Calcium in PDB 3khe: Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii

The structure of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii, PDB code: 3khe was solved by A.K.Wernimont, A.Hutchinson, J.D.Artz, F.Mackenzie, D.Cossar, I.Kozieradzki, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, R.Hui, W.Qiu, M.Amani, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.838, 101.015, 107.870, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 27.7

The structure of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii (pdb code 3khe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii, PDB code: 3khe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


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 the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca192 b:20.8 occ:1.00 OD1 A:ASP97 2.2 13.2 1.0 OD1 A:ASP99 2.2 17.8 1.0 OD1 A:ASN101 2.3 14.7 1.0 O A:TYR103 2.4 11.2 1.0 OE1 A:GLU105 2.4 17.8 1.0 OE2 A:GLU108 2.5 13.4 1.0 OE1 A:GLU108 2.6 10.6 1.0 CD A:GLU108 2.9 11.0 1.0 CG A:ASN101 3.2 18.3 1.0 CG A:ASP97 3.3 16.4 1.0 CD A:GLU105 3.3 16.2 1.0 CG A:ASP99 3.4 19.8 1.0 C A:TYR103 3.6 13.0 1.0 OE2 A:GLU105 3.7 19.3 1.0 ND2 A:ASN101 3.8 18.4 1.0 OD2 A:ASP99 3.9 23.7 1.0 OD2 A:ASP97 4.0 13.5 1.0 CA A:ASP97 4.2 17.4 1.0 N A:GLU105 4.2 10.2 1.0 CB A:ASP97 4.3 17.6 1.0 N A:ASN101 4.3 20.0 1.0 CG A:GLU108 4.3 10.4 1.0 N A:ASP99 4.3 18.8 1.0 CB A:ASN101 4.4 19.2 1.0 N A:TYR103 4.4 15.8 1.0 O A:HOH343 4.4 28.3 1.0 N A:ILE104 4.4 12.0 1.0 CA A:ILE104 4.5 11.1 1.0 CA A:TYR103 4.5 14.3 1.0 C A:ASP97 4.5 18.7 1.0 CB A:ASP99 4.6 19.1 1.0 N A:PHE98 4.6 19.6 1.0 CG A:GLU105 4.7 12.6 1.0 N A:ARG100 4.7 20.5 1.0 CA A:ASP99 4.8 19.0 1.0 CA A:ASN101 4.8 19.4 1.0 C A:ILE104 4.8 10.8 1.0 CB A:GLU105 4.9 10.1 1.0 N A:GLY102 4.9 18.3 1.0 C A:ASP99 5.0 19.3 1.0 CB A:TYR103 5.0 13.7 1.0 O A:HOH313 5.0 24.5 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


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 the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca193 b:20.0 occ:1.00 OD1 A:ASP133 2.2 14.2 1.0 O A:LYS139 2.3 11.6 1.0 OD1 A:ASP135 2.3 12.1 1.0 O A:HOH268 2.4 16.0 1.0 OG A:SER137 2.4 14.7 1.0 OE1 A:GLU144 2.5 14.1 1.0 OE2 A:GLU144 2.5 11.5 1.0 CD A:GLU144 2.9 14.7 1.0 CG A:ASP135 3.4 16.8 1.0 CG A:ASP133 3.4 14.1 1.0 C A:LYS139 3.5 12.0 1.0 CB A:SER137 3.5 16.4 1.0 OD2 A:ASP135 3.8 17.1 1.0 N A:SER137 4.0 17.5 1.0 N