Calcium in PDB 6i4k: Crystal Structure of Plasmodium Falciparum Actin I (G115A Mutant) in the Ca-Atp State

The structure of Crystal Structure of Plasmodium Falciparum Actin I (G115A Mutant) in the Ca-Atp State, PDB code: 6i4k 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)	43.80 / 1.83
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	69.830, 71.380, 110.930, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.7

The structure of Crystal Structure of Plasmodium Falciparum Actin I (G115A 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 (G115A Mutant) in the Ca-Atp State (pdb code 6i4k). 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 (G115A Mutant) in the Ca-Atp State, PDB code: 6i4k:
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 (G115A 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 (G115A Mutant) in the Ca-Atp State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.5 occ:1.00 O1B A:ATP401 2.3 17.1 1.0 O2G A:ATP401 2.3 15.8 1.0 O A:HOH600 2.4 15.3 1.0 O A:HOH641 2.4 18.2 1.0 O A:HOH602 2.4 15.6 1.0 O A:HOH569 2.5 17.4 1.0 O A:HOH557 2.8 16.4 1.0 PG A:ATP401 3.5 17.0 1.0 PB A:ATP401 3.5 14.9 1.0 HZ3 A:LYS19 3.6 38.3 1.0 O3B A:ATP401 3.9 16.2 1.0 HA2 A:GLY14 3.9 22.2 1.0 O3G A:ATP401 3.9 17.3 1.0 HA3 A:GLY14 4.1 22.2 1.0 O A:HOH626 4.1 15.4 1.0 O3A A:ATP401 4.2 16.6 1.0 OE1 A:GLN138 4.3 16.0 1.0 O1A A:ATP401 4.3 19.0 1.0 HA3 A:GLY157 4.3 18.4 1.0 O A:HOH550 4.4 27.3 1.0 HG21 A:VAL340 4.5 20.3 1.0 CA A:GLY14 4.5 18.5 1.0 O A:HOH584 4.5 29.7 0.6 NZ A:LYS19 4.5 31.9 1.0 CD A:GLN138 4.5 15.9 1.0 OD2 A:ASP155 4.6 23.8 1.0 O A:HOH649 4.6 26.5 1.0 OD1 A:ASP155 4.6 26.0 1.0 HG2 A:GLN138 4.6 18.1 1.0 OD1 A:ASP12 4.7 17.4 1.0 HZ1 A:LYS19 4.7 38.3 1.0 OD2 A:ASP12 4.7 17.6 1.0 O1G A:ATP401 4.8 14.6 1.0 PA A:ATP401 4.8 18.8 1.0 H A:SER15 4.8 22.2 1.0 HB3 A:GLN138 4.8 17.9 1.0 O2B A:ATP401 4.8 15.1 1.0 NE2 A:GLN138 4.9 15.8 1.0 HZ2 A:LYS19 4.9 38.3 1.0 HE22 A:GLN138 4.9 18.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (G115A 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 (G115A Mutant) in the Ca-Atp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:11.9 occ:1.00 O G:GLY41 2.3 14.1 1.0 O G:VAL121 2.3 16.3 1.0 OD1 G:ASP42 2.3 17.4 1.0 O G:HOH363 2.3 15.7 1.0 OE2 G:GLU73 2.4 16.4 1.0 O G:HOH386 2.4 14.8 1.0 OE1 G:GLU73 2.4 17.7 1.0 CD G:GLU73 2.8 17.0 1.0 HA G:ASP42 3.2 21.7 1.0 C G:GLY41 3.3 15.1 1.0 C G:VAL121 3.5 17.6 1.0 CG G:ASP42 3.6 18.4 1.0 HG13 G:VAL121 3.6 25.2 1.0 H