Calcium in PDB 6i4h: Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Ca-Atp State

The structure of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Ca-Atp State, PDB code: 6i4h 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)	43.75 / 1.40
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.870, 71.540, 110.600, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.3

The structure of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Ca-Atp State also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Ca-Atp State (pdb code 6i4h). 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 (F54Y Mutant) in the Ca-Atp State, PDB code: 6i4h:
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 (F54Y Mutant) in the Ca-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 (F54Y Mutant) in the Ca-Atp State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:15.3 occ:1.00 O1B A:ATP401 2.3 14.7 1.0 O2G A:ATP401 2.3 14.2 1.0 O A:HOH583 2.4 16.0 1.0 O A:HOH581 2.4 18.5 1.0 O A:HOH621 2.4 17.7 1.0 O A:HOH632 2.5 17.7 1.0 O A:HOH572 2.7 18.4 1.0 PG A:ATP401 3.5 15.0 1.0 HZ1 A:LYS19 3.5 27.3 1.0 PB A:ATP401 3.6 14.4 1.0 HA3 A:GLY14 3.9 18.8 1.0 HA2 A:GLY14 3.9 18.8 1.0 O3B A:ATP401 3.9 14.2 1.0 O3G A:ATP401 4.0 15.1 1.0 O A:HOH657 4.2 11.3 1.0 O3A A:ATP401 4.3 14.2 1.0 OE1 A:GLN138 4.3 16.8 1.0 O1A A:ATP401 4.4 17.0 1.0 CA A:GLY14 4.4 15.6 1.0 O A:HOH535 4.4 31.1 1.0 NZ A:LYS19 4.4 22.8 1.0 HA3 A:GLY157 4.4 17.0 1.0 HG21 A:VAL340 4.4 17.0 1.0 OD1 A:ASP155 4.6 22.7 1.0 OD2 A:ASP155 4.6 20.0 1.0 CD A:GLN138 4.6 15.6 1.0 O A:HOH633 4.6 22.2 1.0 O A:HOH584 4.6 25.7 1.0 OD1 A:ASP12 4.7 15.5 1.0 HZ2 A:LYS19 4.7 27.3 1.0 OD2 A:ASP12 4.7 14.9 1.0 PA A:ATP401 4.7 15.7 1.0 HZ3 A:LYS19 4.7 27.3 1.0 HG2 A:GLN138 4.8 18.6 1.0 H A:SER15 4.8 18.5 1.0 O1G A:ATP401 4.8 15.3 1.0 O2B A:ATP401 4.8 14.9 1.0 HB3 A:GLN138 4.9 17.0 1.0 NE2 A:GLN138 5.0 15.6 1.0 HE22 A:GLN138 5.0 18.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Ca-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 (F54Y Mutant) in the Ca-Atp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:15.1 occ:1.00 OD1 G:ASP42 2.3 16.3 1.0 O G:VAL121 2.4 16.4 1.0 O G:GLY41 2.4 16.0 1.0 O G:HOH394 2.4 17.9 1.0 O G:HOH385 2.4 17.6 1.0 OE2 G:GLU73 2.4 15.2 1.0 OE1 G:GLU73 2.5 15.9 1.0 CD G:GLU73 2.8 14.5 1.0 HA G:ASP42 3.3 16.5 1.0 C G:GLY41 3.4 15.3 1.0 CG G:ASP42 3.5 17.4 1.0 C G:VAL121 3.5 17.2 1.0 HG13 G:VAL121 3.7 23.6 1.0 HG12 G:VAL121 3.7 23.6 1.0 H G:VAL121 3.8 20.1 1.0 HA3 G:GLY120 3.8 21.6 1.0 N G:VAL121 3.9 16.8 1.0 HA G:CYS69 3.9 17.3 1.0 CA G:ASP42 4.0 13.7 1.0 H G:SER70 4.0 17.8 1.0 HA3 G:GLY41 4.1 18.1 1.0 N G:ASP42 4.1 13.8 1.0 CG1 G:VAL121 4.2 19.7 1.0 O G:HOH327 4.2 15.2 1.0 CA G:VAL121 4.3 16.7 1.0 C G:GLY120 4.3 17.2 1.0 CG G:GLU73 4.3 14.8 1.0 CB G:ASP42 4.4 13.4 1.0 CA G:GLY41 4.4 15.1 1.0 OD2 G:ASP42 4.4 15.7 1.0 O G:HOH361 4.4 26.7 1.0 HA G:SER123 4.5 19.7 0.7 HA G:SER123 4.5 20.1 0.3 C G:ALA122 4.5 16.6 1.0 CA G:GLY120 4.5 18.0 1.0 HA G:ALA122 4.6 20.9 1.0 N G:ALA122 4.6 17.1 1.0 OG G:SER70 4.6 17.8 1.0 HB2 G:CYS69 4.6 17.5 1.0 N G:SER123 4.6 14.8 0.7 N G:SER123 4.6 19.4 0.3 HG3 G:GLU73 4.7 17.8 1.0 HG2 G:GLU73 4.7 17.8 1.0 H G:SER123 4.7 17.7 0.7 H G:SER123 4.7 23.3 0.3 HA2 G:GLY41 4.7 18.1 1.0 O G:HOH359 4.7 21.2 0.4 O G:HOH438 4.8 29.5 1.0 N G:SER70 4.8 14.8 1.0 O G:ALA122 4.8 17.6 1.0 CA G:ALA122 4.8 17.4 1.0 HB3 G:ASP42 4.8 16.1 1.0 CA G:CYS69 4.9 14.4 1.0 O G:HOH359 4.9 30.4 0.6 CB G:VAL121 4.9 19.5 1.0 O G:HOH347 4.9 15.8 1.0 O G:GLY120 4.9 20.8 1.0 HG11 G:VAL121 5.0 23.6 1.0 H G:ASP42 5.0 16.6 1.0 HB3 G:SER123 5.0 25.1 0.3