A:LYS139 4.3 13.0 1.0 OD2 A:ASP133 4.3 13.1 1.0 CA A:ASP133 4.3 14.7 1.0 O A:HOH406 4.3 26.5 1.0 CA A:SER137 4.3 16.1 1.0 N A:ILE140 4.3 11.0 1.0 CB A:ASP133 4.3 16.2 1.0 CA A:ILE140 4.4 11.1 1.0 CG A:GLU144 4.4 15.6 1.0 CA A:LYS139 4.5 12.1 1.0 CG2 A:THR141 4.5 13.7 1.0 C A:ASP133 4.5 16.1 1.0 N A:ASP135 4.5 17.6 1.0 O A:HOH331 4.7 25.4 1.0 CB A:ASP135 4.7 18.1 1.0 N A:GLY138 4.7 15.1 1.0 N A:THR141 4.8 12.2 1.0 C A:SER137 4.8 15.0 1.0 N A:SER134 4.8 17.5 1.0 O A:HOH332 4.9 35.7 1.0 O A:ASP133 4.9 15.4 1.0 N A:GLY136 4.9 17.8 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


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 the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca194 b:18.6 occ:1.00 OD1 A:ASP171 2.2 17.5 1.0 OD1 A:ASP167 2.3 11.0 1.0 O A:GLU173 2.4 14.3 1.0 OD1 A:ASN169 2.4 11.0 1.0 OE2 A:GLU178 2.4 10.2 1.0 O A:HOH212 2.4 20.1 1.0 OE1 A:GLU178 2.5 11.3 1.0 CD A:GLU178 2.8 12.7 1.0 CG A:ASP171 3.2 16.1 1.0 CG A:ASP167 3.4 11.9 1.0 CG A:ASN169 3.5 12.2 1.0 C A:GLU173 3.5 13.1 1.0 OD2 A:ASP171 3.6 14.2 1.0 CA A:ASP167 4.1 13.5 1.0 ND2 A:ASN169 4.1 13.7 1.0 CB A:ASP167 4.2 13.2 1.0 N A:ASP171 4.2 14.0 1.0 OD2 A:ASP167 4.3 12.3 1.0 N A:GLU173 4.3 12.5 1.0 CG A:GLU178 4.3 10.7 1.0 N A:VAL174 4.4 11.5 1.0 CA A:GLU173 4.4 13.9 1.0 C A:ASP167 4.5 12.7 1.0 CB A:ASP171 4.5 14.6 1.0 N A:ASN169 4.5 13.0 1.0 CA A:VAL174 4.5 10.0 1.0 N A:ASP175 4.5 9.9 1.0 OD2 A:ASP175 4.6 16.2 1.0 O A:HOH225 4.6 20.1 1.0 N A:ASN170 4.7 12.1 1.0 CB A:ASN169 4.7 12.4 1.0 N A:LYS168 4.7 13.0 1.0 CA A:ASP171 4.8 14.2 1.0 N A:GLY172 4.8 12.5 1.0 CA A:ASN169 4.9 12.7 1.0 C A:ASN169 4.9 12.5 1.0 O A:ASP167 5.0 12.3 1.0 C A:VAL174 5.0 9.5 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca195 b:23.5 occ:1.00 OD1 A:ASN52 2.3 17.8 1.0 OD1 A:ASP54 2.3 15.9 1.0 OD1 A:ASP50 2.3 19.9 1.0 OE2 A:GLU61 2.3 18.1 1.0 O A:GLN56 2.4 14.5 1.0 OE1 A:GLU61 2.4 18.7 1.0 O A:HOH246 2.5 20.9 1.0 CD A:GLU61 2.7 19.9 1.0 CG A:ASN52 3.3 18.8 1.0 CG A:ASP54 3.3 18.6 1.0 CG A:ASP50 3.4 18.0 1.0 C A:GLN56 3.6 14.8 1.0 OD2 A:ASP54 3.8 20.7 1.0 ND2 A:ASN52 3.9 17.0 1.0 OD2 A:ASP50 4.1 16.3 1.0 O A:HOH345 4.2 30.0 1.0 CG A:GLU61 4.2 18.6 1.0 N A:ASP54 4.3 16.9 1.0 N A:ASN52 4.4 19.3 1.0 CA A:ASP50 4.4 19.1 1.0 CA A:LEU57 4.4 14.0 1.0 N A:LEU57 4.4 13.3 1.0 CB A:ASP50 4.5 19.5 1.0 CB A:ASN52 4.5 18.8 1.0 N A:GLN56 4.6 15.6 1.0 C A:ASP50 4.6 20.0 1.0 N A:GLY53 4.6 17.0 1.0 CB