Calcium in PDB 4cbx: Crystal Structure of Plasmodium Berghei Actin II

The structure of Crystal Structure of Plasmodium Berghei Actin II, PDB code: 4cbx was solved by J.Vahokoski, S.P.Bhargav, A.Desfosses, M.Andreadaki, E.P.Kumpula, A.Ignatev, S.Munico Martinez, S.Lepper, F.Frischknecht, I.Siden-Kiamos, C.Sachse, I.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.907 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.248, 60.908, 75.518, 90.00, 97.24, 90.00
R / Rfree (%)	19.59 / 22.75

The structure of Crystal Structure of Plasmodium Berghei Actin II also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Plasmodium Berghei Actin II (pdb code 4cbx). 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 Berghei Actin II, PDB code: 4cbx:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Plasmodium Berghei Actin II


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1378 b:22.0 occ:1.00 O A:HOH2003 2.4 21.8 1.0 O2B A:ATP1374 2.4 20.5 1.0 O A:HOH2006 2.4 19.5 1.0 O3G A:ATP1374 2.4 17.1 1.0 O A:HOH2085 2.4 15.9 1.0 O A:HOH2005 2.4 17.7 1.0 O A:HOH2099 2.4 24.1 1.0 PG A:ATP1374 3.5 17.3 1.0 PB A:ATP1374 3.7 16.8 1.0 O1G A:ATP1374 3.7 15.4 1.0 O A:HOH2101 4.0 15.4 1.0 OE1 A:GLN137 4.0 18.7 1.0 O3B A:ATP1374 4.1 17.1 1.0 O3A A:ATP1374 4.1 14.5 1.0 O A:HOH2086 4.1 45.1 1.0 CA A:GLY13 4.4 19.7 1.0 CD A:GLN137 4.4 23.7 1.0 OD1 A:ASP154 4.5 35.5 1.0 O1A A:ATP1374 4.6 17.3 1.0 NZ A:LYS18 4.6 18.9 1.0 OD2 A:ASP154 4.7 38.0 1.0 O A:HOH2100 4.7 45.4 1.0 OD2 A:ASP11 4.8 25.4 1.0 OD1 A:ASP11 4.8 25.7 1.0 O A:HOH2229 4.8 28.2 1.0 NE2 A:GLN137 4.8 22.4 1.0 O2G A:ATP1374 4.8 14.9 1.0 PA A:ATP1374 4.8 22.9 1.0 O1B A:ATP1374 4.9 22.0 1.0 CG A:ASP154 5.0 35.0 1.0 O A:ASN12 5.0 26.9 1.0 CG A:GLN137 5.0 23.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Plasmodium Berghei Actin II


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1151 b:48.2 occ:1.00 OD2 G:ASP109 2.4 31.6 1.0 O A:HOH2111 2.4 48.7 1.0 OE1 A:GLU167 2.4 32.5 1.0 O G:ALA116 2.4 34.8 1.0 O G:GLY114 2.7 32.5 1.0 CG G:ASP109 3.2 30.5 1.0 OD1 G:ASP109 3.3 31.7 1.0 C G:GLY114 3.4 33.4 1.0 CD A:GLU167 3.5 31.7 1.0 C G:ALA116 3.6 27.5 1.0 O A:HOH2110 3.7 37.7 1.0 O A:HOH2109 3.8 29.6 1.0 O A:HOH2112 3.9 42.1 1.0 N G:ALA116 3.9 28.4 1.0 CA G:GLY114 3.9 31.8 1.0 OE2 A:GLU167 4.0 33.8 1.0 CA G:ALA116 4.3 27.6 1.0 N G:ARG115 4.4 30.1 1.0 C G:ARG115 4.6 32.1 1.0 NE2 G:GLN118 4.6 27.5 1.0 CG A:GLU167 4.7 23.5 1.0 N G:VAL117 4.7 22.8 1.0 CB A:GLU167 4.7 15.1 1.0 CB G:ASP109 4.7 25.0 1.0 O G:HOH2064 4.8 44.2 1.0 CA G:ARG115 4.8 30.4 1.0 CA G:VAL117 4.9 21.1 1.0 CB G:ALA116 5.0 24.3 1.0 CG G:GLN118 5.0 20.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Plasmodium Berghei Actin II


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 Berghei Actin II within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1152 b:27.8 occ:1.00 O G:GLY65 2.2 25.3 1.0 OE2 G:GLU97 2.4 26.6 1.0 OD1 G:ASP66 2.4 32.8 1.0 O G:HOH2046 2.4 31.5 1.0 O G:HOH2045 2.4 22.5 1.0 OE1 G:GLU97 2.4 26.6 1.0 O G:VAL145 2.4 31.1 1.0 CD G:GLU97 2.7 22.5 1.0 C G:GLY65 3.4 27.2 1.0 CG G:ASP66 3.6 30.8 1.0 C G:VAL145 3.6 29.0 1.0 CA G:ASP66 3.9 29.4 1.0 N G:ASP66 4.1 27.2 1.0 N G:VAL145 4.2 30.5 1.0 CG G:GLU97 4.2 19.6 1.0 CG1 G:VAL145 4.2 33.2 1.0 O G:HOH2059 4.3 35.9 1.0 O G:HOH2025 4.3 23.8 1.0 CB G:ASP66 4.3 29.9 1.0 CA G:VAL145 4.4 27.6 1.0 CA G:GLY65 4.4 28.9 1.0 OD2 G:ASP66 4.5 30.6 1.0 C G:ALA146 4.5 28.8 1.0 C G:GLY144 4.6 31.1 1.0 N G:ALA146 4.6 28.7 1.0 CA G:CYS93 4.6 19.3 1.0 O G:ALA146 4.7 29.2 1.0 OG G:SER94 4.7 25.9 1.0 O G:HOH2010 4.7 50.6 1.0 N G:SER94 4.7 18.8 1.0 CA G:ALA146 4.7 26.4 1.0 N G:SER147 4.8 33.5 1.0 O G:HOH2029 4.9 28.2 1.0 CB G:CYS93 4.9 18.7 1.0 CA G:GLY144 5.0 32.1 1.0

J.Vahokoski, S.P.Bhargav, A.Desfosses, M.Andreadaki, E.Kumpula, S.M.Martinez, A.Ignatev, S.Lepper, F.Frischknecht, I.Siden-Kiamos, C.Sachse, I.Kursula. Structural Differences Explain Diverse Functions of Plasmodium Actins. Plos Pathog. V. 10 4091 2014.
ISSN: ISSN 1553-7366
PubMed: 24743229
DOI: 10.1371/JOURNAL.PPAT.1004091