Calcium in PDB 6i4g: Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State

The structure of Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State, PDB code: 6i4g 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)	48.80 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.610, 110.620, 138.830, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.7

The structure of Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State (pdb code 6i4g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State, PDB code: 6i4g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp 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 (H74Q) in the Mg-K- Atp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:34.0 occ:1.00 O G:HOH348 2.4 27.2 1.0 O G:GLY41 2.4 26.7 1.0 O G:VAL121 2.5 29.7 1.0 OD1 G:ASP42 2.5 36.1 1.0 OE1 G:GLU73 2.5 27.2 1.0 OE2 G:GLU73 2.6 26.9 1.0 O G:HOH344 2.7 48.5 1.0 CD G:GLU73 2.9 26.6 1.0 HA G:ASP42 3.2 32.1 1.0 C G:GLY41 3.5 26.8 1.0 C G:VAL121 3.6 29.6 1.0 HG13 G:VAL121 3.7 43.9 1.0 H G:VAL121 3.7 35.9 1.0 HG12 G:VAL121 3.7 43.9 1.0 CG G:ASP42 3.7 35.2 1.0 HA G:CYS69 3.9 30.6 1.0 N G:VAL121 3.9 29.8 1.0 HA3 G:GLY120 4.0 37.4 1.0 CA G:ASP42 4.0 27.1 1.0 O G:HOH316 4.1 23.1 1.0 H G:SER70 4.1 38.8 1.0 N G:ASP42 4.1 26.9 1.0 CG1 G:VAL121 4.1 36.5 1.0 HA3 G:GLY41 4.2 36.4 1.0 CA G:VAL121 4.3 34.8 1.0 CG G:GLU73 4.4 25.6 1.0 CB G:ASP42 4.4 29.1 1.0 C G:GLY120 4.4 31.6 1.0 CA G:GLY41 4.5 30.2 1.0 HA G:SER123 4.5 39.3 0.4 HA G:SER123 4.5 39.2 0.6 HA G:ALA122 4.5 32.4 1.0 HB2 G:CYS69 4.6 34.4 1.0 C G:ALA122 4.6 30.1 1.0 OD2 G:ASP42 4.7 34.5 1.0 N G:ALA122 4.7 26.8 1.0 CA G:GLY120 4.7 31.1 1.0 HG3 G:GLU73 4.7 30.4 1.0 OG G:SER70 4.7 31.0 1.0 N G:SER123 4.8 30.0 1.0 O G:HOH306 4.8 25.2 1.0 HB3 G:ASP42 4.8 35.0 1.0 O G:ALA122 4.8 30.5 1.0 HA2 G:GLY41 4.8 36.4 1.0 HG2 G:GLU73 4.8 30.4 1.0 CA G:CYS69 4.8 25.4 1.0 O G:HOH335 4.9 43.3 1.0 CA G:ALA122 4.9 26.9 1.0 HB2 G:SER123 4.9 42.3 0.4 N G:SER70 4.9 32.3 1.0 HB3 G:SER123 4.9 42.6 0.6 HG11 G:VAL121 4.9 43.9 1.0 CB G:VAL121 4.9 38.8 1.0 H G:ASP42 5.0 31.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp 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 (H74Q) in the Mg-K- Atp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:52.0 occ:1.00 OD2 G:ASP85 2.4 34.9 1.0 O G:ALA92 2.5 38.0 1.0 O G:HOH327 2.5 72.0 1.0 OE1 B:GLU168 2.6 46.8 1.0 O G:GLY90 2.6 42.0 1.0 OD1 G:ASP85 3.1 35.8 1.0 CG G:ASP85 3.1 30.6 1.0 C G:GLY90 3.3 39.6 1.0 HA2 G:GLY90 3.4 48.7 1.0 H G:ALA92 3.5 42.9 1.0 C G:ALA92 3.6 38.6 1.0 CD B:GLU168 3.7 45.1 1.0 N G:ALA92 3.8 35.7 1.0 CA G:GLY90 3.8 40.5 1.0 HE21 G:GLN94 4.1 40.1 1.0 HA3 G:GLY90 4.1 48.7 1.0 OE2 B:GLU168 4.2 43.0 1.0 N G:ARG91 4.2 35.1 1.0 CA G:ALA92 4.3 37.7 1.0 HA G:VAL93 4.3 41.1 1.0 HG3 G:GLN94 4.4 36.6 1.0 C G:ARG91 4.4 38.8 1.0 HB3 B:GLU168 4.4 31.2 1.0 HB3 G:ALA92 4.5 39.4 1.0 CB G:ASP85 4.6 26.6 1.0 HA G:ARG91 4.7 44.6 1.0 CA G:ARG91 4.7 37.1 1.0 N G:VAL93 4.7 35.6 1.0 NE2 G:GLN94 4.7 33.4 1.0 HB3 G:ASP85 4.8 32.0 1.0 H G:ARG91 4.8 41.8 1.0 HB2 B:GLU168 4.9 31.2 1.0 CG B:GLU168 4.9 36.7 1.0 HB2 G:ASP85 5.0 32.0 1.0 CB G:ALA92 5.0 33.1 1.0 CB B:GLU168 5.0 26.