A:ASP54 4.7 16.4 1.0 CA A:GLN56 4.7 14.9 1.0 N A:ASN51 4.7 20.9 1.0 CA A:ASN52 4.7 18.8 1.0 N A:ASP58 4.7 16.9 1.0 C A:ASN52 4.8 16.4 1.0 CG A:GLN56 4.8 15.6 1.0 O A:HOH275 4.8 23.5 1.0 OD2 A:ASP58 4.9 26.7 1.0 CA A:ASP54 4.9 15.8 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca192 b:23.3 occ:1.00 OD1 B:ASP54 2.3 15.5 1.0 O B:GLN56 2.4 11.3 1.0 O B:HOH240 2.4 12.9 1.0 OD1 B:ASN52 2.5 20.9 1.0 OE1 B:GLU61 2.5 17.1 1.0 OD1 B:ASP50 2.5 17.3 1.0 OE2 B:GLU61 2.5 12.3 1.0 CD B:GLU61 2.8 13.3 1.0 CG B:ASP54 3.3 14.4 1.0 CG B:ASN52 3.4 20.1 1.0 C B:GLN56 3.6 11.8 1.0 CG B:ASP50 3.6 14.7 1.0 OD2 B:ASP54 3.7 18.0 1.0 ND2 B:ASN52 3.9 21.4 1.0 N B:ASP54 4.2 14.7 1.0 OD2 B:ASP50 4.3 15.4 1.0 CG B:GLU61 4.3 12.9 1.0 CA B:LEU57 4.3 11.9 1.0 O B:HOH329 4.4 18.9 1.0 N B:GLN56 4.4 12.2 1.0 N B:LEU57 4.4 11.6 1.0 CA B:ASP50 4.4 16.1 1.0 N B:ASN52 4.4 18.0 1.0 CB B:ASP50 4.6 16.5 1.0 CB B:ASP54 4.6 12.4 1.0 N B:GLY53 4.6 15.2 1.0 CA B:GLN56 4.6 10.4 1.0 N B:ASP58 4.6 13.9 1.0 OD2 B:ASP58 4.6 22.6 1.0 N B:ASN51 4.6 17.1 1.0 C B:ASP50 4.6 17.0 1.0 CB B:ASN52 4.7 17.4 1.0 CG B:GLN56 4.7 8.0 1.0 CA B:ASP54 4.8 13.2 1.0 C B:ASN52 4.8 16.0 1.0 N B:GLY55 4.8 12.0 1.0 CA B:ASN52 4.9 17.8 1.0 O B:HOH259 4.9 24.9 1.0 C B:ASP54 5.0 12.8 1.0 C B:LEU57 5.0 12.8 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca193 b:20.0 occ:1.00 O B:TYR103 2.2 9.1 1.0 OD1 B:ASP97 2.3 14.9 1.0 OD1 B:ASP99 2.3 15.2 1.0 OE1 B:GLU105 2.3 16.4 1.0 OD1 B:ASN101 2.5 12.5 1.0 OE1 B:GLU108 2.5 7.7 1.0 OE2 B:GLU108 2.6 13.2 1.0 CD B:GLU108 2.9 12.2 1.0 CG B:ASN101 3.3 15.6 1.0 CD B:GLU105 3.3 13.5 1.0 CG B:ASP97 3.4 17.9 1.0 C B:TYR103 3.5 10.6 1.0 CG B:ASP99 3.5 17.0 1.0 OE2 B:GLU105 3.7 16.6 1.0 ND2 B:ASN101 3.7 15.6 1.0 OD2 B:ASP99 4.0 21.0 1.0 OD2 B:ASP97 4.1 18.2 1.0 CA B:ASP97 4.2 15.4 1.0 N B:GLU105 4.2 8.7 1.0 N B:TYR103 4.2 13.1 1.0 N B:ASP99 4.3 14.7 1.0 CB B:ASP97 4.3 15.2 1.0 N B:ASN101 4.3 16.9 1.0 N B:ILE104 4.3 8.5 1.0 CG B:GLU108 4.4 12.2 1.0 CA B:ILE104 4.4 9.4 1.0 C B:ASP97 4.4 15.5 1.0 CA B:TYR103 4.4 13.0 1.0 CB B:ASN101 4.4 16.3 1.0 MG B:MG197 4.5 39.5 1.0 N B:PHE98 4.6 15.4 1.0 N B:ARG100 4.6 16.0 0.5 CB B:ASP99 4.7 15.4 1.0 CG B:GLU105 4.7 7.3 1.0 N B:ARG100 4.7 15.9 0.5 N B:GLY102 4.7 14.0 1.0 CA B:ASP99 4.8 15.1 1.0 CB B:TYR103 4.8 13.2 1.0 C B:ILE104 4.8 9.5 1.0 CA B:ASN101 4.8 16.3 1.0 CB B:GLU105 4.9 7.7 1.0 C B:ASP99 4.9 15.8 1.0 O B:ASP97 5.0 15.3 1.0 O B:HOH305 