Calcium in PDB 4cbw: Crystal Structure of Plasmodium Berghei Actin I with D-Loop From Muscle Actin

The structure of Crystal Structure of Plasmodium Berghei Actin I with D-Loop From Muscle Actin, PDB code: 4cbw 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)	38.581 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.240, 69.530, 178.830, 90.00, 90.00, 90.00
R / Rfree (%)	21.07 / 26.4

The binding sites of Calcium atom in the Crystal Structure of Plasmodium Berghei Actin I with D-Loop From Muscle Actin (pdb code 4cbw). 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 I with D-Loop From Muscle Actin, PDB code: 4cbw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Plasmodium Berghei Actin I with D-Loop From Muscle Actin


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 I with D-Loop From Muscle Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1377 b:59.6 occ:1.00 O2B A:ATP1379 2.4 54.8 1.0 O A:HOH2015 2.4 39.0 1.0 O A:HOH2005 2.4 38.2 1.0 O A:HOH2006 2.5 41.4 1.0 O A:HOH2003 2.5 59.7 1.0 O A:HOH2022 2.5 68.2 1.0 O3G A:ATP1379 2.6 68.1 1.0 O2G A:ATP1379 2.8 62.1 1.0 PG A:ATP1379 3.1 61.1 1.0 PB A:ATP1379 3.5 65.7 1.0 O3B A:ATP1379 3.5 85.1 1.0 HZ2 A:LYS19 3.7 83.8 1.0 O1A A:ATP1379 4.0 43.5 1.0 HA2 A:GLY14 4.0 69.1 1.0 OE1 A:GLN138 4.0 59.7 1.0 O A:HOH2021 4.1 60.7 1.0 HA3 A:GLY14 4.3 69.1 1.0 HA3 A:GLY157 4.3 78.6 1.0 OD1 A:ASP155 4.4 70.3 1.0 O A:HOH2007 4.4 55.8 1.0 O3A A:ATP1379 4.5 64.0 1.0 CD A:GLN138 4.5 55.7 1.0 NZ A:LYS19 4.5 69.4 1.0 HG22 A:VAL340 4.6 67.3 1.0 O1B A:ATP1379 4.6 60.3 1.0 O1G A:ATP1379 4.6 67.3 1.0 OD2 A:ASP155 4.6 67.0 1.0 O A:ASN13 4.6 64.4 1.0 CA A:GLY14 4.6 57.1 1.0 H A:SER15 4.7 84.5 1.0 HE22 A:GLN138 4.7 64.2 1.0 HZ3 A:LYS19 4.8 83.8 1.0 PA A:ATP1379 4.8 57.4 1.0 OD2 A:ASP12 4.8 64.5 1.0 HZ1 A:LYS19 4.8 83.8 1.0 NE2 A:GLN138 4.9 53.0 1.0 CG A:ASP155 4.9 71.5 1.0 OD1 A:ASP12 5.0 71.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Plasmodium Berghei Actin I with D-Loop From Muscle Actin


