Calcium in PDB 6i4m: Crystal Structure of Plasmodium Berghei Actin II in the Mg-Adp State

The structure of Crystal Structure of Plasmodium Berghei Actin II in the Mg-Adp State, PDB code: 6i4m 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)	64.88 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.410, 61.510, 64.940, 90.00, 92.55, 90.00
R / Rfree (%)	14.3 / 17.9

The structure of Crystal Structure of Plasmodium Berghei Actin II 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 Berghei Actin II in the Mg-Adp State (pdb code 6i4m). 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 Berghei Actin II in the Mg-Adp State, PDB code: 6i4m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Plasmodium Berghei Actin II 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 Berghei Actin II in the Mg-Adp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:27.2 occ:1.00 O G:GLY90 2.5 25.7 1.0 O G:ALA92 2.5 28.0 1.0 OD2 G:ASP85 2.6 24.9 1.0 O G:HOH393 2.6 51.4 1.0 OE1 A:GLU167 2.6 25.2 1.0 O G:HOH391 2.7 54.0 1.0 OD1 G:ASP85 3.1 24.9 1.0 CG G:ASP85 3.2 25.1 1.0 C G:GLY90 3.4 26.4 1.0 CD A:GLU167 3.6 23.2 1.0 C G:ALA92 3.6 27.3 1.0 HA2 G:GLY90 3.6 32.1 1.0 O A:HOH706 3.7 43.1 1.0 H G:ALA92 3.7 33.5 1.0 N G:ALA92 3.9 27.9 1.0 CA G:GLY90 4.0 26.7 1.0 O A:HOH617 4.0 27.3 1.0 OE2 A:GLU167 4.1 23.3 1.0 HB3 A:GLU167 4.2 23.2 1.0 HE21 G:GLN94 4.2 27.4 1.0 HA G:VAL93 4.2 29.8 1.0 N G:ARG91 4.3 28.6 1.0 HG3 G:GLN94 4.3 25.3 1.0 C G:ARG91 4.3 29.2 1.0 CA G:ALA92 4.3 27.0 1.0 HA3 G:GLY90 4.3 32.1 1.0 HA G:ARG91 4.4 37.7 1.0 HB3 G:ALA92 4.5 30.7 1.0 O A:HOH627 4.5 28.6 1.0 CA G:ARG91 4.6 31.4 1.0 N G:VAL93 4.7 25.7 1.0 CB G:ASP85 4.7 23.3 1.0 HB2 A:GLU167 4.7 23.2 1.0 O G:HOH361 4.7 46.5 1.0 CB A:GLU167 4.7 19.4 1.0 CG A:GLU167 4.7 19.8 1.0 NE2 G:GLN94 4.9 22.8 1.0 CA G:VAL93 4.9 24.8 1.0 H G:ARG91 5.0 34.3 1.0 HB3 G:ASP85 5.0 27.9 1.0 HB2 G:ASP85 5.0 27.9 1.0 O G:ARG91 5.0 29.8 1.0 CB G:ALA92 5.0 25.5 1.0 H G:GLN94 5.0 25.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Plasmodium Berghei Actin II 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 Berghei Actin II in the Mg-Adp State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:21.9 occ:1.00 OD1 G:ASP42 2.3 21.2 1.0 O G:VAL121 2.3 25.6 1.0 O G:GLY41 2.4 18.0 1.0 OE2 G:GLU73 2.4 21.4 1.0 O G:HOH373 2.4 20.5 1.0 O G:HOH380 2.4 28.8 1.0 OE1 G:GLU73 2.5 20.7 1.0 CD G:GLU73 2.7 20.4 1.0 HA G:ASP42 3.2 23.0 1.0 C G:GLY41 3.4 20.2 1.0 CG G:ASP42 3.5 20.1 1.0 C G:VAL121 3.5 25.7 1.0 HG13 G:VAL121 3.5 30.0 1.0 H G:VAL121 3.8 29.1 1.0 HA G:CYS69 3.8 23.3 1.0 H G:SER70 4.0 21.8 1.0 CA G:ASP42 4.0 19.2 1.0 N G:VAL121 4.0 24.2 1.0 HA3 G:GLY120 4.1 30.3 1.0 HG12 G:VAL121 4.1 30.0 1.0 N G:ASP42 4.1 21.8 1.0 O G:HOH330 4.1 17.4 1.0 HA3 G:GLY41 4.2 24.6 1.0 CG1 G:VAL121 4.2 25.0 1.0 CG G:GLU73 4.3 18.1 1.0 HA G:ALA122 4.3 33.5 1.0 CA G:VAL121 4.3 25.6 1.0 CB G:ASP42 4.3 18.5 1.0 O G:HOH326 4.4 27.3 1.0 OD2 G:ASP42 4.4 22.5 1.0 C G:GLY120 4.4 25.2 1.0 CA G:GLY41 4.4 20.5 1.0 HB2 G:CYS69 4.5 21.5 1.0 N G:ALA122 4.5 27.8 1.0 C G:ALA122 4.6 26.4 1.0 HG3 G:GLU73 4.6 21.7 1.0 OG G:SER70 4.6 22.2 1.0 HG2 G:GLU73 4.6 21.7 1.0 O G:HOH389 4.7 38.5 1.0 O G:HOH424 4.7 44.2 1.0 CA G:ALA122 4.7 27.9 1.0 HA G:SER123 4.7 30.2 1.0 N G:SER70 4.7 18.1 1.0 HB3 G:ASP42 4.7 22.2 1.0 CA G:GLY120 4.7 25.3 1.0 HA2 G:GLY41 4.8 24.6 1.0 CA G:CYS69 4.8 19.4 1.0 N G:SER123 4.8 25.4 1.0 O G:HOH338 4.8 21.1 1.0 O G:ALA122 4.8 25.9 1.0 CB G:VAL121 4.9 26.7 1.0 H G:SER123 4.9 30.5 1.0 H G:ASP42 5.0 26.1 1.0 HG G:SER70 5.0 26.7 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