5.0 23.6 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca194 b:20.7 occ:1.00 OD1 B:ASP135 2.3 14.9 1.0 O B:LYS139 2.3 11.2 1.0 OD1 B:ASP133 2.3 10.3 1.0 O B:HOH201 2.4 15.0 1.0 OE1 B:GLU144 2.4 15.1 1.0 OG B:SER137 2.4 14.9 1.0 OE2 B:GLU144 2.6 12.0 1.0 CD B:GLU144 2.8 13.7 1.0 CG B:ASP135 3.3 17.5 1.0 C B:LYS139 3.5 12.1 1.0 CB B:SER137 3.5 17.7 1.0 CG B:ASP133 3.5 12.2 1.0 OD2 B:ASP135 3.7 16.4 1.0 N B:SER137 4.0 18.6 1.0 N B:LYS139 4.2 13.1 1.0 O B:HOH328 4.2 27.8 1.0 CA B:ASP133 4.2 12.9 1.0 CA B:SER137 4.3 17.0 1.0 N B:ILE140 4.4 10.8 1.0 OD2 B:ASP133 4.4 11.7 1.0 CG B:GLU144 4.4 13.9 1.0 CB B:ASP133 4.4 13.5 1.0 CA B:ILE140 4.4 10.8 1.0 O B:HOH234 4.4 42.5 1.0 CA B:LYS139 4.5 13.2 1.0 C B:ASP133 4.5 14.0 1.0 N B:ASP135 4.6 18.2 1.0 CG2 B:THR141 4.6 9.4 1.0 CB B:ASP135 4.7 18.8 1.0 N B:GLY138 4.7 15.7 1.0 O B:HOH254 4.7 22.7 1.0 N B:THR141 4.7 11.4 1.0 N B:SER134 4.8 15.5 1.0 C B:SER137 4.8 16.9 1.0 N B:GLY136 4.9 18.7 1.0 O B:ASP133 4.9 14.7 1.0 CA B:ASP135 5.0 17.7 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Calcium-Loaded Calmodulin-Like Domain of the Cdpk, 541.M00134 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca195 b:18.8 occ:1.00 OD1 B:ASP171 2.2 18.1 1.0 OD1 B:ASP167 2.3 15.4 1.0 OD1 B:ASN169 2.3 14.4 1.0 O B:GLU173 2.4 11.8 1.0 O B:HOH274 2.4 15.6 1.0 OE1 B:GLU178 2.5 12.7 1.0 OE2 B:GLU178 2.5 12.3 1.0 CD B:GLU178 2.8 12.8 1.0 CG B:ASP171 3.1 16.4 1.0 CG B:ASN169 3.4 15.2 1.0 CG B:ASP167 3.5 13.9 1.0 C B:GLU173 3.5 12.5 1.0 OD2 B:ASP171 3.5 16.2 1.0 ND2 B:ASN169 4.0 15.2 1.0 CA B:ASP167 4.2 14.5 1.0 OD2 B:ASP167 4.3 14.4 1.0 N B:ASP171 4.3 13.8 1.0 N B:GLU173 4.3 12.6 1.0 CB B:ASP167 4.3 14.5 1.0 N B:VAL174 4.4 11.8 1.0 CB B:ASP171 4.4 15.1 1.0 CG B:GLU178 4.4 13.3 1.0 CA B:GLU173 4.4 13.4 1.0 O B:HOH233 4.5 21.4 1.0 CA B:VAL174 4.5 10.7 1.0 N B:ASP175 4.5 9.2 1.0 C B:ASP167 4.5 14.8 1.0 N B:ASN169 4.5 15.0 1.0 OD2 B:ASP175 4.6 16.2 1.0 CB B:ASN169 4.7 14.7 1.0 N B:LYS168 4.7 15.2 1.0 N B:ASN170 4.7 13.8 1.0 CA B:ASP171 4.8 14.8 1.0 N B:GLY172 4.9 14.1 1.0 CA B:ASN169 4.9 14.6 1.0 C B:ASN169 5.0 14.0 1.0 C B:VAL174 5.0 9.8 1.0 CB B:GLU173 5.0 13.2 1.0

A.K.Wernimont, M.Amani, W.Qiu, J.C.Pizarro, J.D.Artz, Y.H.Lin, J.Lew, A.Hutchinson, R.Hui. Structures of Parasitic Cdpk Domains Point to A Common Mechanism of Activation. Proteins V. 79 803 2011.
ISSN: ISSN 0887-3585
PubMed: 21287613
DOI: 10.1002/PROT.22919