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 I with D-Loop From Muscle Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1150 b:56.1 occ:1.00 O G:ALA116 2.3 40.5 1.0 OE1 A:GLU168 2.4 50.9 1.0 O G:GLY114 2.4 60.1 1.0 OD2 G:ASP109 2.4 51.9 1.0 O A:HOH2024 2.5 62.3 1.0 O A:HOH2025 2.5 39.9 1.0 OD1 G:ASP109 2.8 49.5 1.0 CG G:ASP109 3.0 49.2 1.0 C G:GLY114 3.2 59.9 1.0 H G:ALA116 3.3 58.7 1.0 CD A:GLU168 3.3 48.6 1.0 HA2 G:GLY114 3.3 77.3 1.0 C G:ALA116 3.4 50.4 1.0 OE2 A:GLU168 3.5 50.4 1.0 N G:ALA116 3.6 48.4 1.0 CA G:GLY114 3.8 63.9 1.0 HA3 G:GLY114 4.0 77.3 1.0 CA G:ALA116 4.1 54.7 1.0 HA G:VAL117 4.2 66.9 1.0 N G:ARG115 4.2 61.1 1.0 HB1 G:ALA116 4.3 69.9 1.0 HE21 G:GLN118 4.3 60.5 1.0 C G:ARG115 4.3 55.9 1.0 HG3 G:GLN118 4.4 62.3 1.0 HB3 A:GLU168 4.4 56.6 1.0 CB G:ASP109 4.5 54.9 1.0 N G:VAL117 4.5 55.4 1.0 HA G:ARG115 4.6 66.6 1.0 CA G:ARG115 4.6 55.1 1.0 CG A:GLU168 4.6 45.0 1.0 O A:HOH2023 4.7 41.0 1.0 CB G:ALA116 4.8 57.8 1.0 HB3 G:ASP109 4.8 66.5 1.0 HB2 G:ASP109 4.8 66.5 1.0 CA G:VAL117 4.8 55.2 1.0 H G:ARG115 4.9 73.9 1.0 HA G:ALA116 4.9 66.3 1.0 CB A:GLU168 4.9 46.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Plasmodium Berghei Actin I with D-Loop From Muscle Actin


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 I with D-Loop From Muscle Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1151 b:70.6 occ:1.00 O G:GLY65 2.3 64.6 1.0 O G:VAL145 2.3 62.6 1.0 OE2 G:GLU97 2.4 65.2 1.0 O G:HOH2015 2.5 62.6 1.0 OD1 G:ASP66 2.5 63.4 1.0 O G:HOH2006 2.5 61.9 1.0 OE1 G:GLU97 2.6 64.7 1.0 CD G:GLU97 2.8 63.9 1.0 HA G:ASP66 3.3 75.1 1.0 C G:GLY65 3.4 59.8 1.0 C G:VAL145 3.5 61.7 1.0 HG11 G:VAL145 3.6 95.2 1.0 CG G:ASP66 3.7 60.9 1.0 HG13 G:VAL145 3.9 95.2 1.0 HA3 G:GLY144 3.9 79.2 1.0 CA G:ASP66 4.0 62.1 1.0 N G:VAL145 4.0 60.7 1.0 H G:SER94 4.0 74.7 1.0 H G:VAL145 4.0 73.4 1.0 N G:ASP66 4.1 59.7 1.0 HA G:CYS93 4.1 78.3 1.0 CG1 G:VAL145 4.2 78.9 1.0 CG G:GLU97 4.3 60.7 1.0 HG G:SER94 4.3 78.3 1.0 HA3 G:GLY65 4.3 80.3 1.0 C G:GLY144 4.3 61.3 1.0 OG G:SER94 4.3 64.8 1.0 HA G:ALA146 4.3 89.0 1.0 CA G:VAL145 4.3 62.5 1.0 CB G:ASP66 4.4 58.6 1.0 CA G:GLY65 4.5 66.5 1.0 C G:ALA146 4.5 71.8 1.0 O G:HOH2003 4.5 51.3 1.0 HG3 G:GLU97 4.5 73.4 1.0 N G:ALA146 4.5 72.5 1.0 HG2 G:GLU97 4.6 73.4 1.0 CA G:GLY144 4.6 65.5 1.0 CA G:ALA146 4.7 73.7 1.0 N G:SER147 4.7 64.7 1.0 O G:ALA146 4.7 70.0 1.0 OD2 G:ASP66 4.7 57.2 1.0 HA G:SER147 4.7 79.7 1.0 O G:GLY144 4.8 67.6 1.0 HB3 G:ASP66 4.8 70.9 1.0 HA2 G:GLY65 4.8 80.3 1.0 H G:SER147 4.8 78.2 1.0 N G:SER94 4.8 61.8 1.0 CB G:VAL145 4.9 74.3 1.0 H G:ASP66 4.9 72.2 1.0 HB2 G:CYS93 4.9 83.3 1.0 HG12 G:VAL145 5.0 95.2 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