.5 0.5 OD1 G:ASP85 3.2 19.7 0.7 CG G:ASP85 3.3 19.9 0.7 C G:GLY90 3.5 27.1 1.0 C G:ALA92 3.6 24.8 0.5 O A:HOH574 3.6 28.9 0.7 HA2 G:GLY90 3.6 32.9 1.0 C G:ALA92 3.7 23.1 0.5 CD A:GLU168 3.7 21.4 1.0 H G:ALA92 3.7 27.4 0.5 N G:ALA92 3.9 22.8 0.5 N G:ALA92 4.0 26.4 0.5 HA G:VAL93 4.1 27.3 1.0 CA G:GLY90 4.1 27.4 1.0 HE21 G:GLN94 4.1 20.7 1.0 OE2 A:GLU168 4.2 22.5 1.0 HG3 G:GLN94 4.2 19.8 1.0 O A:HOH613 4.3 46.9 1.0 HA3 G:GLY90 4.3 32.9 1.0 CA G:ALA92 4.3 25.8 0.5 C G:ARG91 4.4 24.3 0.5 N G:ARG91 4.4 26.5 0.5 HB3 A:GLU168 4.4 20.0 1.0 HH A:TYR170 4.4 25.8 0.2 N G:ARG91 4.4 28.3 0.5 HB3 G:ALA92 4.4 30.6 0.5 O G:HOH335 4.5 46.3 1.0 CA G:ALA92 4.5 23.1 0.5 N G:VAL93 4.6 23.0 1.0 C G:ARG91 4.6 28.2 0.5 HA G:ARG91 4.6 35.5 0.5 HA G:ARG91 4.7 31.8 0.5 CB G:ASP85 4.7 19.1 1.0 NE2 G:GLN94 4.7 17.3 1.0 CA G:ARG91 4.7 26.5 0.5 CA G:VAL93 4.8 22.8 1.0 HB3 G:ALA92 4.8 27.4 0.5 CA G:ARG91 4.8 29.6 0.5 CG A:GLU168 4.9 18.8 1.0 HB2 A:GLU168 4.9 20.0 1.0 H G:GLN94 4.9 22.1 1.0 O G:ARG91 4.9 23.9 0.5 CB A:GLU168 4.9 16.7 1.0 CB G:ALA92 5.0 25.5 0.5 H G:ARG91 5.0 31.9 0.5 HE1 A:TYR170 5.0 23.7 0.2 HB3 G:ASP85 5.0 22.9 1.0 HB2 G:ASP85 5.0 22.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I in the Mg-Adp State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Plasmodium Falciparum Actin I in the Mg-Adp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:13.8 occ:1.00 OD1 G:ASP42 2.3 15.4 1.0 O G:GLY41 2.3 12.9 1.0 O G:VAL121 2.3 15.5 1.0 O G:HOH387 2.4 17.6 1.0 OE2 G:GLU73 2.4 14.7 1.0 O G:HOH390 2.4 17.6 1.0 OE1 G:GLU73 2.6 14.4 1.0 CD G:GLU73 2.8 13.1 1.0 HA G:ASP42 3.3 14.3 1.0 C G:GLY41 3.4 12.3 1.0 C G:VAL121 3.5 16.6 1.0 CG G:ASP42 3.5 13.6 1.0 HG12 G:VAL121 3.7 20.7 1.0 HG13 G:VAL121 3.8 20.7 1.0 H G:VAL121 3.8 19.3 1.0 HA3 G:GLY120 3.9 22.8 1.0 HA G:CYS69 3.9 17.0 1.0 N G:VAL121 3.9 16.1 1.0 CA G:ASP42 4.0 11.9 1.0 H G:SER70 4.1 14.7 1.0 HA3 G:GLY41 4.1 16.1 1.0 N G:ASP42 4.1 11.8 1.0 CG1 G:VAL121 4.2 17.2 1.0 O G:HOH333 4.2 13.9 1.0 CA G:VAL121 4.3 17.4 1.0 CA G:GLY41 4.3 13.4 1.0 CG G:GLU73 4.3 12.2 1.0 CB G:ASP42 4.3 12.0 1.0 C G:GLY120 4.4 17.7 1.0 OD2 G:ASP42 4.4 14.1 1.0 O G:HOH316 4.4 25.1 1.0 HA G:ALA122 4.5 22.1 1.0 C G:ALA122 4.5 17.3 1.0 N G:ALA122 4.5 16.8 1.0 N G:SER123 4.5 16.8 1.0 CA G:GLY120 4.6 19.0 1.0 HA G:SER123 4.6 21.8 1.0 H G:SER123 4.6 20.2 1.0 HB2 G:CYS69 4.6 16.1 1.0 OG G:SER70 4.6 17.9 1.0 HA2 G:GLY41 4.6 16.1 1.0 O G:HOH386 4.7 28.9 0.5 HG3 G:GLU73 4.7 14.7 1.0 O G:HOH389 4.7 29.3 1.0 HG2 G:GLU73 4.7 14.7 1.0 O G:HOH410 4.7 13.1 0.2 CA G:ALA122 4.7 18.4 1.0 O G:HOH410 4.8 40.3 0.8 HB3 G:ASP42 4.8 14.4 1.0 N G:SER70 4.8 12.2 1.0 O G:ALA122 4.8 17.4 1.0 CA G:CYS69 4.8 14.2 1.0 CB G:VAL121 4.9 18.7 1.0 H G:ASP42 4.9 14.2 1.0 O G:HOH360 5.0 16.2 1.0 HG11 G:VAL121 5.0 20.7 1.0 O G:GLY120 5.0 20.6 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