G:VAL121 3.7 19.1 1.0 HA G:CYS69 3.8 19.5 1.0 HA3 G:GLY120 3.8 20.4 1.0 N G:VAL121 3.9 16.0 1.0 HG12 G:VAL121 3.9 25.2 1.0 CA G:ASP42 3.9 18.0 1.0 H G:SER70 4.0 18.0 1.0 N G:ASP42 4.1 15.7 1.0 HA3 G:GLY41 4.1 18.7 1.0 CG1 G:VAL121 4.2 21.0 1.0 O G:HOH336 4.2 14.4 1.0 CA G:VAL121 4.3 17.8 1.0 O G:HOH346 4.3 30.6 1.0 CG G:GLU73 4.3 16.2 1.0 CB G:ASP42 4.3 18.3 1.0 CA G:GLY41 4.3 15.5 1.0 C G:GLY120 4.4 18.1 1.0 HA G:ALA122 4.4 25.1 1.0 OD2 G:ASP42 4.5 19.5 1.0 OG G:SER70 4.5 22.2 1.0 HB2 G:CYS69 4.5 20.9 1.0 N G:ALA122 4.6 20.7 1.0 CA G:GLY120 4.6 17.0 1.0 O G:HOH367 4.6 16.8 1.0 O G:HOH403 4.6 32.9 1.0 C G:ALA122 4.6 19.8 1.0 N G:SER123 4.6 18.5 1.0 HG3 G:GLU73 4.7 19.4 1.0 H G:SER123 4.7 22.3 1.0 HA2 G:GLY41 4.7 18.7 1.0 HG2 G:GLU73 4.7 19.4 1.0 HA G:SER123 4.7 20.9 1.0 CA G:CYS69 4.8 16.2 1.0 CA G:ALA122 4.8 20.9 1.0 HB3 G:ASP42 4.8 22.0 1.0 N G:SER70 4.8 15.0 1.0 O G:HOH340 4.8 16.7 1.0 HG G:SER70 4.9 26.7 1.0 CB G:VAL121 4.9 21.7 1.0 H G:ASP42 4.9 18.9 1.0 O G:ALA122 5.0 19.6 1.0 HG11 G:VAL121 5.0 25.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (G115A 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 (G115A Mutant) in the Ca-Atp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:19.5 occ:0.72 OD2 G:ASP85 2.3 23.1 1.0 O G:HOH378 2.3 41.7 1.0 O G:HOH374 2.3 33.0 1.0 O G:ALA92 2.3 28.2 1.0 O G:GLY90 2.5 31.3 1.0 OE1 A:GLU168 2.5 23.8 1.0 OD1 G:ASP85 2.9 21.8 1.0 CG G:ASP85 2.9 21.9 1.0 C G:GLY90 3.4 30.1 1.0 HA2 G:GLY90 3.4 34.0 1.0 C G:ALA92 3.5 24.1 1.0 CD A:GLU168 3.6 23.0 1.0 H G:ALA92 3.7 26.7 0.5 H G:ALA92 3.7 26.7 0.5 N G:ALA92 3.9 22.2 1.0 CA G:GLY90 3.9 28.3 1.0 O A:HOH771 3.9 43.8 1.0 HE21 G:GLN94 3.9 25.9 1.0 HA G:VAL93 4.1 29.1 1.0 HG3 G:GLN94 4.1 25.5 1.0 OE2 A:GLU168 4.1 23.0 1.0 HA3 G:GLY90 4.2 34.0 1.0 CA G:ALA92 4.2 22.4 1.0 HB3 A:GLU168 4.2 20.7 1.0 HB3 G:ALA92 4.3 28.0 1.0 N G:ARG91 4.3 29.5 0.5 C G:ARG91 4.3 25.4 0.5 N G:ARG91 4.3 29.5 0.5 O A:HOH560 4.3 30.2 1.0 C G:ARG91 4.4 25.4 0.5 CB G:ASP85 4.4 18.9 1.0 O A:HOH640 4.5 48.3 1.0 N G:VAL93 4.6 23.1 1.0 HA G:ARG91 4.6 33.8 0.5 NE2 G:GLN94 4.6 21.5 1.0 HB3 G:ASP85 4.6 22.7 1.0 CA G:ARG91 4.7 28.2 0.5 CA G:ARG91 4.7 28.3 0.5 HB2 G:ASP85 4.8 22.7 1.0 CG A:GLU168 4.8 20.1 1.0 CA G:VAL93 4.8 24.2 1.0 HA G:ARG91 4.8 34.0 0.5 CB G:ALA92 4.8 23.3 1.0 CB A:GLU168 4.8 17.2 1.0 O G:ARG91 4.9 24.4 0.5 HB2 A:GLU168 4.9 20.7 1.0 H G:ARG91 4.9 35.4 0.5 H G:ARG91 4.9 35.4 0.5 H G:GLN94 5.0 21.5 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