Calcium in PDB 1rfj: Crystal Structure of Potato Calmodulin PCM6

The structure of Crystal Structure of Potato Calmodulin PCM6, PDB code: 1rfj was solved by D.C.Liang, C.H.Yun, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.95 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.440, 68.980, 109.890, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 25

The binding sites of Calcium atom in the Crystal Structure of Potato Calmodulin PCM6 (pdb code 1rfj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Potato Calmodulin PCM6, PDB code: 1rfj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Potato Calmodulin PCM6


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 Potato Calmodulin PCM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:24.0 occ:1.00 OD2 A:ASP20 2.2 34.0 1.0 OD2 A:ASP24 2.3 24.4 1.0 OD1 A:ASP22 2.4 33.2 1.0 O A:CYS26 2.4 23.1 1.0 OE1 A:GLU31 2.4 28.0 1.0 O A:HOH4109 2.5 33.9 1.0 OE2 A:GLU31 2.5 26.1 1.0 CD A:GLU31 2.8 29.5 1.0 CG A:ASP24 3.2 28.4 1.0 CG A:ASP22 3.3 37.5 1.0 CG A:ASP20 3.4 35.1 1.0 C A:CYS26 3.6 24.7 1.0 OD2 A:ASP22 3.6 38.0 1.0 OD1 A:ASP24 3.7 30.4 1.0 N A:ASP24 4.0 31.2 1.0 OD1 A:ASP20 4.1 36.7 1.0 N A:CYS26 4.2 23.5 1.0 CA A:ASP20 4.2 34.8 1.0 N A:ASP22 4.3 34.4 1.0 CG A:GLU31 4.3 27.4 1.0 CB A:ASP24 4.3 28.2 1.0 CB A:ASP20 4.3 35.2 1.0 C A:ASP20 4.4 36.0 1.0 SG A:CYS26 4.4 36.7 1.0 CA A:CYS26 4.4 26.1 1.0 CB A:ASP22 4.5 35.2 1.0 N A:ILE27 4.5 23.2 1.0 N A:GLY23 4.5 33.3 1.0 CA A:ILE27 4.6 22.4 1.0 CA A:ASP24 4.6 28.3 1.0 C A:ASP22 4.7 34.2 1.0 CA A:ASP22 4.7 34.4 1.0 N A:LYS21 4.7 36.6 1.0 O A:ASP20 4.7 33.5 1.0 CG2 A:THR28 4.7 23.2 1.0 N A:GLY25 4.8 27.4 1.0 N A:THR28 4.8 22.1 1.0 O A:HOH4041 4.9 34.7 1.0 C A:ASP24 5.0 28.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Potato Calmodulin PCM6


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 Potato Calmodulin PCM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:16.4 occ:1.00 OD2 A:ASP56 2.2 23.1 1.0 O A:HOH4056 2.3 18.5 1.0 OE1 A:GLU67 2.4 14.3 1.0 OD1 A:ASN60 2.4 18.1 1.0 O A:THR62 2.4 17.1 1.0 OD2 A:ASP58 2.5 23.6 1.0 OE2 A:GLU67 2.5 12.0 1.0 CD A:GLU67 2.8 15.5 1.0 CG A:ASN60 3.2 20.7 1.0 O A:HOH4006 3.3 29.8 1.0 CG A:ASP56 3.3 24.8 1.0 CG A:ASP58 3.3 25.2 1.0 ND2 A:ASN60 3.6 22.6 1.0 C A:THR62 3.6 19.4 1.0 OD1 A:ASP58 3.6 23.8 1.0 OD1 A:ASP56 4.0 22.8 1.0 N A:ASN60 4.3 23.9 1.0 CB A:ASP56 4.3 21.6 1.0 CA A:ASP56 4.3 23.2 1.0 CG A:GLU67 4.3 12.5 1.0 N A:THR62 4.3 20.3 1.0 N A:ASP64 4.4 15.6 1.0 CB A:ASN60 4.4 22.5 1.0 CA A:ILE63 4.4 18.3 1.0 N A:ILE63 4.4 17.0 1.0 N A:ASP58 4.5 24.0 1.0 CA A:THR62 4.5 20.3 1.0 OG1 A:THR62 4.6 20.8 1.0 CG A:ASP64 4.6 15.7 1.0 OD1 A:ASP64 4.6 14.7 1.0 C A:ASP56 4.6 23.4 1.0 CB A:ASP58 4.6 24.9 1.0 N A:GLY59 4.8 24.4 1.0 CA A:ASN60 4.8 23.6 1.0 C A:ILE63 4.8 15.5 1.0 N A:ALA57 4.8 23.2 1.0 OD2 A:ASP64 4.8 14.0 1.0 CA A:ASP58 4.9 23.7 1.0 O A:HOH4004 4.9 18.3 1.0 N A:GLY61 4.9 21.2 1.0 C A:ASP58 5.0 24.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Potato Calmodulin PCM6