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp 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 (H74Q) in the Mg-K- Atp State within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca201 b:25.0 occ:1.00 O H:HOH342 2.3 25.4 1.0 O H:VAL121 2.3 39.0 1.0 O H:GLY41 2.4 25.5 1.0 OD1 H:ASP42 2.4 32.4 1.0 O H:HOH340 2.5 33.1 1.0 OE2 H:GLU73 2.5 24.8 1.0 OE1 H:GLU73 2.7 24.8 1.0 CD H:GLU73 2.9 25.0 1.0 HA H:ASP42 3.3 27.2 1.0 C H:GLY41 3.4 24.0 1.0 C H:VAL121 3.5 37.8 1.0 HG13 H:VAL121 3.6 48.0 1.0 CG H:ASP42 3.6 32.0 1.0 H H:VAL121 3.7 44.8 1.0 N H:VAL121 3.8 37.6 1.0 HA3 H:GLY120 3.8 44.5 1.0 HA H:CYS69 3.9 32.7 1.0 HG12 H:VAL121 4.0 48.0 1.0 CA H:ASP42 4.0 22.7 1.0 HA3 H:GLY41 4.1 36.0 1.0 N H:ASP42 4.1 22.9 1.0 H H:SER70 4.1 32.0 1.0 CG1 H:VAL121 4.2 40.2 1.0 O H:HOH314 4.2 22.6 1.0 CA H:VAL121 4.2 37.3 1.0 C H:GLY120 4.3 36.6 1.0 CA H:GLY41 4.3 30.0 1.0 HA H:ALA122 4.4 44.5 1.0 CB H:ASP42 4.4 28.3 1.0 CG H:GLU73 4.5 25.5 1.0 OD2 H:ASP42 4.5 34.7 1.0 O H:HOH329 4.5 32.7 1.0 N H:ALA122 4.5 36.9 1.0 CA H:GLY120 4.6 37.3 1.0 C H:ALA122 4.6 39.0 1.0 HA H:SER123 4.6 49.3 0.6 HA H:SER123 4.6 49.3 0.4 OG H:SER70 4.7 32.5 1.0 HB2 H:CYS69 4.7 37.0 1.0 HA2 H:GLY41 4.7 36.0 1.0 CA H:ALA122 4.7 37.4 1.0 N H:SER123 4.7 39.7 1.0 O H:HOH306 4.8 30.1 1.0 HG3 H:GLU73 4.8 30.2 1.0 O H:ALA122 4.8 39.6 1.0 HG2 H:GLU73 4.8 30.2 1.0 HB3 H:ASP42 4.9 34.1 1.0 CA H:CYS69 4.9 27.2 1.0 CB H:VAL121 4.9 38.4 1.0 N H:SER70 4.9 27.0 1.0 HB3 H:SER123 4.9 50.3 0.6 H H:ASP42 4.9 27.5 1.0 HB2 H:SER123 5.0 50.3 0.4 H H:SER123 5.0 47.4 0.4 H H:SER123 5.0 47.4 0.6 O H:GLY120 5.0 35.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Plasmodium Falciparum Actin I (H74Q) in the Mg-K- Atp State within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca202 b:46.0 occ:1.00 O H:ALA92 2.4 37.0 1.0 OD2 H:ASP85 2.4 38.5 1.0 OE1 A:GLU168 2.5 36.3 1.0 O A:HOH608 2.5 36.0 1.0 O H:GLY90 2.8 35.5 1.0 CG H:ASP85 3.1 33.6 1.0 OD1 H:ASP85 3.1 38.8 1.0 C H:GLY90 3.5 31.8 1.0 C H:ALA92 3.6 34.9 1.0 HA2 H:GLY90 3.6 40.0 1.0 CD A:GLU168 3.6 38.1 1.0 H H:ALA92 3.7 42.3 1.0 N H:ALA92 3.9 35.2 1.0 CA H:GLY90 4.1 33.3 1.0 OE2 A:GLU168 4.1 35.5 1.0 HA H:VAL93 4.1 43.6 1.0 HE21 H:GLN94 4.2 33.4 1.0 HA3 H:GLY90 4.3 40.0 1.0 HG3 H:GLN94 4.3 34.3 1.0 CA H:ALA92 4.3 34.0 1.0 HB3 A:GLU168 4.4 35.1 1.0 N H:ARG91 4.5 30.4 1.0 C H:ARG91 4.5 38.1 1.0 HB3 H:ALA92 4.5 37.2 1.0 N H:VAL93 4.6 34.8 1.0 CB H:ASP85 4.6 26.3 1.0 HA H:ARG91 4.8 43.9 1.0 CA H:VAL93 4.8 36.3 1.0 NE2 H:GLN94 4.8 27.7 1.0 HB3 H:ASP85 4.8 31.6 1.0 CA H:ARG91 4.9 36.5 1.0 CG A:GLU168 4.9 29.8 1.0 HB2 A:GLU168 4.9 35.1 1.0 CB A:GLU168 4.9 29.6 1.0 HB2 H:ASP85 4.9 31.6 1.0 CB H:ALA92 5.0 30.9 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