Calcium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Ca-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 (F54Y Mutant) in the Ca-Atp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:19.4 occ:0.92 O G:HOH391 2.3 30.4 1.0 O G:ALA92 2.3 25.2 1.0 OD2 G:ASP85 2.4 22.1 1.0 O G:GLY90 2.4 25.9 1.0 OE1 A:GLU168 2.5 22.4 1.0 O G:HOH402 2.5 31.2 1.0 OD1 G:ASP85 2.9 19.7 1.0 CG G:ASP85 3.0 20.2 1.0 C G:GLY90 3.3 23.6 1.0 C G:ALA92 3.5 22.7 1.0 HA2 G:GLY90 3.5 28.7 1.0 CD A:GLU168 3.6 20.7 1.0 H G:ALA92 3.7 23.7 1.0 O A:HOH815 3.8 33.2 1.0 N G:ALA92 3.9 19.8 1.0 CA G:GLY90 3.9 23.9 1.0 HE21 G:GLN94 4.0 20.8 1.0 OE2 A:GLU168 4.1 19.4 1.0 HA G:VAL93 4.1 24.6 1.0 HG3 G:GLN94 4.1 18.9 1.0 HB3 A:GLU168 4.2 19.9 1.0 HA3 G:GLY90 4.2 28.7 1.0 CA G:ALA92 4.3 18.4 1.0 N G:ARG91 4.3 22.4 1.0 HB3 G:ALA92 4.3 25.6 1.0 O A:HOH610 4.3 30.3 1.0 C G:ARG91 4.3 20.4 1.0 CB G:ASP85 4.5 17.2 1.0 HA G:ARG91 4.5 28.8 1.0 O G:HOH432 4.6 64.4 1.0 N G:VAL93 4.6 21.4 1.0 O G:HOH450 4.6 56.7 1.0 O A:HOH755 4.6 32.1 1.0 CA G:ARG91 4.6 24.0 1.0 NE2 G:GLN94 4.7 17.3 1.0 HB3 G:ASP85 4.7 20.6 1.0 CG A:GLU168 4.8 17.1 1.0 HB2 A:GLU168 4.8 19.9 1.0 CB A:GLU168 4.8 16.6 1.0 CA G:VAL93 4.8 20.5 1.0 CB G:ALA92 4.8 21.3 1.0 HB2 G:ASP85 4.8 20.6 1.0 H G:GLN94 4.9 20.5 1.0 H G:ARG91 4.9 26.8 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