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 Potato Calmodulin PCM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:15.0 occ:1.00 O A:PHE99 2.3 15.3 1.0 OD1 A:ASP95 2.3 20.3 1.0 OE1 A:GLU104 2.3 18.8 1.0 OD2 A:ASP93 2.3 17.4 1.0 OD1 A:ASN97 2.3 17.5 1.0 O A:HOH4063 2.4 24.1 1.0 OE2 A:GLU104 2.4 16.1 1.0 CD A:GLU104 2.7 18.7 1.0 CG A:ASN97 3.3 21.6 1.0 CG A:ASP95 3.3 22.4 1.0 CG A:ASP93 3.4 17.5 1.0 C A:PHE99 3.5 14.8 1.0 OD2 A:ASP95 3.8 20.8 1.0 ND2 A:ASN97 3.9 18.2 1.0 CA A:ASP93 4.0 18.5 1.0 N A:ASN97 4.1 19.0 1.0 N A:ASP95 4.2 17.9 1.0 CG A:GLU104 4.2 20.1 1.0 N A:PHE99 4.2 15.8 1.0 OD1 A:ASP93 4.2 15.2 1.0 CB A:ASP93 4.3 17.7 1.0 C A:ASP93 4.3 19.8 1.0 CA A:PHE99 4.3 15.9 1.0 CB A:ASN97 4.4 19.0 1.0 N A:ILE100 4.4 12.9 1.0 CA A:ILE100 4.5 13.3 1.0 N A:LYS94 4.5 19.4 1.0 N A:GLN96 4.5 19.9 1.0 CB A:ASP95 4.5 19.9 1.0 N A:SER101 4.6 13.7 1.0 CA A:ASP95 4.7 18.5 1.0 C A:ASP95 4.7 20.5 1.0 CA A:ASN97 4.7 18.7 1.0 O A:HOH4032 4.8 35.8 1.0 CB A:PHE99 4.8 18.2 1.0 O A:ASP93 4.8 16.6 1.0 O A:HOH4016 4.9 20.5 1.0 N A:GLY98 4.9 17.6 1.0 C A:ILE100 5.0 14.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Potato Calmodulin PCM6


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 Potato Calmodulin PCM6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:14.3 occ:1.00 OD1 A:ASP129 2.3 14.3 1.0 OD2 A:ASP133 2.4 14.7 1.0 OD2 A:ASP131 2.4 13.8 1.0 O A:GLN135 2.4 14.2 1.0 O A:HOH4062 2.5 14.3 1.0 OE2 A:GLU140 2.5 11.3 1.0 OE1 A:GLU140 2.6 11.4 1.0 CD A:GLU140 2.9 12.5 1.0 CG A:ASP133 3.2 16.2 1.0 CG A:ASP131 3.3 16.9 1.0 CG A:ASP129 3.4 17.1 1.0 C A:GLN135 3.6 13.6 1.0 OD1 A:ASP131 3.6 19.2 1.0 OD1 A:ASP133 3.7 15.2 1.0 N A:ASP133 4.1 16.2 1.0 OD2 A:ASP129 4.2 15.5 1.0 N A:GLN135 4.2 14.2 1.0 CA A:ASP129 4.3 16.7 1.0 CB A:ASP129 4.3 16.3 1.0 N A:ASP131 4.3 17.2 1.0 CB A:ASP133 4.4 15.6 1.0 CA A:ILE136 4.4 13.6 1.0 CG A:GLU140 4.4 12.2 1.0 N A:ASN137 4.5 15.0 1.0 N A:ILE136 4.5 12.3 1.0 N A:GLY132 4.5 18.9 1.0 CA A:GLN135 4.5 13.1 1.0 CG A:GLN135 4.6 11.0 1.0 CB A:ASP131 4.6 17.8 1.0 C A:ASP129 4.6 17.8 1.0 CA A:ASP133 4.7 16.2 1.0 N A:VAL130 4.7 16.1 1.0 N A:GLY134 4.7 16.5 1.0 CA A:ASP131 4.8 19.4 1.0 C A:ASP131 4.8 19.7 1.0 OD1 A:ASN137 4.9 20.9 1.0 C A:ILE136 4.9 13.3 1.0 C A:ASP133 5.0 17.9 1.0

C.H.Yun, J.Bai, D.Y.Sun, D.F.Cui, W.R.Chang, D.C.Liang. Structure of Potato Calmodulin PCM6: the First Report of the Three-Dimensional Structure of A Plant Calmodulin. Acta Crystallogr.,Sect.D V. 60 1214 2004.
ISSN: ISSN 0907-4449
PubMed: 15213382
DOI: 10.1107/S0907444904009771